/* sqnutil1.c * =========================================================================== * * PUBLIC DOMAIN NOTICE * National Center for Biotechnology Information (NCBI) * * This software/database is a "United States Government Work" under the * terms of the United States Copyright Act. It was written as part of * the author's official duties as a United States Government employee and * thus cannot be copyrighted. This software/database is freely available * to the public for use. The National Library of Medicine and the U.S. * Government do not place any restriction on its use or reproduction. * We would, however, appreciate having the NCBI and the author cited in * any work or product based on this material * * Although all reasonable efforts have been taken to ensure the accuracy * and reliability of the software and data, the NLM and the U.S. * Government do not and cannot warrant the performance or results that * may be obtained by using this software or data. The NLM and the U.S. * Government disclaim all warranties, express or implied, including * warranties of performance, merchantability or fitness for any particular * purpose. * * =========================================================================== * * File Name: sqnutil1.c * * Author: Jonathan Kans * * Version Creation Date: 9/2/97 * * $Revision: 6.676 $ * * File Description: * * Modifications: * -------------------------------------------------------------------------- * Date Name Description of modification * ------- ---------- ----------------------------------------------------- * * * ========================================================================== */ #include #include #include #include #include #include /* #include */ #include #include #include #include #include #include #include #include #include #include #include #include #include #define NLM_GENERATED_CODE_PROTO #include #include static int descr_insert_order [] = { Seq_descr_title, Seq_descr_source, Seq_descr_molinfo, Seq_descr_het, Seq_descr_pub, Seq_descr_comment, Seq_descr_name, Seq_descr_user, Seq_descr_maploc, Seq_descr_region, Seq_descr_num, Seq_descr_dbxref, Seq_descr_mol_type, Seq_descr_modif, Seq_descr_method, Seq_descr_org, Seq_descr_sp, Seq_descr_pir, Seq_descr_prf, Seq_descr_pdb, Seq_descr_embl, Seq_descr_genbank, Seq_descr_modelev, Seq_descr_create_date, Seq_descr_update_date, 0 }; static void NormalizeDescriptorProc ( SeqEntryPtr sep, Pointer data, Int4 index, Int2 indent ) { BioseqPtr bsp; BioseqSetPtr bssp; /* arrays are SEQDESCR_MAX + 1, last slot stores unexpected descriptor numbers */ SeqDescrPtr first [SEQDESCR_MAX + 1]; SeqDescrPtr last [SEQDESCR_MAX + 1]; int i; int idx; SeqDescrPtr PNTR head = NULL; SeqDescrPtr PNTR prev = NULL; SeqDescrPtr next; SeqDescrPtr sdp; if (sep == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp == NULL) return; head = &(bsp->descr); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return; head = &(bssp->descr); } if (head == NULL) return; MemSet ((Pointer) &first, 0, sizeof (first)); MemSet ((Pointer) &last, 0, sizeof (last)); prev = head; sdp = *prev; while (sdp != NULL) { next = sdp->next; *prev = sdp->next; sdp->next = NULL; idx = (int) sdp->choice; /* unexpected descriptor numbers go into last slot */ if (idx <= 0 || idx >= SEQDESCR_MAX) { idx = SEQDESCR_MAX; } if (idx > 0 && idx <= SEQDESCR_MAX) { if (first [idx] == NULL) { first [idx] = sdp; } if (last [idx] != NULL) { (last [idx])->next = sdp; } last [idx] = sdp; } sdp = next; } for (i = 0; descr_insert_order [i] != 0; i++) { idx = descr_insert_order [i]; sdp = first [idx]; if (sdp == NULL) continue; ValNodeLink (head, sdp); } } NLM_EXTERN void NormalizeDescriptorOrder ( SeqEntryPtr sep ) { SeqEntryExplore (sep, NULL, NormalizeDescriptorProc); } NLM_EXTERN DatePtr DateAdvance (DatePtr dp, Uint1 monthsToAdd) { if (dp == NULL) { dp = DateCurr (); } if (dp != NULL && dp->data [0] == 1 && dp->data [1] > 0) { while (monthsToAdd > 12) { monthsToAdd--; (dp->data [1])++; } if (dp->data [2] < 13 - monthsToAdd) { (dp->data [2]) += monthsToAdd; } else { (dp->data [1])++; (dp->data [2]) -= (12 - monthsToAdd); } if (dp->data [2] == 0) { dp->data [2] = 1; } if (dp->data [3] == 0) { switch (dp->data [2]) { case 4 : case 6 : case 9 : case 11 : dp->data [3] = 30; break; case 2 : dp->data [3] = 28; break; default : dp->data [3] = 31; break; } } } if (dp != NULL) { switch (dp->data [2]) { case 4 : case 6 : case 9 : case 11 : if (dp->data [3] > 30) { dp->data [3] = 30; } break; case 2 : if (dp->data [3] > 28) { dp->data [3] = 28; } break; default : if (dp->data [3] > 31) { dp->data [3] = 31; } break; } } return dp; } typedef struct orgscan { ObjMgrPtr omp; Int2 nuclCode; Int2 mitoCode; Int2 pstdCode; Boolean mito; Boolean plastid; Char taxname [196]; BioSourcePtr biop; } OrgScan, PNTR OrgScanPtr; static Boolean OrgScanGatherFunc (GatherContextPtr gcp) { BioSourcePtr biop; Boolean doCodes = FALSE; Boolean doMito = FALSE; Boolean doTaxname = FALSE; Boolean mito = FALSE; Int2 mitoCode = 0; Int2 nuclCode = 0; Int2 pstdCode = 0; ObjMgrTypePtr omtp; OrgNamePtr onp; OrgRefPtr orp; OrgScanPtr osp; ValNodePtr sdp; SeqFeatPtr sfp; Uint2 subtype; CharPtr taxname = NULL; Int2 val; ValNodePtr vnp; if (gcp == NULL || gcp->thisitem == NULL) return TRUE; if (gcp->thistype != OBJ_SEQFEAT && gcp->thistype != OBJ_SEQDESC) return TRUE; osp = (OrgScanPtr) gcp->userdata; if (osp == NULL) return TRUE; subtype = 0; if (gcp->thistype == OBJ_SEQFEAT || gcp->thistype == OBJ_SEQDESC) { omtp = ObjMgrTypeFind (osp->omp, gcp->thistype, NULL, NULL); if (omtp == NULL) { return TRUE; } if (omtp->subtypefunc != NULL) { subtype = (*(omtp->subtypefunc)) (gcp->thisitem); } } orp = NULL; biop = NULL; switch (gcp->thistype) { case OBJ_SEQFEAT : sfp = (SeqFeatPtr) gcp->thisitem; switch (subtype) { case FEATDEF_ORG : orp = (OrgRefPtr) sfp->data.value.ptrvalue; break; case FEATDEF_BIOSRC : biop = (BioSourcePtr) sfp->data.value.ptrvalue; break; default : break; } break; case OBJ_SEQDESC : sdp = (ValNodePtr) gcp->thisitem; switch (subtype) { case Seq_descr_modif : vnp = (ValNodePtr) sdp->data.ptrvalue; while (vnp != NULL) { val = (Int2) vnp->data.intvalue; if (val == MODIF_mitochondrial || val == MODIF_kinetoplast) { mito = TRUE; doMito = TRUE; /* osp->mito = TRUE; */ } vnp = vnp->next; } break; case Seq_descr_org : orp = (OrgRefPtr) sdp->data.ptrvalue; break; case Seq_descr_source : biop = (BioSourcePtr) sdp->data.ptrvalue; break; default : break; } break; default : break; } if (orp == NULL && biop != NULL) { orp = biop->org; mito = (Boolean) (biop->genome == GENOME_kinetoplast || biop->genome == GENOME_mitochondrion || biop->genome == GENOME_hydrogenosome); doMito = TRUE; /* osp->mito = (Boolean) (biop->genome == 4 || biop->genome == 5); */ } if (orp != NULL) { taxname = orp->taxname; doTaxname = TRUE; /* StringNCpy_0 (osp->taxname, orp->taxname, sizeof (osp->taxname)); */ onp = orp->orgname; if (onp != NULL) { nuclCode = onp->gcode; mitoCode = onp->mgcode; pstdCode = onp->pgcode; doCodes = TRUE; /* osp->nuclCode = onp->gcode; osp->mitoCode = onp->mgcode; */ } } if (biop != NULL) { if (osp->biop == NULL || biop->is_focus) { osp->biop = biop; if (doMito) { osp->mito = mito; } osp->plastid = (Boolean) (biop->genome == GENOME_chloroplast || biop->genome == GENOME_chromoplast || biop->genome == GENOME_plastid || biop->genome == GENOME_cyanelle || biop->genome == GENOME_apicoplast || biop->genome == GENOME_leucoplast || biop->genome == GENOME_proplastid || biop->genome == GENOME_chromatophore); if (doCodes) { osp->nuclCode = nuclCode; osp->mitoCode = mitoCode; osp->pstdCode = pstdCode; } if (doTaxname) { StringNCpy_0 (osp->taxname, taxname, sizeof (osp->taxname)); } } } return TRUE; } static Int2 SeqEntryOrEntityIDToGeneticCode (SeqEntryPtr sep, Uint2 entityID, BoolPtr mito, CharPtr taxname, size_t maxsize, BioSourcePtr PNTR biopp) { GatherScope gs; OrgScan osp; if (mito != NULL) { *mito = FALSE; } if (taxname != NULL && maxsize > 0) { *taxname = '\0'; } osp.mito = FALSE; osp.plastid = FALSE; osp.nuclCode = 0; osp.mitoCode = 0; osp.pstdCode = 0; osp.omp = ObjMgrGet (); osp.taxname [0] = '\0'; osp.biop = NULL; MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.get_feats_location = TRUE; MemSet ((Pointer) (gs.ignore), (int)(TRUE), (size_t) (OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQDESC] = FALSE; if (sep != NULL) { gs.scope = sep; GatherSeqEntry (sep, (Pointer) &osp, OrgScanGatherFunc, &gs); } else if (entityID > 0) { GatherEntity (entityID, (Pointer) &osp, OrgScanGatherFunc, &gs); } if (mito != NULL) { *mito = osp.mito; } if (taxname != NULL && maxsize > 0) { StringNCpy_0 (taxname, osp.taxname, maxsize); } if (biopp != NULL) { *biopp = osp.biop; } if (osp.plastid) { if (osp.pstdCode > 0) { return osp.pstdCode; } else { return 11; } } else if (osp.mito) { return osp.mitoCode; } else { return osp.nuclCode; } } NLM_EXTERN Int2 EntityIDToGeneticCode (Uint2 entityID, BoolPtr mito, CharPtr taxname, size_t maxsize) { return SeqEntryOrEntityIDToGeneticCode (NULL, entityID, mito, taxname, maxsize, NULL); } NLM_EXTERN Int2 SeqEntryToGeneticCode (SeqEntryPtr sep, BoolPtr mito, CharPtr taxname, size_t maxsize) { return SeqEntryOrEntityIDToGeneticCode (sep, 0, mito, taxname, maxsize, NULL); } NLM_EXTERN Int2 SeqEntryToBioSource (SeqEntryPtr sep, BoolPtr mito, CharPtr taxname, size_t maxsize, BioSourcePtr PNTR biopp) { return SeqEntryOrEntityIDToGeneticCode (sep, 0, mito, taxname, maxsize, biopp); } NLM_EXTERN Boolean BioseqToGeneticCode ( BioseqPtr bsp, Int2Ptr gencodep, BoolPtr mitop, BoolPtr plastidp, CharPtr taxnamep, size_t maxsize, BioSourcePtr PNTR biopp ) { BioSourcePtr biop = NULL; SeqMgrDescContext dcontext; SeqMgrFeatContext fcontext; Int2 gencode = 0; Boolean mito = FALSE; Int2 mitoCode = 0; Int2 nuclCode = 0; Int2 pstdCode = 0; OrgNamePtr onp; OrgRefPtr orp; Boolean plastid = FALSE; SeqDescrPtr sdp; SeqFeatPtr sfp; CharPtr taxname = NULL; if (bsp == NULL) return FALSE; sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_source, &dcontext); if (sdp != NULL) { biop = (BioSourcePtr) sdp->data.ptrvalue; } if (biop == NULL) { sfp = SeqMgrGetNextFeature (bsp, NULL, SEQFEAT_BIOSRC, 0, &fcontext); if (sfp != NULL) { biop = (BioSourcePtr) sfp->data.value.ptrvalue; } } if (biop == NULL) return FALSE; orp = biop->org; if (orp == NULL) return FALSE; taxname = orp->taxname; if (StringHasNoText (taxname)) return FALSE; onp = orp->orgname; if (onp != NULL) { nuclCode = onp->gcode; mitoCode = onp->mgcode; pstdCode = onp->pgcode; } mito = (Boolean) (biop->genome == GENOME_kinetoplast || biop->genome == GENOME_mitochondrion || biop->genome == GENOME_hydrogenosome); plastid = (Boolean) (biop->genome == GENOME_chloroplast || biop->genome == GENOME_chromoplast || biop->genome == GENOME_plastid || biop->genome == GENOME_cyanelle || biop->genome == GENOME_apicoplast || biop->genome == GENOME_leucoplast || biop->genome == GENOME_proplastid || biop->genome == GENOME_chromatophore); if (plastid) { if (pstdCode > 0) { gencode = pstdCode; } else { gencode = 11; } } else if (mito) { gencode = mitoCode; } else { gencode = nuclCode; } if (gencodep != NULL) { *gencodep = gencode; } if (mitop != NULL) { *mitop = mito; } if (plastidp != NULL) { *plastidp = plastid; } if (taxnamep != NULL && maxsize > 0) { StringNCpy_0 (taxnamep, taxname, maxsize); } if (biopp != NULL) { *biopp = biop; } return TRUE; } static Boolean FindBspItem (GatherContextPtr gcp) { BioseqPtr PNTR bspp; bspp = (BioseqPtr PNTR) gcp->userdata; if (bspp != NULL && gcp->thistype == OBJ_BIOSEQ) { *bspp = (BioseqPtr) gcp->thisitem; } return TRUE; } NLM_EXTERN BioseqPtr GetBioseqGivenIDs (Uint2 entityID, Uint4 itemID, Uint2 itemtype) { BioseqPtr bsp; bsp = NULL; if (entityID > 0 && itemID > 0 && itemtype == OBJ_BIOSEQ) { GatherItem (entityID, itemID, itemtype, (Pointer) (&bsp), FindBspItem); } return bsp; } NLM_EXTERN BioseqPtr GetBioseqGivenSeqLoc (SeqLocPtr slp, Uint2 entityID) { BioseqPtr bsp; SeqEntryPtr sep; SeqIdPtr sip; if (slp == NULL) return NULL; bsp = NULL; sip = SeqLocId (slp); if (sip != NULL) { bsp = BioseqFind (sip); } else if (entityID > 0) { slp = SeqLocFindNext (slp, NULL); if (slp != NULL) { sip = SeqLocId (slp); if (sip != NULL) { bsp = BioseqFind (sip); if (bsp != NULL) { sep = GetBestTopParentForData (entityID, bsp); if (sep != NULL) { sep = FindNucSeqEntry (sep); if (sep != NULL && sep->choice == 1) { bsp = (BioseqPtr) sep->data.ptrvalue; } } } } } } return bsp; } typedef struct tripletdata { Uint2 entityID; Uint4 itemID; Uint2 itemtype; Pointer lookfor; } TripletData, PNTR TripletDataPtr; static Boolean FindIDsFromPointer (GatherContextPtr gcp) { TripletDataPtr tdp; tdp = (TripletDataPtr) gcp->userdata; if (tdp != NULL && gcp->thisitem == tdp->lookfor) { tdp->entityID = gcp->entityID; tdp->itemID = gcp->itemID; tdp->itemtype = gcp->thistype; } return TRUE; } NLM_EXTERN Uint4 GetItemIDGivenPointer (Uint2 entityID, Uint2 itemtype, Pointer lookfor) { GatherScope gs; TripletData td; if (entityID > 0 && itemtype > 0 && itemtype < OBJ_MAX && lookfor != NULL) { td.entityID = 0; td.itemID = 0; td.itemtype = 0; td.lookfor = lookfor; MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.get_feats_location = FALSE; MemSet ((Pointer)(gs.ignore), (int)(FALSE), (size_t)(OBJ_MAX * sizeof(Boolean))); /* gs.ignore[itemtype] = FALSE; */ GatherEntity (entityID, (Pointer) (&td), FindIDsFromPointer, &gs); if (td.entityID == entityID && td.itemID > 0 && td.itemtype == itemtype) { return td.itemID; } } return 0; } static void AddNucPart (BioseqPtr segseq, BioseqSetPtr parts, SeqEntryPtr addme) { BioseqPtr bsp; SeqLocPtr slp; SeqEntryPtr tmp; if (segseq == NULL || addme == NULL) return; if (addme->choice != 1 || addme->data.ptrvalue == NULL) return; bsp = (BioseqPtr) addme->data.ptrvalue; slp = ValNodeNew ((ValNodePtr) segseq->seq_ext); if (slp == NULL) return; if (segseq->seq_ext == NULL) { segseq->seq_ext = (Pointer) slp; } if (bsp->length >= 0) { segseq->length += bsp->length; slp->choice = SEQLOC_WHOLE; slp->data.ptrvalue = (Pointer) SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); } else { slp->choice = SEQLOC_NULL; addme = SeqEntryFree (addme); return; } if (parts == NULL) { addme = SeqEntryFree (addme); return; } if (parts->seq_set != NULL) { tmp = parts->seq_set; while (tmp->next != NULL) { tmp = tmp->next; } tmp->next = addme; } else { parts->seq_set = addme; } } NLM_EXTERN void GetSeqEntryParent (SeqEntryPtr target, Pointer PNTR parentptr, Uint2Ptr parenttype) { ObjMgrPtr omp; ObjMgrDataPtr omdp; if (parentptr == NULL || parenttype == NULL) return; *parenttype = 0; *parentptr = NULL; if (target == NULL || target->data.ptrvalue == NULL) return; omp = ObjMgrGet (); if (omp == NULL) return; omdp = ObjMgrFindByData (omp, target->data.ptrvalue); if (omdp == NULL) return; *parenttype = omdp->parenttype; *parentptr = omdp->parentptr; } NLM_EXTERN void SaveSeqEntryObjMgrData (SeqEntryPtr target, ObjMgrDataPtr PNTR omdptopptr, ObjMgrData PNTR omdataptr) { ObjMgrPtr omp; ObjMgrDataPtr omdp, omdptop = NULL; if (target == NULL || omdptopptr == NULL || omdataptr == NULL) return; *omdptopptr = NULL; MemSet ((Pointer) omdataptr, 0, sizeof (ObjMgrData)); omp = ObjMgrGet (); if (omp == NULL) return; omdp = ObjMgrFindByData (omp, target->data.ptrvalue); if (omdp == NULL) return; omdptop = ObjMgrFindTop (omp, omdp); if (omdptop == NULL) return; if (omdptop->EntityID == 0) return; *omdptopptr = omdptop; MemCopy ((Pointer) omdataptr, omdptop, sizeof (ObjMgrData)); omdptop->userdata = NULL; } extern void ObjMgrRemoveEntityIDFromRecycle (Uint2 entityID, ObjMgrPtr omp); extern void ObjMgrRecordOmdpByEntityID (Uint2 entityID, ObjMgrDataPtr omdp); NLM_EXTERN void RestoreSeqEntryObjMgrData (SeqEntryPtr target, ObjMgrDataPtr omdptop, ObjMgrData PNTR omdataptr) { ObjMgrPtr omp; ObjMgrDataPtr omdp, omdpnew = NULL; if (target == NULL || omdptop == NULL || omdataptr == NULL) return; if (omdataptr->EntityID == 0) return; omp = ObjMgrGet (); if (omp == NULL) return; omdp = ObjMgrFindByData (omp, target->data.ptrvalue); if (omdp == NULL) return; omdpnew = ObjMgrFindTop (omp, omdp); if (omdpnew == NULL) return; if (omdpnew != omdptop) { omdpnew->EntityID = omdataptr->EntityID; omdptop->EntityID = 0; omdpnew->lockcnt = omdataptr->lockcnt; omdpnew->tempload = omdataptr->tempload; omdpnew->clipboard = omdataptr->clipboard; omdpnew->dirty = omdataptr->dirty; omdpnew->being_freed = omdataptr->being_freed; omdpnew->free = omdataptr->free; omdpnew->options = omdataptr->options; ObjMgrRemoveEntityIDFromRecycle (omdpnew->EntityID, omp); ObjMgrRecordOmdpByEntityID (omdpnew->EntityID, omdpnew); } omdpnew->userdata = omdataptr->userdata; } NLM_EXTERN void AddSeqEntryToSeqEntry (SeqEntryPtr target, SeqEntryPtr insert, Boolean relink) { SeqEntryPtr first; BioseqPtr insertbsp; BioseqSetPtr nuc_prot; Uint2 parenttype; Pointer parentptr; BioseqSetPtr parts; BioseqPtr seg; BioseqSetPtr segs; BioseqPtr targetbsp; BioseqSetPtr targetbssp; SeqEntryPtr the_nuc; SeqEntryPtr the_prt; SeqEntryPtr tmp; ObjMgrDataPtr omdptop; ObjMgrData omdata; if (target == NULL || insert == NULL) return; if (target->data.ptrvalue == NULL || insert->data.ptrvalue == NULL) return; if (relink) { SaveSeqEntryObjMgrData (target, &omdptop, &omdata); GetSeqEntryParent (target, &parentptr, &parenttype); } if (IS_Bioseq (target) && IS_Bioseq (insert)) { targetbsp = (BioseqPtr) target->data.ptrvalue; insertbsp = (BioseqPtr) insert->data.ptrvalue; if (ISA_na (targetbsp->mol)) { if (ISA_na (insertbsp->mol)) { seg = BioseqNew (); if (seg == NULL) return; seg->mol = targetbsp->mol; seg->repr = Seq_repr_seg; seg->seq_ext_type = 1; seg->length = 0; /* seg->id = MakeSeqID ("SEG_dna"); */ /* seg->id = MakeNewProteinSeqId (NULL, NULL); */ seg->id = MakeUniqueSeqID ("segseq_"); SeqMgrAddToBioseqIndex (seg); the_nuc = SeqEntryNew (); if (the_nuc == NULL) return; the_nuc->choice = 1; the_nuc->data.ptrvalue = (Pointer) seg; segs = BioseqSetNew (); if (segs == NULL) return; segs->_class = 2; segs->seq_set = the_nuc; parts = BioseqSetNew (); if (parts == NULL) return; parts->_class = 4; tmp = SeqEntryNew (); if (tmp == NULL) return; tmp->choice = 2; tmp->data.ptrvalue = (Pointer) parts; the_nuc->next = tmp; first = SeqEntryNew (); if (first == NULL) return; first->choice = 1; first->data.ptrvalue = (Pointer) targetbsp; target->choice = 2; target->data.ptrvalue = (Pointer) segs; AddNucPart (seg, parts, first); AddNucPart (seg, parts, insert); } else if (ISA_aa (insertbsp->mol)) { nuc_prot = BioseqSetNew (); if (nuc_prot == NULL) return; nuc_prot->_class = 1; the_nuc = SeqEntryNew (); if (the_nuc == NULL) return; the_nuc->choice = 1; the_nuc->data.ptrvalue = (Pointer) targetbsp; target->choice = 2; target->data.ptrvalue = (Pointer) nuc_prot; nuc_prot->seq_set = the_nuc; the_nuc->next = insert; } } else if (ISA_aa (targetbsp->mol)) { if (ISA_na (insertbsp->mol)) { nuc_prot = BioseqSetNew (); if (nuc_prot == NULL) return; nuc_prot->_class = 1; the_prt = SeqEntryNew (); if (the_prt == NULL) return; the_prt->choice = 1; the_prt->data.ptrvalue = (Pointer) targetbsp; target->choice = 2; target->data.ptrvalue = (Pointer) nuc_prot; nuc_prot->seq_set = insert; the_prt->next = insert->next; insert->next = the_prt; } } } else if (IS_Bioseq_set (target)) { targetbssp = (BioseqSetPtr) target->data.ptrvalue; if (targetbssp->_class == 1 && IS_Bioseq (insert)) { insertbsp = (BioseqPtr) insert->data.ptrvalue; if (ISA_aa (insertbsp->mol)) { nuc_prot = targetbssp; if (nuc_prot->seq_set != NULL) { tmp = nuc_prot->seq_set; while (tmp->next != NULL) { tmp = tmp->next; } tmp->next = insert; } else { nuc_prot->seq_set = insert; } } } else if (targetbssp->_class == 2 && IS_Bioseq (insert)) { insertbsp = (BioseqPtr) insert->data.ptrvalue; if (ISA_na (insertbsp->mol)) { the_nuc = FindNucSeqEntry (target); if (the_nuc != NULL && the_nuc->next != NULL) { tmp = the_nuc->next; if (tmp->choice == 2 && tmp->data.ptrvalue != NULL) { parts = (BioseqSetPtr) tmp->data.ptrvalue; if (parts->_class == 4 && the_nuc->choice == 1) { seg = (BioseqPtr) the_nuc->data.ptrvalue; AddNucPart (seg, parts, insert); } } } } else if (ISA_aa (insertbsp->mol)) { nuc_prot = BioseqSetNew (); if (nuc_prot == NULL) return; nuc_prot->_class = 1; first = SeqEntryNew (); if (first == NULL) return; first->choice = 2; first->data.ptrvalue = (Pointer) targetbssp; target->choice = 2; target->data.ptrvalue = (Pointer) nuc_prot; nuc_prot->seq_set = first; first->next = insert; } } else if (targetbssp->_class == 7) { if (targetbssp->seq_set != NULL) { tmp = targetbssp->seq_set; while (tmp->next != NULL) { tmp = tmp->next; } tmp->next = insert; } else { targetbssp->seq_set = insert; } } else if ((targetbssp->_class >= BioseqseqSet_class_mut_set && targetbssp->_class <= BioseqseqSet_class_eco_set) || targetbssp->_class == BioseqseqSet_class_wgs_set || targetbssp->_class == BioseqseqSet_class_small_genome_set) { if (targetbssp->seq_set != NULL) { tmp = targetbssp->seq_set; while (tmp->next != NULL) { tmp = tmp->next; } tmp->next = insert; } else { targetbssp->seq_set = insert; } } else if (targetbssp->_class == BioseqseqSet_class_gen_prod_set) { if (targetbssp->seq_set != NULL) { tmp = targetbssp->seq_set; while (tmp->next != NULL) { tmp = tmp->next; } tmp->next = insert; } else { targetbssp->seq_set = insert; } } } if (relink) { SeqMgrLinkSeqEntry (target, parenttype, parentptr); RestoreSeqEntryObjMgrData (target, omdptop, &omdata); } } NLM_EXTERN void ReplaceSeqEntryWithSeqEntry (SeqEntryPtr target, SeqEntryPtr replaceWith, Boolean relink) { Uint2 parenttype; Pointer parentptr; ObjMgrDataPtr omdptop; ObjMgrData omdata; if (target == NULL || replaceWith == NULL) return; if (relink) { SaveSeqEntryObjMgrData (target, &omdptop, &omdata); GetSeqEntryParent (target, &parentptr, &parenttype); } if (target->choice == 1) { BioseqFree ((BioseqPtr) target->data.ptrvalue); } else if (target->choice == 2) { BioseqSetFree ((BioseqSetPtr) target->data.ptrvalue); } target->choice = replaceWith->choice; target->data.ptrvalue = replaceWith->data.ptrvalue; MemFree (replaceWith); if (relink) { SeqMgrLinkSeqEntry (target, parenttype, parentptr); RestoreSeqEntryObjMgrData (target, omdptop, &omdata); } } static void SeqEntryRemoveLoop (SeqEntryPtr sep, SeqEntryPtr del, SeqEntryPtr PNTR prev) { BioseqSetPtr bssp; SeqEntryPtr next; while (sep != NULL) { next = sep->next; if (sep == del) { *prev = sep->next; sep->next = NULL; SeqEntryFree (sep); } else { prev = (SeqEntryPtr PNTR) &(sep->next); if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL) { SeqEntryRemoveLoop (bssp->seq_set, del, &(bssp->seq_set)); } } } sep = next; } } NLM_EXTERN void RemoveSeqEntryFromSeqEntry (SeqEntryPtr top, SeqEntryPtr del, Boolean relink) { SeqEntryPtr dummy; ObjMgrDataPtr omdptop; ObjMgrData omdata; Uint2 parenttype; Pointer parentptr; if (top == NULL || del == NULL) return; if (top->data.ptrvalue == NULL || del->data.ptrvalue == NULL) return; if (relink) { SaveSeqEntryObjMgrData (top, &omdptop, &omdata); GetSeqEntryParent (top, &parentptr, &parenttype); } dummy = NULL; SeqEntryRemoveLoop (top, del, &dummy); if (relink) { SeqMgrLinkSeqEntry (top, parenttype, parentptr); RestoreSeqEntryObjMgrData (top, omdptop, &omdata); } } typedef struct commontitle { BioseqPtr bsp; SeqDescPtr sdp; } CommonTitleData, PNTR CommonTitlePtr; static CommonTitlePtr CommonTitleNew (BioseqPtr bsp, SeqDescPtr sdp) { CommonTitlePtr c = (CommonTitlePtr) MemNew (sizeof (CommonTitleData)); c->bsp = bsp; c->sdp = sdp; return c; } static CommonTitlePtr CommonTitleFree (CommonTitlePtr c) { if (c != NULL) { c = MemFree (c); } return c; } static ValNodePtr CommonTitleListFree (ValNodePtr vnp) { ValNodePtr vnp_next; while (vnp != NULL) { vnp_next = vnp->next; vnp->next = NULL; vnp->data.ptrvalue = CommonTitleFree (vnp->data.ptrvalue); vnp = ValNodeFree (vnp); vnp = vnp_next; } return vnp; } static void RemoveCommonTitles (ValNodePtr vnp, CharPtr common_title) { CommonTitlePtr c; ObjValNodePtr ovp; while (vnp != NULL) { c = vnp->data.ptrvalue; if (StringCmp (c->sdp->data.ptrvalue, common_title) == 0 && c->sdp->extended > 0) { ovp = (ObjValNodePtr) c->sdp; ovp->idx.deleteme = TRUE; } vnp = vnp->next; } } static int LIBCALLBACK SortCommonTitle (VoidPtr ptr1, VoidPtr ptr2) { CommonTitlePtr c1; CommonTitlePtr c2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { c1 = (CommonTitlePtr) vnp1->data.ptrvalue; c2 = (CommonTitlePtr) vnp2->data.ptrvalue; if (c1 != NULL && c2 != NULL && c1->sdp != NULL && c2->sdp != NULL && c1->sdp->data.ptrvalue != NULL && c2->sdp->data.ptrvalue != NULL) { return StringCmp (c1->sdp->data.ptrvalue, c2->sdp->data.ptrvalue); } } } return 0; } static void CollectCommonTitle (BioseqPtr bsp, Pointer data) { SeqDescPtr sdp; if (bsp == NULL || ISA_aa (bsp->mol) || data == NULL) { return; } sdp = bsp->descr; while (sdp != NULL) { if (sdp->choice == Seq_descr_title) { ValNodeAddPointer ((ValNodePtr PNTR) data, 0, CommonTitleNew (bsp, sdp)); } sdp = sdp->next; } } static CharPtr FindCommonTitleFromList (ValNodePtr list) { ValNodePtr vnp; CommonTitlePtr c; Int4 num_common = 0, num_total, num_expected; CharPtr common_title; if (list == NULL) { return NULL; } num_total = ValNodeLen (list); if (num_total % 2 != 0 || num_total < 4) { return NULL; } num_expected = num_total / 2; c = list->data.ptrvalue; common_title = c->sdp->data.ptrvalue; num_common = 1; for (vnp = list->next; vnp != NULL; vnp = vnp->next) { c = (CommonTitlePtr) vnp->data.ptrvalue; if (StringCmp (common_title, c->sdp->data.ptrvalue) == 0) { num_common++; } else { num_common = 1; common_title = c->sdp->data.ptrvalue; } } if (num_common == num_expected) { return StringSave (common_title); } return NULL; } static void PromoteCommonTitlesSetCallback (BioseqSetPtr bssp, Pointer data) { ValNodePtr list = NULL; CharPtr common_title = NULL; SeqDescrPtr sdp; Int4 num_member = 0; SeqEntryPtr s; CharPtr set_title = NULL; if (bssp == NULL || !GetsDocsumTitle (bssp->_class)) { return; } VisitBioseqsInSet (bssp, &list, CollectCommonTitle); list = ValNodeSort (list, SortCommonTitle); common_title = FindCommonTitleFromList (list); if (common_title != NULL) { s = bssp->seq_set; while (s != NULL) { num_member++; s = s->next; } if (ValNodeLen (list) == num_member) { for (sdp = bssp->descr; sdp != NULL && set_title == NULL; sdp = sdp->next) { if (sdp->choice == Seq_descr_title) { set_title = sdp->data.ptrvalue; } } if (set_title != NULL && StringCmp (set_title, common_title) != 0) { /* don't remove, the seq titles just happen to be identical */ common_title = MemFree (common_title); } } } if (common_title != NULL) { sdp = SeqDescrNew (NULL); sdp->choice = Seq_descr_title; sdp->data.ptrvalue = common_title; sdp->next = bssp->descr; bssp->descr = sdp; RemoveCommonTitles (list, common_title); } list = CommonTitleListFree(list); } NLM_EXTERN void PromoteCommonTitlesToSet (SeqEntryPtr sep) { VisitSetsInSep (sep, NULL, PromoteCommonTitlesSetCallback); } NLM_EXTERN void DeleteMultipleTitles (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; Boolean hastitle; ValNodePtr nextsdp; Pointer PNTR prevsdp; ValNodePtr sdp; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sdp = bsp->descr; prevsdp = (Pointer PNTR) &(bsp->descr); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sdp = bssp->descr; prevsdp = (Pointer PNTR) &(bssp->descr); } else return; hastitle = FALSE; while (sdp != NULL) { nextsdp = sdp->next; if (sdp->choice == Seq_descr_title) { if (hastitle) { *(prevsdp) = sdp->next; sdp->next = NULL; SeqDescFree (sdp); } else { hastitle = TRUE; prevsdp = (Pointer PNTR) &(sdp->next); } } else { prevsdp = (Pointer PNTR) &(sdp->next); } sdp = nextsdp; } } NLM_EXTERN void RenormalizeNucProtSets (SeqEntryPtr sep, Boolean relink) { SeqAnnotPtr annot; BioseqPtr bsp; BioseqSetPtr bssp; ValNodePtr descr; ObjMgrDataPtr omdptop; ObjMgrData omdata; Uint2 parenttype; Pointer parentptr; SeqAnnotPtr sap, tmp_sap; SeqEntryPtr seqentry; if (sep == NULL) return; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && (bssp->_class == 7 || (bssp->_class >= 13 && bssp->_class <= 16) || bssp->_class == BioseqseqSet_class_wgs_set || bssp->_class == BioseqseqSet_class_gen_prod_set || bssp->_class == BioseqseqSet_class_small_genome_set)) { for (sep = bssp->seq_set; sep != NULL; sep = sep->next) { RenormalizeNucProtSets (sep, relink); } return; } if (bssp != NULL && bssp->_class == 1) { seqentry = bssp->seq_set; if (seqentry != NULL && seqentry->next == NULL) { if (relink) { SaveSeqEntryObjMgrData (sep, &omdptop, &omdata); GetSeqEntryParent (sep, &parentptr, &parenttype); } descr = bssp->descr; bssp->descr = NULL; annot = bssp->annot; bssp->annot = NULL; sep->choice = seqentry->choice; sep->data.ptrvalue = seqentry->data.ptrvalue; seqentry->data.ptrvalue = NULL; bssp->seq_set = NULL; bssp->seqentry = NULL; MemFree (seqentry); BioseqSetFree (bssp); sap = NULL; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; ValNodeLink (&(bsp->descr), descr); if (bsp->annot == NULL) { bsp->annot = annot; annot = NULL; } else { sap = bsp->annot; } } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; ValNodeLink (&(bssp->descr), descr); if (bssp->annot == NULL) { bssp->annot = annot; annot = NULL; } else { sap = bssp->annot; } } if (sap != NULL) { tmp_sap = sap; while (tmp_sap->next != NULL) { tmp_sap = tmp_sap->next; } tmp_sap->next = annot; MergeAdjacentAnnotsInList (sap); } DeleteMultipleTitles (sep, NULL, 0, 0); if (relink) { SeqMgrLinkSeqEntry (sep, parenttype, parentptr); RestoreSeqEntryObjMgrData (sep, omdptop, &omdata); } } } } } NLM_EXTERN ValNodePtr ExtractBioSourceAndPubs (SeqEntryPtr sep) { BioseqPtr bsp; BioseqSetPtr bssp; ValNodePtr descr; ValNodePtr last; ValNodePtr nextsdp; Pointer PNTR prevsdp; ValNodePtr sdp; if (sep == NULL || sep->data.ptrvalue == NULL) return NULL; descr = NULL; last = NULL; sdp = NULL; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sdp = bsp->descr; prevsdp = (Pointer PNTR) &(bsp->descr); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sdp = bssp->descr; prevsdp = (Pointer PNTR) &(bssp->descr); } else return NULL; while (sdp != NULL) { nextsdp = sdp->next; if (sdp->choice == Seq_descr_pub || sdp->choice == Seq_descr_source) { *(prevsdp) = sdp->next; sdp->next = NULL; if (descr == NULL) { descr = sdp; last = descr; } else if (last != NULL) { last->next = sdp; last = last->next; } } else { prevsdp = (Pointer PNTR) &(sdp->next); } sdp = nextsdp; } return descr; } NLM_EXTERN void ReplaceBioSourceAndPubs (SeqEntryPtr sep, ValNodePtr descr) { BioseqPtr bsp; BioseqSetPtr bssp; ValNodePtr last; Pointer PNTR prevsdp; ValNodePtr sdp; if (sep == NULL || descr == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sdp = bsp->descr; prevsdp = (Pointer PNTR) &(bsp->descr); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sdp = bssp->descr; prevsdp = (Pointer PNTR) &(bssp->descr); } else return; last = descr; while (last->next != NULL) { last = last->next; } last->next = sdp; *(prevsdp) = descr; } typedef struct targetdata { BioseqPtr bsp; SeqEntryPtr nps; Boolean skipGenProdSet; } TargetData, PNTR TargetDataPtr; static Boolean ReturnStackToItem (GatherContextPtr gcp) { BioseqSetPtr bssp; Int2 i; Uint2 itemtype; TargetDataPtr tdp; if (gcp == NULL) return TRUE; tdp = (TargetDataPtr) gcp->userdata; if (tdp == NULL) return TRUE; if (gcp->gatherstack != NULL && gcp->numstack > 0) { for (i = 0; i < gcp->numstack; i++) { itemtype = gcp->gatherstack [i].itemtype; if (itemtype == OBJ_BIOSEQ || itemtype == OBJ_BIOSEQSET) { tdp->nps = SeqMgrGetSeqEntryForData (gcp->gatherstack [i].thisitem); if (gcp->gatherstack [i].itemtype == OBJ_BIOSEQSET) { bssp = (BioseqSetPtr) gcp->gatherstack [i].thisitem; if (bssp->_class != BioseqseqSet_class_genbank && bssp->_class != BioseqseqSet_class_mut_set && bssp->_class != BioseqseqSet_class_pop_set && bssp->_class != BioseqseqSet_class_phy_set && bssp->_class != BioseqseqSet_class_eco_set && bssp->_class != BioseqseqSet_class_wgs_set && bssp->_class != BioseqseqSet_class_small_genome_set && (bssp->_class != BioseqseqSet_class_gen_prod_set || (! tdp->skipGenProdSet))) { return FALSE; } } else if (gcp->gatherstack [i].itemtype == OBJ_BIOSEQ) { return FALSE; } } } } return FALSE; } static Boolean GetStackToTarget (GatherContextPtr gcp) { TargetDataPtr tdp; if (gcp == NULL) return TRUE; tdp = (TargetDataPtr) gcp->userdata; if (tdp == NULL) return TRUE; if (gcp->thistype == OBJ_BIOSEQ) { if (tdp->bsp == (BioseqPtr) gcp->thisitem) { return ReturnStackToItem (gcp); } } return TRUE; } NLM_EXTERN SeqEntryPtr LIBCALL GetBestTopParentForDataEx (Uint2 entityID, BioseqPtr bsp, Boolean skipGenProdSet) { BioseqSetPtr bssp; BioseqSetPtr parent; GatherScope gs; TargetData td; td.bsp = bsp; td.nps = NULL; td.skipGenProdSet = skipGenProdSet; if (entityID > 0 && bsp != NULL) { if (bsp->idx.parenttype == OBJ_BIOSEQSET) { bssp = (BioseqSetPtr) bsp->idx.parentptr; if (bssp != NULL && bssp->_class == BioseqseqSet_class_parts && bssp->idx.parenttype == OBJ_BIOSEQSET) { parent = (BioseqSetPtr) bssp->idx.parentptr; if (parent != NULL && parent->_class == BioseqseqSet_class_segset) { bssp = parent; } } if (bssp != NULL && bssp->_class == BioseqseqSet_class_segset && bssp->idx.parenttype == OBJ_BIOSEQSET) { parent = (BioseqSetPtr) bssp->idx.parentptr; if (parent != NULL && parent->_class == BioseqseqSet_class_nuc_prot) { bssp = parent; } } if (bssp != NULL && bssp->seqentry != NULL) { if (bssp->_class == BioseqseqSet_class_nuc_prot || bssp->_class == BioseqseqSet_class_segset || bssp->_class == BioseqseqSet_class_parts) { return bssp->seqentry; } } if (bsp->seqentry != NULL) { return bsp->seqentry; } } MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; MemSet ((Pointer) (gs.ignore), (int) (TRUE), (size_t) (OBJ_MAX * sizeof (Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; GatherEntity (entityID, (Pointer) &td, GetStackToTarget, &gs); } return td.nps; } NLM_EXTERN SeqEntryPtr LIBCALL GetBestTopParentForData (Uint2 entityID, BioseqPtr bsp) { return GetBestTopParentForDataEx (entityID, bsp, FALSE); } NLM_EXTERN SeqEntryPtr LIBCALL GetBestTopParentForItemIDEx (Uint2 entityID, Uint4 itemID, Uint2 itemtype, Boolean skipGenProdSet) { TargetData td; td.bsp = NULL; td.nps = NULL; td.skipGenProdSet = skipGenProdSet; if (entityID > 0 && itemID > 0 && itemtype > 0) { GatherItem (entityID, itemID, itemtype, (Pointer) &td, ReturnStackToItem); } return td.nps; } NLM_EXTERN SeqEntryPtr LIBCALL GetBestTopParentForItemID (Uint2 entityID, Uint4 itemID, Uint2 itemtype) { return GetBestTopParentForItemIDEx (entityID, itemID, itemtype, FALSE); } NLM_EXTERN SeqEntryPtr LIBCALL GetTopSeqEntryForEntityID (Uint2 entityID) { ObjMgrDataPtr omdp; SeqSubmitPtr ssp; omdp = ObjMgrGetData (entityID); if (omdp != NULL) { switch (omdp->datatype) { case OBJ_SEQSUB : ssp = (SeqSubmitPtr) omdp->dataptr; if (ssp != NULL && ssp->datatype == 1) { return (SeqEntryPtr) ssp->data; } break; case OBJ_BIOSEQ : return (SeqEntryPtr) omdp->choice; case OBJ_BIOSEQSET : return (SeqEntryPtr) omdp->choice; default : break; } } return NULL; } NLM_EXTERN Boolean CheckSeqLocForPartialEx (SeqLocPtr location, BoolPtr p5ptr, BoolPtr p3ptr, Int4Ptr limptr) { SeqLocPtr firstSlp; IntFuzzPtr ifp; SeqLocPtr lastSlp; Int4 lim; Boolean partial5; Boolean partial3; SeqIntPtr sip; SeqLocPtr slp; SeqPntPtr spp; partial5 = FALSE; partial3 = FALSE; lim = -1; if (location != NULL) { firstSlp = NULL; lastSlp = NULL; slp = SeqLocFindNext (location, NULL); while (slp != NULL) { if (firstSlp == NULL) { firstSlp = slp; } lastSlp = slp; slp = SeqLocFindNext (location, slp); } if (firstSlp != NULL) { if (firstSlp->choice == SEQLOC_INT && firstSlp->data.ptrvalue != NULL) { sip = (SeqIntPtr) firstSlp->data.ptrvalue; if (sip->strand == Seq_strand_minus || sip->strand == Seq_strand_both_rev) { ifp = sip->if_to; if (ifp != NULL && ifp->choice == 4 && ifp->a == 1) { partial5 = TRUE; } } else { ifp = sip->if_from; if (ifp != NULL && ifp->choice == 4 && ifp->a == 2) { partial5 = TRUE; } } } else if (firstSlp->choice == SEQLOC_PNT && firstSlp->data.ptrvalue != NULL) { spp = (SeqPntPtr) firstSlp->data.ptrvalue; if (spp->strand == Seq_strand_minus || spp->strand == Seq_strand_both_rev) { ifp = spp->fuzz; if (ifp != NULL && ifp->choice == 4 && ifp->a == 1) { partial5 = TRUE; } } else { ifp = spp->fuzz; if (ifp != NULL && ifp->choice == 4 && ifp->a == 2) { partial5 = TRUE; } } ifp = spp->fuzz; if (ifp != NULL && ifp->choice == 4) { lim = ifp->a; } } } if (lastSlp != NULL) { if (lastSlp->choice == SEQLOC_INT && lastSlp->data.ptrvalue != NULL) { sip = (SeqIntPtr) lastSlp->data.ptrvalue; if (sip->strand == Seq_strand_minus || sip->strand == Seq_strand_both_rev) { ifp = sip->if_from; if (ifp != NULL && ifp->choice == 4 && ifp->a == 2) { partial3 = TRUE; } } else { ifp = sip->if_to; if (ifp != NULL && ifp->choice == 4 && ifp->a == 1) { partial3 = TRUE; } } } else if (lastSlp->choice == SEQLOC_PNT && lastSlp->data.ptrvalue != NULL) { spp = (SeqPntPtr) lastSlp->data.ptrvalue; if (spp->strand == Seq_strand_minus || spp->strand == Seq_strand_both_rev) { ifp = spp->fuzz; if (ifp != NULL && ifp->choice == 4 && ifp->a == 2) { partial3 = TRUE; } } else { ifp = spp->fuzz; if (ifp != NULL && ifp->choice == 4 && ifp->a == 1) { partial3 = TRUE; } } ifp = spp->fuzz; if (ifp != NULL && ifp->choice == 4) { lim = ifp->a; } } } } if (p5ptr != NULL) { *p5ptr = partial5; } if (p3ptr != NULL) { *p3ptr = partial3; } if (limptr != NULL) { *limptr = lim; } return (Boolean) (partial5 || partial3 || lim == 3 || lim == 4); } NLM_EXTERN Boolean CheckSeqLocForPartial (SeqLocPtr location, BoolPtr p5ptr, BoolPtr p3ptr) { return CheckSeqLocForPartialEx (location, p5ptr, p3ptr, NULL); } static void ConvertWholeToIntLoc (SeqLocPtr slp) { BioseqPtr bsp; SeqIntPtr sip; if (slp == NULL || slp->choice != SEQLOC_WHOLE || slp->data.ptrvalue == NULL) { return; } bsp = BioseqFind (slp->data.ptrvalue); if (bsp == NULL) { return; } sip = SeqIntNew (); if (sip != NULL) { sip->from = 0; sip->to = bsp->length - 1; sip->id = SeqIdDup (SeqIdFindBest (bsp->id, 0)); sip->strand = bsp->strand; slp->data.ptrvalue = SeqIdFree (slp->data.ptrvalue); slp->data.ptrvalue = sip; slp->choice = SEQLOC_INT; } } NLM_EXTERN void SetSeqLocPartialEx (SeqLocPtr location, Boolean partial5, Boolean partial3, Int4 lim) { SeqLocPtr firstSlp; IntFuzzPtr ifp; SeqLocPtr lastSlp; SeqIntPtr sip; SeqLocPtr slp; SeqPntPtr spp; if (location != NULL) { /* if whole, need to convert to int */ if (partial5 || partial3) { ConvertWholeToIntLoc (location); } firstSlp = NULL; lastSlp = NULL; slp = SeqLocFindNext (location, NULL); while (slp != NULL) { if (firstSlp == NULL) { firstSlp = slp; } lastSlp = slp; slp = SeqLocFindNext (location, slp); } if (firstSlp != NULL) { if (firstSlp->choice == SEQLOC_INT && firstSlp->data.ptrvalue != NULL) { sip = (SeqIntPtr) firstSlp->data.ptrvalue; if (partial5) { ifp = IntFuzzNew (); if (ifp != NULL) { ifp->choice = 4; if (sip->strand == Seq_strand_minus || sip->strand == Seq_strand_both_rev) { sip->if_to = IntFuzzFree (sip->if_to); sip->if_to = ifp; ifp->a = 1; } else { sip->if_from = IntFuzzFree (sip->if_from); sip->if_from = ifp; ifp->a = 2; } } } else { if (sip->strand == Seq_strand_minus || sip->strand == Seq_strand_both_rev) { sip->if_to = IntFuzzFree (sip->if_to); } else { sip->if_from = IntFuzzFree (sip->if_from); } } } else if (firstSlp->choice == SEQLOC_PNT && firstSlp->data.ptrvalue != NULL) { spp = (SeqPntPtr) firstSlp->data.ptrvalue; if (partial5) { ifp = IntFuzzNew (); if (ifp != NULL) { ifp->choice = 4; if (spp->strand == Seq_strand_minus || spp->strand == Seq_strand_both_rev) { spp->fuzz = IntFuzzFree (spp->fuzz); spp->fuzz = ifp; ifp->a = 1; } else { spp->fuzz = IntFuzzFree (spp->fuzz); spp->fuzz = ifp; ifp->a = 2; } } } else if (lim == 3 || lim == 4) { ifp = IntFuzzNew (); if (ifp != NULL) { ifp->choice = 4; spp->fuzz = IntFuzzFree (spp->fuzz); spp->fuzz = ifp; ifp->a = lim; } } else { if (spp->strand == Seq_strand_minus || spp->strand == Seq_strand_both_rev) { spp->fuzz = IntFuzzFree (spp->fuzz); } else { spp->fuzz = IntFuzzFree (spp->fuzz); } } } } if (lastSlp != NULL) { if (lastSlp->choice == SEQLOC_INT && lastSlp->data.ptrvalue != NULL) { sip = (SeqIntPtr) lastSlp->data.ptrvalue; if (partial3) { ifp = IntFuzzNew (); if (ifp != NULL) { ifp->choice = 4; if (sip->strand == Seq_strand_minus || sip->strand == Seq_strand_both_rev) { sip->if_from = IntFuzzFree (sip->if_from); sip->if_from = ifp; ifp->a = 2; } else { sip->if_to = IntFuzzFree (sip->if_to); sip->if_to = ifp; ifp->a = 1; } } } else { if (sip->strand == Seq_strand_minus || sip->strand == Seq_strand_both_rev) { sip->if_from = IntFuzzFree (sip->if_from); } else { sip->if_to = IntFuzzFree (sip->if_to); } } } else if (lastSlp->choice == SEQLOC_PNT && lastSlp->data.ptrvalue != NULL) { spp = (SeqPntPtr) lastSlp->data.ptrvalue; if (partial3) { ifp = IntFuzzNew (); if (ifp != NULL) { ifp->choice = 4; if (spp->strand == Seq_strand_minus || spp->strand == Seq_strand_both_rev) { spp->fuzz = IntFuzzFree (spp->fuzz); spp->fuzz = ifp; ifp->a = 2; } else { spp->fuzz = IntFuzzFree (spp->fuzz); spp->fuzz = ifp; ifp->a = 1; } } } else if (lim == 3 || lim == 4) { ifp = IntFuzzNew (); if (ifp != NULL) { ifp->choice = 4; spp->fuzz = IntFuzzFree (spp->fuzz); spp->fuzz = ifp; ifp->a = lim; } } else { if (spp->strand == Seq_strand_minus || spp->strand == Seq_strand_both_rev) { spp->fuzz = IntFuzzFree (spp->fuzz); } else { spp->fuzz = IntFuzzFree (spp->fuzz); } } } } } } NLM_EXTERN void SetSeqLocPartial (SeqLocPtr location, Boolean partial5, Boolean partial3) { SetSeqLocPartialEx (location, partial5, partial3, -1); } NLM_EXTERN ValNodePtr GetSeqLocPartialSet (SeqLocPtr location) { ValNodePtr head = NULL, last = NULL, vnp; Int4 lim; Boolean noLeft; Boolean noRight; SeqLocPtr slp; Int4 val; if (location == NULL) return NULL; slp = SeqLocFindNext (location, NULL); while (slp != NULL) { CheckSeqLocForPartialEx (slp, &noLeft, &noRight, &lim); val = 0; if (noLeft) { val |= 2; } if (noRight) { val |= 1; } if (lim == 3) { val |= 4; } else if (lim == 4) { val |= 8; } vnp = ValNodeAddInt (&last, 0, val); if (head == NULL) { head = vnp; } last = vnp; slp = SeqLocFindNext (location, slp); } return head; } NLM_EXTERN void SetSeqLocPartialSet (SeqLocPtr location, ValNodePtr vnp) { Int4 lim; Boolean noLeft; Boolean noRight; SeqLocPtr slp; Int4 val; if (location == NULL || vnp == NULL) return; slp = SeqLocFindNext (location, NULL); while (slp != NULL && vnp != NULL) { val = (Int4) vnp->data.intvalue; noLeft = (Boolean) ((val & 2) != 0); noRight = (Boolean) ((val & 1) != 0); lim = -1; if ((val & 4) != 0) { lim = 3; } else if ((val & 8) != 0) { lim = 4; } SetSeqLocPartialEx (slp, noLeft, noRight, lim); slp = SeqLocFindNext (location, slp); vnp = vnp->next; } } /* KeyTag section */ NLM_EXTERN int LIBCALLBACK SortVnpByString (VoidPtr ptr1, VoidPtr ptr2) { CharPtr str1; CharPtr str2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { str1 = (CharPtr) vnp1->data.ptrvalue; str2 = (CharPtr) vnp2->data.ptrvalue; if (str1 != NULL && str2 != NULL) { return StringICmp (str1, str2); } } } return 0; } NLM_EXTERN int LIBCALLBACK SortVnpByStringCS (VoidPtr ptr1, VoidPtr ptr2) { CharPtr str1; CharPtr str2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { str1 = (CharPtr) vnp1->data.ptrvalue; str2 = (CharPtr) vnp2->data.ptrvalue; if (str1 != NULL && str2 != NULL) { return StringCmp (str1, str2); } } } return 0; } NLM_EXTERN int LIBCALLBACK SortVnpByStringCI (VoidPtr ptr1, VoidPtr ptr2) { CharPtr str1; CharPtr str2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { str1 = (CharPtr) vnp1->data.ptrvalue; str2 = (CharPtr) vnp2->data.ptrvalue; if (str1 != NULL && str2 != NULL) { return StringCmp (str1, str2); } } } return 0; } NLM_EXTERN int LIBCALLBACK SortVnpByStringCIUCFirst (VoidPtr ptr1, VoidPtr ptr2) { int comp; CharPtr str1; CharPtr str2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { str1 = (CharPtr) vnp1->data.ptrvalue; str2 = (CharPtr) vnp2->data.ptrvalue; if (str1 != NULL && str2 != NULL) { comp = StringICmp (str1, str2); if (comp != 0) return comp; return StringCmp (str1, str2); } } } return 0; } NLM_EXTERN int LIBCALLBACK SortVnpByStringCILCFirst (VoidPtr ptr1, VoidPtr ptr2) { int comp; CharPtr str1; CharPtr str2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { str1 = (CharPtr) vnp1->data.ptrvalue; str2 = (CharPtr) vnp2->data.ptrvalue; if (str1 != NULL && str2 != NULL) { comp = StringICmp (str1, str2); if (comp != 0) return comp; return StringCmp (str2, str1); } } } return 0; } NLM_EXTERN int LIBCALLBACK SortVnpByNaturalCS (VoidPtr ptr1, VoidPtr ptr2) { CharPtr str1, str2; ValNodePtr vnp1, vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; str1 = (CharPtr) vnp1->data.ptrvalue; str2 = (CharPtr) vnp2->data.ptrvalue; if (str1 == NULL || str2 == NULL) return 0; return NaturalStringCmp (str1, str2); } NLM_EXTERN int LIBCALLBACK SortVnpByNaturalCI (VoidPtr ptr1, VoidPtr ptr2) { CharPtr str1, str2; ValNodePtr vnp1, vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; str1 = (CharPtr) vnp1->data.ptrvalue; str2 = (CharPtr) vnp2->data.ptrvalue; if (str1 == NULL || str2 == NULL) return 0; return NaturalStringICmp (str1, str2); } NLM_EXTERN ValNodePtr UniqueValNode (ValNodePtr list) { CharPtr last; ValNodePtr next; Pointer PNTR prev; CharPtr str; ValNodePtr vnp; if (list == NULL) return NULL; last = (CharPtr) list->data.ptrvalue; vnp = list->next; prev = (Pointer PNTR) &(list->next); while (vnp != NULL) { next = vnp->next; str = (CharPtr) vnp->data.ptrvalue; if (StringICmp (last, str) == 0) { vnp->next = NULL; *prev = next; ValNodeFreeData (vnp); } else { last = (CharPtr) vnp->data.ptrvalue; prev = (Pointer PNTR) &(vnp->next); } vnp = next; } return list; } NLM_EXTERN ValNodePtr UniqueStringValNodeCS (ValNodePtr list) { CharPtr last; ValNodePtr next; Pointer PNTR prev; CharPtr str; ValNodePtr vnp; if (list == NULL) return NULL; last = (CharPtr) list->data.ptrvalue; vnp = list->next; prev = (Pointer PNTR) &(list->next); while (vnp != NULL) { next = vnp->next; str = (CharPtr) vnp->data.ptrvalue; if (StringCmp (last, str) == 0) { vnp->next = NULL; *prev = next; ValNodeFreeData (vnp); } else { last = (CharPtr) vnp->data.ptrvalue; prev = (Pointer PNTR) &(vnp->next); } vnp = next; } return list; } NLM_EXTERN ValNodePtr UniqueStringValNodeCI (ValNodePtr list) { CharPtr last; ValNodePtr next; Pointer PNTR prev; CharPtr str; ValNodePtr vnp; if (list == NULL) return NULL; last = (CharPtr) list->data.ptrvalue; vnp = list->next; prev = (Pointer PNTR) &(list->next); while (vnp != NULL) { next = vnp->next; str = (CharPtr) vnp->data.ptrvalue; if (StringICmp (last, str) == 0) { vnp->next = NULL; *prev = next; ValNodeFreeData (vnp); } else { last = (CharPtr) vnp->data.ptrvalue; prev = (Pointer PNTR) &(vnp->next); } vnp = next; } return list; } NLM_EXTERN int LIBCALLBACK SortByIntvalue (VoidPtr ptr1, VoidPtr ptr2) { Int4 val1; Int4 val2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; val1 = (Int4) vnp1->data.intvalue; val2 = (Int4) vnp2->data.intvalue; if (val1 > val2) { return 1; } else if (val1 < val2) { return -1; } return 0; } NLM_EXTERN ValNodePtr UniqueIntValNode (ValNodePtr list) { Int4 curr, last; ValNodePtr next; Pointer PNTR prev; ValNodePtr vnp; if (list == NULL) return NULL; last = (Int4) list->data.intvalue; vnp = list->next; prev = (Pointer PNTR) &(list->next); while (vnp != NULL) { next = vnp->next; curr = (Int4) vnp->data.intvalue; if (last == curr) { vnp->next = NULL; *prev = next; ValNodeFree (vnp); } else { last = (Int4) vnp->data.intvalue; prev = (Pointer PNTR) &(vnp->next); } vnp = next; } return list; } NLM_EXTERN int LIBCALLBACK SortByPtrvalue (VoidPtr ptr1, VoidPtr ptr2) { VoidPtr val1; VoidPtr val2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; val1 = (VoidPtr) vnp1->data.ptrvalue; val2 = (VoidPtr) vnp2->data.ptrvalue; if (val1 > val2) { return 1; } else if (val1 < val2) { return -1; } return 0; } NLM_EXTERN ValNodePtr UniquePtrValNode (ValNodePtr list) { VoidPtr curr, last; ValNodePtr next; Pointer PNTR prev; ValNodePtr vnp; if (list == NULL) return NULL; last = (VoidPtr) list->data.ptrvalue; vnp = list->next; prev = (Pointer PNTR) &(list->next); while (vnp != NULL) { next = vnp->next; curr = (VoidPtr) vnp->data.ptrvalue; if (last == curr) { vnp->next = NULL; *prev = next; ValNodeFree (vnp); } else { last = (VoidPtr) vnp->data.ptrvalue; prev = (Pointer PNTR) &(vnp->next); } vnp = next; } return list; } NLM_EXTERN void KeyTagInit (KeyTag PNTR ktp, ValNodePtr list) { Int2 i; CharPtr PNTR index; Int2 num; ValNodePtr vnp; if (ktp == NULL || list == NULL) return; list = ValNodeSort (list, SortVnpByString); list = UniqueValNode (list); num = ValNodeLen (list); index = MemNew (sizeof (CharPtr) * (num + 1)); for (vnp = list, i = 0; vnp != NULL && i < num; vnp = vnp->next, i++) { index [i] = (CharPtr) vnp->data.ptrvalue; } ktp->num = num; ktp->list = list; ktp->index = index; } NLM_EXTERN void KeyTagClear (KeyTag PNTR ktp) { if (ktp == NULL) return; ktp->num = 0; ktp->list = ValNodeFreeData (ktp->list); ktp->index = MemFree (ktp->index); } NLM_EXTERN Int2 KeyFromTag (KeyTag PNTR ktp, CharPtr tag) { Int2 L, R, mid, compare; if (ktp == NULL || ktp->list == NULL || ktp->index == NULL) return 0; if (tag == NULL) return 0; L = 0; R = ktp->num - 1; while (L < R) { mid = (L + R) / 2; compare = StringICmp (ktp->index [mid], tag); if (compare < 0) { L = mid + 1; } else { R = mid; } } if (StringICmp (ktp->index [R], tag) == 0) { return (R + 1); } return 0; } NLM_EXTERN CharPtr TagFromKey (KeyTag PNTR ktp, Int2 key) { if (ktp == NULL || ktp->list == NULL || ktp->index == NULL) return 0; if (key < 1 || key > ktp->num) return 0; key--; return ktp->index [key]; } /* begin PromoteXrefs section */ typedef struct geneextendlist { GeneRefPtr grp; SeqLocPtr slp; ObjMgrPtr omp; Boolean rsult; Char label [41]; } GeneExtendList, PNTR GeneExtendPtr; static Boolean GeneExtendFunc (GatherContextPtr gcp) { BioseqPtr bsp; GeneExtendPtr gep; GeneRefPtr grp; Boolean hasNulls; ObjMgrTypePtr omtp; SeqFeatPtr sfp; SeqLocPtr slp; Char thislabel [41]; if (gcp == NULL) return TRUE; gep = (GeneExtendPtr) gcp->userdata; if (gep == NULL ) return TRUE; thislabel [0] = '\0'; if (gcp->thistype == OBJ_SEQFEAT) { sfp = (SeqFeatPtr) gcp->thisitem; if (sfp != NULL && sfp->data.choice == SEQFEAT_GENE && sfp->data.value.ptrvalue != NULL) { grp = (GeneRefPtr) sfp->data.value.ptrvalue; omtp = ObjMgrTypeFind (gep->omp, gcp->thistype, NULL, NULL); if (omtp == NULL) { return TRUE; } if (omtp->labelfunc != NULL) { (*(omtp->labelfunc)) (gcp->thisitem, thislabel, 40, OM_LABEL_CONTENT); } if (thislabel [0] != '\0') { if (StringICmp (thislabel, gep->label) == 0) { if (SeqLocCompare (gep->slp, sfp->location) != SLC_NO_MATCH) { bsp = GetBioseqGivenSeqLoc (sfp->location, gcp->entityID); if (bsp != NULL) { slp = SeqLocMerge (bsp, sfp->location, gep->slp, TRUE, FALSE, FALSE); if (slp != NULL) { sfp->location = SeqLocFree (sfp->location); sfp->location = slp; if (bsp->repr == Seq_repr_seg) { slp = SegLocToPartsEx (bsp, sfp->location, TRUE); sfp->location = SeqLocFree (sfp->location); sfp->location = slp; hasNulls = LocationHasNullsBetween (sfp->location); sfp->partial = (sfp->partial || hasNulls); } FreeAllFuzz (slp); gep->rsult = TRUE; } } } return FALSE; } } } } return TRUE; } /* static Boolean ExtendGene (GeneRefPtr grp, SeqEntryPtr nsep, SeqLocPtr slp) { GeneExtendList gel; GatherScope gs; ObjMgrTypePtr omtp; SeqFeatPtr sfp; if (grp == NULL || nsep == NULL || slp == NULL) return FALSE; gel.grp = grp; gel.slp = slp; gel.omp = ObjMgrGet (); gel.label [0] = '\0'; gel.rsult = FALSE; omtp = ObjMgrTypeFind (gel.omp, OBJ_SEQFEAT, NULL, NULL); if (omtp != NULL && omtp->labelfunc != NULL) { sfp = SeqFeatNew (); if (sfp != NULL) { sfp->data.choice = SEQFEAT_GENE; sfp->data.value.ptrvalue = (Pointer) grp; (*(omtp->labelfunc)) ((Pointer) sfp, gel.label, 40, OM_LABEL_CONTENT); sfp->data.value.ptrvalue = NULL; SeqFeatFree (sfp); } } MemSet ((Pointer)(&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; gs.get_feats_location = TRUE; MemSet((Pointer)(gs.ignore), (int)(TRUE), (size_t)(OBJ_MAX * sizeof(Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQFEAT] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; GatherSeqEntry (nsep, (Pointer) &gel, GeneExtendFunc, &gs); return gel.rsult; } */ NLM_EXTERN void SetEmptyGeneticCodes (SeqAnnotPtr sap, Int2 genCode) { CdRegionPtr crp; GeneticCodePtr gc; SeqFeatPtr sfp; ValNodePtr vnp; if (sap == NULL || sap->type != 1) return; for (sfp = (SeqFeatPtr) sap->data; sfp != NULL; sfp = sfp->next) { if (sfp->data.choice == SEQFEAT_CDREGION) { crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { gc = crp->genetic_code; if (gc != NULL) { vnp = gc->data.ptrvalue; if (vnp != NULL && vnp->choice == 2) { vnp->data.intvalue = (Int4) genCode; /* if (vnp->data.intvalue == 0) { vnp->data.intvalue = (Int4) genCode; } */ } } } } } } NLM_EXTERN void PromoteXrefsExEx ( SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID, Boolean include_stop, Boolean remove_trailingX, Boolean gen_prod_set, Boolean force_local_id, BoolPtr seq_fetch_failP ) { Int2 adv; ByteStorePtr bs; BioseqSetPtr bssp; Char ch; CharPtr comment; CdRegionPtr crp; Int2 ctr = 1; ValNodePtr descr; SeqFeatPtr first; GBQualPtr gbq; Int4 i; Char id [128]; SeqEntryPtr last; Char lcl [128]; BioseqPtr mbsp; MolInfoPtr mip; SeqEntryPtr msep; SeqFeatXrefPtr next; GBQualPtr nextqual; SeqEntryPtr old; ObjMgrDataPtr omdptop; ObjMgrData omdata; Uint2 parenttype; Pointer parentptr; Boolean partial5; Boolean partial3; BioseqPtr pbsp; SeqFeatXrefPtr PNTR prev; GBQualPtr PNTR prevqual; SeqFeatPtr prot; CharPtr protseq; ProtRefPtr prp, prp2; SeqEntryPtr psep; CharPtr ptr; CharPtr rnaseq; SeqEntryPtr sep; SeqHistPtr shp; SeqIdPtr sip; SeqEntryPtr target = NULL; Uint4 version = 0; long int val; ValNodePtr vnp; SeqFeatXrefPtr xref; Boolean ok_to_remove; /* DbtagPtr dbt; SeqFeatPtr gene; GeneRefPtr grp; */ if (seq_fetch_failP != NULL) { *seq_fetch_failP = FALSE; } if (sfp == NULL || bsp == NULL) return; /* set subtypes, used to find mRNA features for genomic product sets */ first = sfp; while (sfp != NULL) { if (sfp->idx.subtype == 0) { sfp->idx.subtype = FindFeatDefType (sfp); } sfp = sfp->next; } /* no longer expand genes specified by qualifiers on other features (except repeat_region) */ /* sfp = first; while (sfp != NULL) { prev = &(sfp->xref); xref = sfp->xref; while (xref != NULL) { next = xref->next; if (xref->data.choice == SEQFEAT_GENE && sfp->data.choice != SEQFEAT_GENE && sfp->idx.subtype != FEATDEF_repeat_region) { grp = (GeneRefPtr) xref->data.value.ptrvalue; if (grp != NULL && SeqMgrGeneIsSuppressed (grp)) { } else { xref->data.value.ptrvalue = NULL; if (grp != NULL) { sep = SeqMgrGetSeqEntryForData (bsp); if (ExtendGene (grp, sep, sfp->location)) { GeneRefFree (grp); } else { gene = CreateNewFeature (sep, NULL, SEQFEAT_GENE, NULL); if (gene != NULL) { gene->data.value.ptrvalue = (Pointer) grp; gene->location = SeqLocFree (gene->location); gene->location = AsnIoMemCopy (sfp->location, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); for (vnp = sfp->dbxref; vnp != NULL; vnp = vnp->next) { dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt == NULL) continue; ValNodeAddPointer (&(gene->dbxref), 0, (Pointer) DbtagDup (dbt)); } } } } *(prev) = next; xref->next = NULL; xref->data.choice = 0; SeqFeatXrefFree (xref); } } else { prev = &(xref->next); } xref = next; } sfp = sfp->next; } */ /* expand mRNA features into cDNA product sequences */ bssp = NULL; sep = NULL; last = NULL; if (gen_prod_set) { sep = GetTopSeqEntryForEntityID (entityID); if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->seq_set != NULL) { last = bssp->seq_set; while (last->next != NULL) { last = last->next; } } } } if (gen_prod_set && sep != NULL && bssp != NULL && last != NULL) { target = sep; SaveSeqEntryObjMgrData (target, &omdptop, &omdata); GetSeqEntryParent (target, &parentptr, &parenttype); sfp = first; while (sfp != NULL) { if (sfp->data.choice == SEQFEAT_RNA && /* sfp->idx.subtype != FEATDEF_tRNA && */ sfp->product == NULL && (! sfp->pseudo)) { gbq = sfp->qual; prevqual = (GBQualPtr PNTR) &(sfp->qual); id [0] = '\0'; sip = NULL; comment = NULL; while (gbq != NULL) { nextqual = gbq->next; if (StringICmp (gbq->qual, "transcript_id") == 0) { if (StringDoesHaveText (id) && StringDoesHaveText (gbq->val)) { ErrPostEx (SEV_WARNING, ERR_FEATURE_QualWrongThisFeat, "RNA transcript_id %s replacing %s", gbq->val, id); } *(prevqual) = gbq->next; gbq->next = NULL; StringNCpy_0 (id, gbq->val, sizeof (id)); GBQualFree (gbq); } else if (StringICmp (gbq->qual, "comment") == 0 && StringDoesHaveText (gbq->val)) { *(prevqual) = gbq->next; gbq->next = NULL; comment = StringSave (gbq->val); GBQualFree (gbq); } else { prevqual = (GBQualPtr PNTR) &(gbq->next); } gbq = nextqual; } if (! StringHasNoText (id)) { if (StringChr (id, '|') != NULL) { sip = SeqIdParse (id); } else if (force_local_id) { sprintf (lcl, "lcl|%s", id); sip = SeqIdParse (lcl); } else { adv = ValidateAccnDotVer (id); if (adv == 0 || adv == -5) { ptr = StringChr (id, '.'); if (ptr != NULL) { *ptr = '\0'; ptr++; if (sscanf (ptr, "%ld", &val) == 1) { version = (Uint4) val; } } sip = SeqIdFromAccession (id, version, NULL); } else { sprintf (lcl, "lcl|%s", id); sip = SeqIdParse (lcl); } } } if (sip != NULL || sfp->idx.subtype == FEATDEF_mRNA) { rnaseq = GetSequenceByFeature (sfp); if (rnaseq == NULL && seq_fetch_failP != NULL) { *seq_fetch_failP = TRUE; } if (rnaseq != NULL) { i = (Int4) StringLen (rnaseq); bs = BSNew (i + 2); if (bs != NULL) { BSWrite (bs, (VoidPtr) rnaseq, (Int4) StringLen (rnaseq)); mbsp = BioseqNew (); if (mbsp != NULL) { mbsp->repr = Seq_repr_raw; mbsp->mol = Seq_mol_rna; mbsp->seq_data_type = Seq_code_iupacna; mbsp->seq_data = (SeqDataPtr) bs; mbsp->length = BSLen (bs); BioseqPack (mbsp); bs = NULL; /* sep = GetTopSeqEntryForEntityID (entityID); */ old = SeqEntrySetScope (sep); if (sip != NULL) { mbsp->id = sip; } else if (sfp->idx.subtype == FEATDEF_mRNA) { /* actually just making rapid unique ID for mRNA */ mbsp->id = MakeNewProteinSeqIdEx (sfp->location, NULL, NULL, &ctr); } CheckSeqLocForPartial (sfp->location, &partial5, &partial3); SeqMgrAddToBioseqIndex (mbsp); SeqEntrySetScope (old); msep = SeqEntryNew (); if (msep != NULL) { msep->choice = 1; msep->data.ptrvalue = (Pointer) mbsp; SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) mbsp, msep); mip = MolInfoNew (); if (mip != NULL) { switch (sfp->idx.subtype) { case FEATDEF_preRNA : mip->biomol = MOLECULE_TYPE_PRE_MRNA; break; case FEATDEF_mRNA : mip->biomol = MOLECULE_TYPE_MRNA; break; case FEATDEF_tRNA : mip->biomol = MOLECULE_TYPE_TRNA; break; case FEATDEF_rRNA : mip->biomol = MOLECULE_TYPE_RRNA; break; case FEATDEF_snRNA : mip->biomol = MOLECULE_TYPE_SNRNA; break; case FEATDEF_scRNA : mip->biomol = MOLECULE_TYPE_SCRNA; break; case FEATDEF_otherRNA : mip->biomol = MOLECULE_TYPE_TRANSCRIBED_RNA; break; case FEATDEF_snoRNA : mip->biomol = MOLECULE_TYPE_SNORNA; break; case FEATDEF_ncRNA : mip->biomol = MOLECULE_TYPE_NCRNA; break; case FEATDEF_tmRNA : mip->biomol = MOLECULE_TYPE_TMRNA; break; default : mip->biomol = 0; break; } if (partial5 && partial3) { mip->completeness = 5; } else if (partial5) { mip->completeness = 3; } else if (partial3) { mip->completeness = 4; } vnp = CreateNewDescriptor (msep, Seq_descr_molinfo); if (vnp != NULL) { vnp->data.ptrvalue = (Pointer) mip; } } if (comment != NULL) { vnp = CreateNewDescriptor (msep, Seq_descr_comment); if (vnp != NULL) { vnp->data.ptrvalue = (Pointer) comment; } } /* add mRNA sequence to genomic product set */ last->next = msep; last = msep; SetSeqFeatProduct (sfp, mbsp); } } } rnaseq = MemFree (rnaseq); } } } sfp = sfp->next; } SeqMgrLinkSeqEntry (target, parenttype, parentptr); RestoreSeqEntryObjMgrData (target, omdptop, &omdata); } /* expand coding region features into protein product sequences */ last = NULL; sfp = first; while (sfp != NULL) { prev = &(sfp->xref); xref = sfp->xref; while (xref != NULL) { next = xref->next; if (xref->data.choice == SEQFEAT_PROT && sfp->data.choice == SEQFEAT_CDREGION && sfp->product == NULL && (! sfp->pseudo)) { prp = (ProtRefPtr) xref->data.value.ptrvalue; ok_to_remove = TRUE; if (prp != NULL) { crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { /** crp->frame = 0; **/ bs = ProteinFromCdRegionEx (sfp, include_stop, remove_trailingX); if (bs == NULL && seq_fetch_failP != NULL) { *seq_fetch_failP = TRUE; } if (bs != NULL) { protseq = BSMerge (bs, NULL); bs = BSFree (bs); if (protseq != NULL) { ptr = protseq; ch = *ptr; while (ch != '\0') { *ptr = TO_UPPER (ch); ptr++; ch = *ptr; } i = (Int4) StringLen (protseq); if (i > 0 && protseq [i - 1] == '*') { protseq [i - 1] = '\0'; } bs = BSNew (i + 2); if (bs != NULL) { ptr = protseq; /* if (protseq [0] == '-') { ptr++; } */ BSWrite (bs, (VoidPtr) ptr, (Int4) StringLen (ptr)); } protseq = MemFree (protseq); } pbsp = BioseqNew (); if (pbsp != NULL) { pbsp->repr = Seq_repr_raw; pbsp->mol = Seq_mol_aa; pbsp->seq_data_type = Seq_code_ncbieaa; pbsp->seq_data = (SeqDataPtr) bs; pbsp->length = BSLen (bs); bs = NULL; sep = NULL; mbsp = NULL; if (gen_prod_set) { gbq = sfp->qual; prevqual = (GBQualPtr PNTR) &(sfp->qual); id [0] = '\0'; sip = NULL; while (gbq != NULL) { nextqual = gbq->next; if (StringICmp (gbq->qual, "transcript_id") == 0) { if (StringDoesHaveText (id) && StringDoesHaveText (gbq->val)) { ErrPostEx (SEV_WARNING, ERR_FEATURE_QualWrongThisFeat, "CDS transcript_id %s replacing %s", gbq->val, id); } *(prevqual) = gbq->next; gbq->next = NULL; StringNCpy_0 (id, gbq->val, sizeof (id)); GBQualFree (gbq); } else if (StringICmp (gbq->qual, "secondary_accession") == 0) { *(prevqual) = gbq->next; gbq->next = NULL; shp = ParseStringIntoSeqHist (NULL, gbq->val); if (shp != NULL) { pbsp->hist = shp; } GBQualFree (gbq); } else { prevqual = (GBQualPtr PNTR) &(gbq->next); } gbq = nextqual; } if (StringHasNoText (id)) { Message (MSG_POSTERR, "No transcript_id on CDS - unable to create nuc-prot set"); } else { if (StringChr (id, '|') != NULL) { sip = SeqIdParse (id); } else if (force_local_id) { sprintf (lcl, "lcl|%s", id); sip = SeqIdParse (lcl); } else { adv = ValidateAccnDotVer (id); if (adv == 0 || adv == -5) { ptr = StringChr (id, '.'); if (ptr != NULL) { *ptr = '\0'; ptr++; if (sscanf (ptr, "%ld", &val) == 1) { version = (Uint4) val; } } sip = SeqIdFromAccession (id, version, NULL); } else { sprintf (lcl, "lcl|%s", id); sip = SeqIdParse (lcl); } } } mbsp = BioseqFind (sip); SeqIdFree (sip); if (mbsp != NULL) { sep = SeqMgrGetSeqEntryForData (mbsp); /* } else { sep = GetBestTopParentForDataEx (entityID, bsp, TRUE); */ } } else { sep = GetBestTopParentForData (entityID, bsp); } if (sep == NULL) { Message (MSG_POSTERR, "No location for nuc-prot set for CDS - unable to create nuc-prot set"); pbsp = BioseqFree (pbsp); ok_to_remove = FALSE; } else { old = SeqEntrySetScope (sep); gbq = sfp->qual; prevqual = (GBQualPtr PNTR) &(sfp->qual); id [0] = '\0'; sip = NULL; while (gbq != NULL) { nextqual = gbq->next; if (StringICmp (gbq->qual, "protein_id") == 0) { if (StringDoesHaveText (id) && StringDoesHaveText (gbq->val)) { ErrPostEx (SEV_WARNING, ERR_FEATURE_QualWrongThisFeat, "CDS protein_id %s replacing %s", gbq->val, id); } *(prevqual) = gbq->next; gbq->next = NULL; StringNCpy_0 (id, gbq->val, sizeof (id)); GBQualFree (gbq); } else { prevqual = (GBQualPtr PNTR) &(gbq->next); } gbq = nextqual; } if (! StringHasNoText (id)) { if (StringChr (id, '|') != NULL) { sip = SeqIdParse (id); } else if (force_local_id) { sprintf (lcl, "lcl|%s", id); sip = SeqIdParse (lcl); } else { adv = ValidateAccnDotVer (id); if (adv == 0 || adv == -5) { ptr = StringChr (id, '.'); if (ptr != NULL) { *ptr = '\0'; ptr++; if (sscanf (ptr, "%ld", &val) == 1) { version = (Uint4) val; } } sip = SeqIdFromAccession (id, version, NULL); } else { sprintf (lcl, "lcl|%s", id); sip = SeqIdParse (lcl); } } } if (sip != NULL) { pbsp->id = sip; } else { pbsp->id = MakeNewProteinSeqIdEx (sfp->location, NULL, NULL, &ctr); } CheckSeqLocForPartial (sfp->location, &partial5, &partial3); SeqMgrAddToBioseqIndex (pbsp); SeqEntrySetScope (old); psep = SeqEntryNew (); if (psep != NULL) { psep->choice = 1; psep->data.ptrvalue = (Pointer) pbsp; SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) pbsp, psep); mip = MolInfoNew (); if (mip != NULL) { mip->biomol = 8; mip->tech = 8; if (partial5 && partial3) { mip->completeness = 5; } else if (partial5) { mip->completeness = 3; } else if (partial3) { mip->completeness = 4; } vnp = CreateNewDescriptor (psep, Seq_descr_molinfo); if (vnp != NULL) { vnp->data.ptrvalue = (Pointer) mip; } } /* the first protein may change the set/seq structure, so goes through AddSeqEntryToSeqEntry */ if (gen_prod_set || last == NULL) { descr = ExtractBioSourceAndPubs (sep); AddSeqEntryToSeqEntry (sep, psep, TRUE); ReplaceBioSourceAndPubs (sep, descr); last = psep; } else { last->next = psep; last = psep; } if (target == NULL) { target = sep; SaveSeqEntryObjMgrData (target, &omdptop, &omdata); GetSeqEntryParent (target, &parentptr, &parenttype); } SetSeqFeatProduct (sfp, pbsp); psep = SeqMgrGetSeqEntryForData (pbsp); if (psep != NULL) { last = psep; prot = CreateNewFeature (psep, NULL, SEQFEAT_PROT, NULL); if (prot != NULL) { prot->data.value.ptrvalue = (Pointer) prp; SetSeqLocPartial (prot->location, partial5, partial3); prot->partial = (Boolean) (partial5 || partial3); } } } } } } } } if (ok_to_remove) { xref->data.value.ptrvalue = NULL; *(prev) = next; xref->next = NULL; xref->data.choice = 0; SeqFeatXrefFree (xref); } else { prev = &(xref->next); } } else { prev = &(xref->next); } xref = next; } sfp = sfp->next; } /* expand mat_peptide features with protein_id qualifiers into protein product sequences */ last = NULL; sfp = first; while (sfp != NULL) { if (sfp->data.choice == SEQFEAT_PROT && sfp->product == NULL) { prp = (ProtRefPtr) sfp->data.value.ptrvalue; gbq = sfp->qual; prevqual = (GBQualPtr PNTR) &(sfp->qual); id [0] = '\0'; sip = NULL; while (gbq != NULL) { nextqual = gbq->next; if (StringICmp (gbq->qual, "protein_id") == 0) { if (StringDoesHaveText (id) && StringDoesHaveText (gbq->val)) { ErrPostEx (SEV_WARNING, ERR_FEATURE_QualWrongThisFeat, "Protein protein_id %s replacing %s", gbq->val, id); } *(prevqual) = gbq->next; gbq->next = NULL; StringNCpy_0 (id, gbq->val, sizeof (id)); GBQualFree (gbq); } else { prevqual = (GBQualPtr PNTR) &(gbq->next); } gbq = nextqual; } if (! StringHasNoText (id)) { if (StringChr (id, '|') != NULL) { sip = SeqIdParse (id); } else if (force_local_id) { sprintf (lcl, "lcl|%s", id); sip = SeqIdParse (lcl); } else { adv = ValidateAccnDotVer (id); if (adv == 0 || adv == -5) { ptr = StringChr (id, '.'); if (ptr != NULL) { *ptr = '\0'; ptr++; if (sscanf (ptr, "%ld", &val) == 1) { version = (Uint4) val; } } sip = SeqIdFromAccession (id, version, NULL); } else { sprintf (lcl, "lcl|%s", id); sip = SeqIdParse (lcl); } } } if (sip != NULL) { protseq = GetSequenceByFeature (sfp); if (protseq == NULL && seq_fetch_failP != NULL) { *seq_fetch_failP = TRUE; } if (protseq != NULL) { i = (Int4) StringLen (protseq); bs = BSNew (i + 2); if (bs != NULL) { BSWrite (bs, (VoidPtr) protseq, (Int4) StringLen (protseq)); pbsp = BioseqNew (); if (pbsp != NULL) { pbsp->repr = Seq_repr_raw; pbsp->mol = Seq_mol_aa; pbsp->seq_data_type = Seq_code_ncbieaa; pbsp->seq_data = (SeqDataPtr) bs; pbsp->length = BSLen (bs); bs = NULL; /* sep = GetTopSeqEntryForEntityID (entityID); */ sep = GetBestTopParentForData (entityID, bsp); old = SeqEntrySetScope (sep); if (sip != NULL) { pbsp->id = sip; } else { pbsp->id = MakeNewProteinSeqIdEx (sfp->location, NULL, NULL, &ctr); } CheckSeqLocForPartial (sfp->location, &partial5, &partial3); SeqMgrAddToBioseqIndex (pbsp); SeqEntrySetScope (old); psep = SeqEntryNew (); if (psep != NULL) { psep->choice = 1; psep->data.ptrvalue = (Pointer) pbsp; SeqMgrSeqEntry (SM_BIOSEQ, (Pointer) pbsp, psep); mip = MolInfoNew (); if (mip != NULL) { mip->biomol = MOLECULE_TYPE_PEPTIDE; if (partial5 && partial3) { mip->completeness = 5; } else if (partial5) { mip->completeness = 3; } else if (partial3) { mip->completeness = 4; } vnp = CreateNewDescriptor (psep, Seq_descr_molinfo); if (vnp != NULL) { vnp->data.ptrvalue = (Pointer) mip; } } if (last == NULL) { AddSeqEntryToSeqEntry (sep, psep, TRUE); last = psep; } else { last->next = psep; last = psep; } SetSeqFeatProduct (sfp, pbsp); if (prp != NULL) { prp2 = AsnIoMemCopy ((Pointer) prp, (AsnReadFunc) ProtRefAsnRead, (AsnWriteFunc) ProtRefAsnWrite); if (prp2 != NULL) { psep = SeqMgrGetSeqEntryForData (pbsp); if (psep != NULL) { prot = CreateNewFeature (psep, NULL, SEQFEAT_PROT, NULL); if (prot != NULL) { prot->data.value.ptrvalue = prp2; SetSeqLocPartial (prot->location, partial5, partial3); prot->partial = (Boolean) (partial5 || partial3); } } } } } } } protseq = MemFree (protseq); } } } sfp = sfp->next; } if (target != NULL) { SeqMgrLinkSeqEntry (target, parenttype, parentptr); RestoreSeqEntryObjMgrData (target, omdptop, &omdata); } } NLM_EXTERN void PromoteXrefsEx (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID, Boolean include_stop, Boolean remove_trailingX, Boolean gen_prod_set) { PromoteXrefsExEx (sfp, bsp, entityID, include_stop, remove_trailingX, gen_prod_set, FALSE, NULL); } NLM_EXTERN void PromoteXrefs (SeqFeatPtr sfp, BioseqPtr bsp, Uint2 entityID) { PromoteXrefsExEx (sfp, bsp, entityID, TRUE, FALSE, FALSE, FALSE, NULL); } /* begin BasicSeqEntryCleanup section */ static Boolean HasNoText (CharPtr str) { Uchar ch; /* to use 8bit characters in multibyte languages */ if (str != NULL) { ch = *str; while (ch != '\0') { if (ch > ' ') { return FALSE; } str++; ch = *str; } } return TRUE; } static Boolean AlreadyInVnpList (ValNodePtr head, ValNodePtr curr) { if (head == NULL || curr == NULL) return FALSE; /* since we cannot sort these lists, must check against all previous entries */ while (head != curr && head != NULL) { if (StringICmp (head->data.ptrvalue, curr->data.ptrvalue) == 0) return TRUE; head = head->next; } return FALSE; } NLM_EXTERN CharPtr TrimSpacesAndSemicolons (CharPtr str) { CharPtr amp; Uchar ch; /* to use 8bit characters in multibyte languages */ CharPtr dst; CharPtr ptr; if (str != NULL && str [0] != '\0') { dst = str; ptr = str; ch = *ptr; if (ch != '\0' && (ch <= ' ' || ch == ';')) { while (ch != '\0' && (ch <= ' ' || ch == ';')) { ptr++; ch = *ptr; } while (ch != '\0') { *dst = ch; dst++; ptr++; ch = *ptr; } *dst = '\0'; } amp = NULL; dst = NULL; ptr = str; ch = *ptr; while (ch != '\0') { if (ch == '&') { amp = ptr; dst = NULL; } else if (ch <= ' ') { if (dst == NULL) { dst = ptr; } amp = NULL; } else if (ch == ';') { if (dst == NULL && amp == NULL) { dst = ptr; } } else { dst = NULL; } ptr++; ch = *ptr; } if (dst != NULL) { *dst = '\0'; } } return str; } NLM_EXTERN CharPtr TrimSpacesAndJunkFromEnds ( CharPtr str, Boolean allowEllipsis ) { Uchar ch; /* to use 8bit characters in multibyte languages */ CharPtr dst; Boolean isPeriod; Boolean isTilde; CharPtr ptr; if (str != NULL && str [0] != '\0') { dst = str; ptr = str; ch = *ptr; if (ch != '\0' && ch <= ' ') { while (ch != '\0' && ch <= ' ') { ptr++; ch = *ptr; } while (ch != '\0') { *dst = ch; dst++; ptr++; ch = *ptr; } *dst = '\0'; } dst = NULL; ptr = str; ch = *ptr; isPeriod = FALSE; isTilde = FALSE; while (ch != '\0') { if (ch <= ' ' || ch == '.' || ch == ',' || ch == '~' || ch == ';') { if (dst == NULL) { dst = ptr; } isPeriod = (Boolean) (isPeriod || ch == '.'); isTilde = (Boolean) (isTilde || ch == '~'); } else { dst = NULL; isPeriod = FALSE; isTilde = FALSE; } ptr++; ch = *ptr; } if (dst != NULL) { /* allow one period at end */ if (isPeriod) { *dst = '.'; dst++; /* ellipsis are now okay */ if (allowEllipsis && *dst == '.' && dst [1] == '.') { dst += 2; } } else if (isTilde) { /* allow double tilde at end */ if (*dst == '~' && dst [1] == '~') { dst += 2; } } *dst = '\0'; } } return str; } static CharPtr TrimSpacesSemicolonsAndCommas (CharPtr str) { CharPtr amp; Uchar ch; /* to use 8bit characters in multibyte languages */ CharPtr dst; CharPtr ptr; if (str != NULL && str [0] != '\0') { dst = str; ptr = str; ch = *ptr; if (ch != '\0' && (ch <= ' ' || ch == ';' || ch == ',')) { while (ch != '\0' && (ch <= ' ' || ch == ';' || ch == ',')) { ptr++; ch = *ptr; } while (ch != '\0') { *dst = ch; dst++; ptr++; ch = *ptr; } *dst = '\0'; } amp = NULL; dst = NULL; ptr = str; ch = *ptr; while (ch != '\0') { if (ch == '&') { amp = ptr; dst = NULL; } else if (ch <= ' ') { if (dst == NULL) { dst = ptr; } amp = NULL; } else if (ch == ';') { if (dst == NULL && amp == NULL) { dst = ptr; } } else if (ch == ',') { if (dst == NULL) { dst = ptr; } amp = NULL; } else { dst = NULL; } ptr++; ch = *ptr; } if (dst != NULL) { *dst = '\0'; } } return str; } static CharPtr TrimSpacesSemicolonsAndCommasAndParens (CharPtr str) { CharPtr amp; Uchar ch; /* to use 8bit characters in multibyte languages */ CharPtr dst; CharPtr ptr; if (str != NULL && str [0] != '\0') { dst = str; ptr = str; ch = *ptr; if (ch != '\0' && (ch <= ' ' || ch == ';' || ch == ',' || ch == '(')) { while (ch != '\0' && (ch <= ' ' || ch == ';' || ch == ',' || ch == '(')) { ptr++; ch = *ptr; } while (ch != '\0') { *dst = ch; dst++; ptr++; ch = *ptr; } *dst = '\0'; } amp = NULL; dst = NULL; ptr = str; ch = *ptr; while (ch != '\0') { if (ch == '&') { amp = ptr; dst = NULL; } else if (ch <= ' ') { if (dst == NULL) { dst = ptr; } amp = NULL; } else if (ch == ';') { if (dst == NULL && amp == NULL) { dst = ptr; } } else if (ch == ',') { if (dst == NULL) { dst = ptr; } amp = NULL; } else if (ch == ')') { if (dst == NULL) { dst = ptr; } amp = NULL; } else { dst = NULL; } ptr++; ch = *ptr; } if (dst != NULL) { *dst = '\0'; } } return str; } static CharPtr TrimFlankingQuotes (CharPtr str) { size_t len; if (str != NULL && str [0] != '\0') { len = StringLen (str); while (len > 0) { if (str [0] == '"' && str [len - 1] == '"') { str [0] = ' '; str [len - 1] = ' '; } else if (str [0] == '\'' && str [len - 1] == '\'') { str [0] = ' '; str [len - 1] = ' '; } else { return str; } TrimSpacesAroundString (str); len = StringLen (str); } } return str; } static void RemoveFlankingQuotes (CharPtr PNTR strp) { if (strp == NULL) return; if (*strp == NULL) return; TrimFlankingQuotes (*strp); if (HasNoText (*strp)) { *strp = MemFree (*strp); } } static void RemoveFlankingQuotesList (ValNodePtr PNTR vnpp) { ValNodePtr next; ValNodePtr PNTR prev; ValNodePtr vnp; if (vnpp == NULL) return; prev = vnpp; vnp = *vnpp; while (vnp != NULL) { next = vnp->next; TrimFlankingQuotes (vnp->data.ptrvalue); if (HasNoText (vnp->data.ptrvalue) || AlreadyInVnpList (*vnpp, vnp)) { *prev = vnp->next; vnp->next = NULL; ValNodeFreeData (vnp); } else { prev = &(vnp->next); } vnp = next; } } static void CleanVisString (CharPtr PNTR strp) { if (strp == NULL) return; if (*strp == NULL) return; TrimSpacesSemicolonsAndCommas (*strp); if (HasNoText (*strp)) { *strp = MemFree (*strp); } } static void CleanVisStringAndCompress (CharPtr PNTR strp) { if (strp == NULL) return; if (*strp == NULL) return; TrimSpacesSemicolonsAndCommas (*strp); Asn2gnbkCompressSpaces (*strp); if (HasNoText (*strp)) { *strp = MemFree (*strp); } } static void CleanVisStringJunk (CharPtr PNTR strp) { if (strp == NULL) return; if (*strp == NULL) return; TrimSpacesAndJunkFromEnds (*strp, TRUE); if (HasNoText (*strp)) { *strp = MemFree (*strp); } } static void CleanVisStringJunkAndCompress (CharPtr PNTR strp) { if (strp == NULL) return; if (*strp == NULL) return; TrimSpacesAndJunkFromEnds (*strp, TRUE); Asn2gnbkCompressSpaces (*strp); if (HasNoText (*strp)) { *strp = MemFree (*strp); } } static void CleanDoubleQuote (CharPtr str) { Char ch; if (str == NULL) return; ch = *str; while (ch != '\0') { if (ch == '"') { *str = '\''; } str++; ch = *str; } } static CharPtr RemoveSpacesBetweenTildes (CharPtr str) { Char ch; CharPtr dst; CharPtr ptr; CharPtr tmp; if (str == NULL || str [0] == '\0') return str; dst = str; ptr = str; ch = *ptr; while (ch != '\0') { *dst = ch; dst++; ptr++; if (ch == '~') { tmp = ptr; ch = *tmp; while (ch != 0 && ch <= ' ') { tmp++; ch = *tmp; } if (ch == '~') { ptr = tmp; } } ch = *ptr; } *dst = '\0'; return str; } static void CleanVisStringList (ValNodePtr PNTR vnpp) { ValNodePtr next; ValNodePtr PNTR prev; ValNodePtr vnp; if (vnpp == NULL) return; prev = vnpp; vnp = *vnpp; while (vnp != NULL) { next = vnp->next; TrimSpacesSemicolonsAndCommas (vnp->data.ptrvalue); if (HasNoText (vnp->data.ptrvalue) || AlreadyInVnpList (*vnpp, vnp)) { *prev = vnp->next; vnp->next = NULL; ValNodeFreeData (vnp); } else { prev = &(vnp->next); } vnp = next; } } static void CleanVisStringListAndCompress (ValNodePtr PNTR vnpp) { ValNodePtr next; ValNodePtr PNTR prev; ValNodePtr vnp; if (vnpp == NULL) return; prev = vnpp; vnp = *vnpp; while (vnp != NULL) { next = vnp->next; TrimSpacesSemicolonsAndCommas (vnp->data.ptrvalue); Asn2gnbkCompressSpaces (vnp->data.ptrvalue); if (HasNoText (vnp->data.ptrvalue) || AlreadyInVnpList (*vnpp, vnp)) { *prev = vnp->next; vnp->next = NULL; ValNodeFreeData (vnp); } else { prev = &(vnp->next); } vnp = next; } } static Boolean AlreadyInVnpListCaseSensitive (ValNodePtr head, ValNodePtr curr) { if (head == NULL || curr == NULL) return FALSE; /* since we cannot sort these lists, must check against all previous entries */ while (head != curr && head != NULL) { if (StringCmp (head->data.ptrvalue, curr->data.ptrvalue) == 0) return TRUE; head = head->next; } return FALSE; } static void CleanVisStringListCaseSensitive (ValNodePtr PNTR vnpp) { ValNodePtr next; ValNodePtr PNTR prev; ValNodePtr vnp; if (vnpp == NULL) return; prev = vnpp; vnp = *vnpp; while (vnp != NULL) { next = vnp->next; TrimSpacesSemicolonsAndCommas (vnp->data.ptrvalue); if (HasNoText (vnp->data.ptrvalue) || AlreadyInVnpListCaseSensitive (*vnpp, vnp)) { *prev = vnp->next; vnp->next = NULL; ValNodeFreeData (vnp); } else { prev = &(vnp->next); } vnp = next; } } static void CleanDoubleQuoteList (ValNodePtr vnp) { while (vnp != NULL) { CleanDoubleQuote ((CharPtr) vnp->data.ptrvalue); vnp = vnp->next; } } static Boolean HandledGBQualOnGene (SeqFeatPtr sfp, GBQualPtr gbq) { Int2 choice = 0; GeneRefPtr grp; if (StringICmp (gbq->qual, "map") == 0) { choice = 2; } else if (StringICmp (gbq->qual, "allele") == 0) { choice = 3; } else if (StringICmp (gbq->qual, "locus_tag") == 0) { choice = 4; } else if (StringICmp (gbq->qual, "old_locus_tag") == 0) { choice = 5; } if (choice > 0) { grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (grp == NULL) return FALSE; switch (choice) { case 2 : if (grp->maploc != NULL) return FALSE; if (StringHasNoText (gbq->val)) return FALSE; grp->maploc = StringSave (gbq->val); break; case 3 : if (StringHasNoText (gbq->val)) return FALSE; if (grp->allele != NULL) { if (StringICmp (gbq->val, grp->allele) == 0) return TRUE; return FALSE; } grp->allele = StringSave (gbq->val); break; case 4 : if (grp->locus_tag != NULL) return FALSE; if (StringHasNoText (gbq->val)) return FALSE; grp->locus_tag = StringSave (gbq->val); break; case 5 : /* removed by indexer request */ /* if (StringHasNoText (gbq->val)) return FALSE; * if (grp->locus_tag != NULL) { * if (StringICmp (gbq->val, grp->locus_tag) == 0) return TRUE; * return FALSE; * } */ return FALSE; break; default : break; } return TRUE; } return FALSE; } /* code break parser functions from the flatfile parser */ static Uint1 GetQualValueAa (CharPtr qval) { CharPtr str, eptr, ptr; Uint1 aa; str = StringStr(qval, "aa:"); if (str != NULL) { str += 3; } else { ErrPostEx (SEV_WARNING, ERR_QUALIFIER_InvalidDataFormat, "bad transl_except %s", qval); str = StringStr(qval, ","); if (str != NULL) { str = StringStr(str, ":"); if (str != NULL) { str++; } } } if (str == NULL) return (Uint1) 'X'; while (*str == ' ') ++str; for (eptr = str; *eptr != ')' && *eptr != ' ' && *eptr != '\0'; eptr++) continue; ptr = TextSave(str, eptr-str); aa = ValidAminoAcid(ptr); MemFree(ptr); return (aa); } static CharPtr SimpleValuePos (CharPtr qval) { CharPtr bptr, eptr; if ((bptr = StringStr(qval, "(pos:")) == NULL) { return NULL; } bptr += 5; while (*bptr == ' ') ++bptr; for (eptr = bptr; *eptr != ',' && *eptr != '\0'; eptr++) continue; return (TextSave(bptr, eptr-bptr)); } extern Boolean ParseAnticodon (SeqFeatPtr sfp, CharPtr val, Int4 offset); extern Boolean ParseAnticodon (SeqFeatPtr sfp, CharPtr val, Int4 offset) { Int4 diff; Int2 j; Boolean locmap; int num_errs; CharPtr pos; Boolean pos_range = FALSE; RnaRefPtr rrp; SeqIntPtr sintp; SeqIdPtr sip; Boolean sitesmap; SeqLocPtr slp; SeqPntPtr spp; Uint1 strand; Int4 temp; tRNAPtr trp; if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return FALSE; if (StringHasNoText (val)) return FALSE; rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp == NULL) return FALSE; if (rrp->ext.choice == 0 && rrp->ext.value.ptrvalue == NULL) { rrp->ext.choice = 2; trp = (tRNAPtr) MemNew (sizeof (tRNA)); rrp->ext.value.ptrvalue = (Pointer) trp; if (trp != NULL) { trp->aatype = 2; for (j = 0; j < 6; j++) { trp->codon [j] = 255; } } } if (rrp->ext.choice != 2) return FALSE; trp = (tRNAPtr) rrp->ext.value.ptrvalue; if (trp == NULL) return FALSE; /* find SeqId to use */ sip = SeqLocId (sfp->location); if (sip == NULL) { slp = SeqLocFindNext (sfp->location, NULL); if (slp != NULL) { sip = SeqLocId (slp); } } if (sip == NULL) return FALSE; /* parse location */ pos = SimpleValuePos (val); if (pos == NULL) { ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing, "anticodon parsing failed, %s, drop the anticodon", val); return FALSE; } trp->anticodon = Nlm_gbparseint (pos, &locmap, &sitesmap, &num_errs, sip); if (trp->anticodon == NULL) { ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing, "anticodon parsing failed, %s, drop the anticodon", pos); MemFree (pos); return FALSE; } if (trp->anticodon->choice == SEQLOC_PNT) { /* allow a single point */ spp = trp->anticodon->data.ptrvalue; if (spp != NULL) { spp->point += offset; } } if (trp->anticodon->choice == SEQLOC_INT) { sintp = trp->anticodon->data.ptrvalue; if (sintp == NULL) { MemFree (pos); return FALSE; } sintp->from += offset; sintp->to += offset; if (sintp->from > sintp->to) { temp = sintp->from; sintp->from = sintp->to; sintp->to = temp; } sintp->strand = SeqLocStrand (sfp->location); strand = sintp->strand; diff = SeqLocStop(trp->anticodon) - SeqLocStart(trp->anticodon); /* SeqLocStop/Start does not do what you think */ /* if ((diff != 2 && (strand != Seq_strand_minus)) || (diff != -2 && (strand == Seq_strand_minus))) { pos_range = TRUE; } */ if (diff != 2) { pos_range = TRUE; } if (num_errs > 0 || pos_range) { ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing, "anticodon range is wrong, %s, drop the anticodon", pos); MemFree (pos); return FALSE; } if (SeqLocCompare (sfp->location, trp->anticodon) != SLC_B_IN_A) { ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing, "/anticodon not in tRNA: %s", val); MemFree (pos); return FALSE; } } MemFree (pos); return TRUE; } extern Boolean ParseCodeBreak (SeqFeatPtr sfp, CharPtr val, Int4 offset); extern Boolean ParseCodeBreak (SeqFeatPtr sfp, CharPtr val, Int4 offset) { CodeBreakPtr cbp; CdRegionPtr crp; Int4 diff; CodeBreakPtr lastcbp; Boolean locmap; int num_errs; CharPtr pos; Boolean pos_range = FALSE; SeqIntPtr sintp; SeqIdPtr sip; Boolean sitesmap; SeqLocPtr slp; SeqPntPtr spp; Uint1 strand; Int4 temp; if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION) return FALSE; if (StringHasNoText (val)) return FALSE; crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp == NULL) return FALSE; /* find SeqId to use */ sip = SeqLocId (sfp->location); if (sip == NULL) { slp = SeqLocFindNext (sfp->location, NULL); if (slp != NULL) { sip = SeqLocId (slp); } } if (sip == NULL) return FALSE; cbp = CodeBreakNew (); if (cbp == NULL) return FALSE; cbp->aa.choice = 1; /* ncbieaa */ cbp->aa.value.intvalue = (Int4) GetQualValueAa (val); /* parse location */ pos = SimpleValuePos (val); if (pos == NULL) { ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing, "transl_except parsing failed, %s, drop the transl_except", val); return FALSE; } cbp->loc = Nlm_gbparseint (pos, &locmap, &sitesmap, &num_errs, sip); if (cbp->loc == NULL) { CodeBreakFree (cbp); ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing, "transl_except parsing failed, %s, drop the transl_except", pos); MemFree (pos); return FALSE; } if (cbp->loc->choice == SEQLOC_PNT) { /* allow a single point */ spp = cbp->loc->data.ptrvalue; if (spp != NULL) { spp->point += offset; } } if (cbp->loc->choice == SEQLOC_INT) { sintp = cbp->loc->data.ptrvalue; if (sintp == NULL) { MemFree (pos); return FALSE; } sintp->from += offset; sintp->to += offset; if (sintp->from > sintp->to) { temp = sintp->from; sintp->from = sintp->to; sintp->to = temp; } sintp->strand = SeqLocStrand (sfp->location); strand = sintp->strand; diff = SeqLocStop(cbp->loc) - SeqLocStart(cbp->loc); /* SeqLocStop/Start does not do what you think */ /* if ((diff != 2 && (strand != Seq_strand_minus)) || (diff != -2 && (strand == Seq_strand_minus))) { pos_range = TRUE; } */ if (diff != 2) { pos_range = TRUE; } if (num_errs > 0 || pos_range) { CodeBreakFree (cbp); ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing, "transl_except range is wrong, %s, drop the transl_except", pos); MemFree (pos); return FALSE; } if (SeqLocCompare (sfp->location, cbp->loc) != SLC_B_IN_A) { CodeBreakFree (cbp); ErrPostEx (SEV_WARNING, ERR_FEATURE_LocationParsing, "/transl_except not in CDS: %s", val); MemFree (pos); return FALSE; } } /* add to code break list */ lastcbp = crp->code_break; if (lastcbp == NULL) { crp->code_break = cbp; } else { while (lastcbp->next != NULL) { lastcbp = lastcbp->next; } lastcbp->next = cbp; } MemFree (pos); return TRUE; } static Boolean CodonsAlreadyInOrder (tRNAPtr trp) { Int2 i, j; if (trp == NULL) return TRUE; for (i = 0, j = 1; i < 5; i++, j++) { if (trp->codon [i] > trp->codon [j]) return FALSE; } return TRUE; } static int LIBCALLBACK SortCodons (VoidPtr ptr1, VoidPtr ptr2) { Uint1 codon1, codon2; if (ptr1 == NULL || ptr2 == NULL) return 0; codon1 = *((Uint1Ptr) ptr1); codon2 = *((Uint1Ptr) ptr2); if (codon1 > codon2) { return 1; } else if (codon1 < codon2) { return -1; } return 0; } static void UniqueCodons (tRNAPtr trp) { Int2 i, j; Uint1 last = 255, next; if (trp == NULL) return; for (i = 0, j = 0; i < 6; i++) { next = trp->codon [i]; if (next != last) { trp->codon [j] = next; last = next; j++; } } while (j < 6) { trp->codon [j] = 255; j++; } } static CharPtr codonLetterExpand [] = { "?", "A", "C", "AC", "G", "AG", "CG", "ACG", "T", "AT", "CT", "ACT", "GT", "AGT", "CGT", "ACGT", NULL }; NLM_EXTERN Boolean ParseDegenerateCodon (tRNAPtr trp, Uint1Ptr codon) { Uint1 ch; Uint1 chrToInt [256]; Int2 k; Uint1 i, j; Uint1 idx; CharPtr intToChr = "?ACMGRSVTWYHKDBN"; CharPtr ptr, str; if (trp == NULL || codon == NULL) return FALSE; for (i = 0; i < 2; i++) { ch = codon [i]; if (ch != 'A' && ch != 'C' && ch != 'G' && ch != 'T') return FALSE; } for (k = 0; k < 256; k++) { chrToInt [k] = 0; } for (i = 1; i < 16; i++) { ch = intToChr [i]; chrToInt [(int) ch] = i; } idx = chrToInt [(int) codon [2]]; if (idx > 15) return FALSE; str = codonLetterExpand [idx]; ptr = str; ch = *ptr; j = 0; codon [3] = '\0'; while (ch != '\0' && j < 6) { codon [2] = ch; trp->codon [j] = IndexForCodon (codon, Seq_code_iupacna); ptr++; ch = *ptr; j++; } return TRUE; } static void CleanupTrna (SeqFeatPtr sfp, tRNAPtr trp) { Uint1 aa = 0; Char codon [16]; Uint1 curraa; Uint1 from = 0; Int2 i; Int2 j; Boolean justTrnaText; Boolean okayToFree = TRUE; SeqMapTablePtr smtp; CharPtr str; Uint1 trpcodon [6]; /* look for tRNA-OTHER with actual amino acid in comment */ if (trp == NULL) return; if (sfp != NULL && sfp->comment != NULL && trp->codon [0] == 255) { codon [0] = '\0'; if (StringNICmp (sfp->comment, "codon recognized: ", 18) == 0) { StringNCpy_0 (codon, sfp->comment + 18, sizeof (codon)); } else if (StringNICmp (sfp->comment, "codons recognized: ", 19) == 0) { StringNCpy_0 (codon, sfp->comment + 19, sizeof (codon)); } if (StringDoesHaveText (codon)) { if (StringLen (codon) > 3 && codon [3] == ';') { codon [3] = '\0'; okayToFree = FALSE; } if (StringLen (codon) == 3) { for (i = 0; i < 3; i++) { if (codon [i] == 'U') { codon [i] = 'T'; } } if (ParseDegenerateCodon (trp, (Uint1Ptr) codon)) { if (okayToFree) { sfp->comment = MemFree (sfp->comment); } else { str = StringSave (sfp->comment + 22); TrimSpacesAroundString (str); sfp->comment = MemFree (sfp->comment); if (StringHasNoText (str)) { str = MemFree (str); } sfp->comment = str; } } } } } if (! CodonsAlreadyInOrder (trp)) { StableMergeSort ((VoidPtr) &(trp->codon), 6, sizeof (Uint1), SortCodons); } UniqueCodons (trp); /* now always switch iupacaa to ncbieaa (was just for selenocysteine) */ if (trp->aatype == 1 /* && trp->aa == 'U' */) { trp->aatype = 2; } if (sfp == NULL || sfp->comment == NULL) return; if (trp->aatype == 2) { aa = trp->aa; } else { switch (trp->aatype) { case 0 : from = 0; break; case 1 : from = Seq_code_iupacaa; break; case 2 : from = Seq_code_ncbieaa; break; case 3 : from = Seq_code_ncbi8aa; break; case 4 : from = Seq_code_ncbistdaa; break; default: break; } smtp = SeqMapTableFind (Seq_code_ncbieaa, from); if (smtp != NULL) { aa = SeqMapTableConvert (smtp, trp->aa); } } if (aa != 'X') { curraa = ParseTRnaString (sfp->comment, &justTrnaText, trpcodon, TRUE); if (aa == 0 && curraa != 0) { aa = curraa; trp->aa = curraa; trp->aatype = 2; } if (aa != 0 && aa == curraa) { if (justTrnaText) { for (j = 0; j < 6; j++) { if (trp->codon [j] == 255) { trp->codon [j] = trpcodon [j]; } } if (StringCmp (sfp->comment, "fMet") != 0) { sfp->comment = MemFree (sfp->comment); } } } return; } aa = ParseTRnaString (sfp->comment, &justTrnaText, trpcodon, TRUE); if (aa == 0) return; trp->aa = aa; trp->aatype = 2; if (justTrnaText) { for (j = 0; j < 6; j++) { if (trp->codon [j] == 255) { trp->codon [j] = trpcodon [j]; } } if (StringCmp (sfp->comment, "fMet") != 0) { sfp->comment = MemFree (sfp->comment); } } } NLM_EXTERN SeqFeatPtr LIBCALL GetBestProteinFeatureUnindexed (SeqLocPtr product) { BioseqPtr bsp; SeqFeatPtr prot = NULL; SeqAnnotPtr sap; SeqFeatPtr tmp; ValNode vn; if (product == NULL) return NULL; bsp = BioseqFindFromSeqLoc (product); if (bsp == NULL || bsp->repr != Seq_repr_raw) return NULL; vn.choice = SEQLOC_WHOLE; vn.data.ptrvalue = (Pointer) SeqIdFindBest (bsp->id, 0); vn.next = NULL; for (sap = bsp->annot; sap != NULL && prot == NULL; sap = sap->next) { if (sap->type == 1) { for (tmp = (SeqFeatPtr) sap->data; tmp != NULL && prot == NULL; tmp = tmp->next) { if (tmp->data.choice == SEQFEAT_PROT) { if (SeqLocCompare (tmp->location, &vn)) { /* find first protein feature packaged on and located on bioseq */ prot = tmp; } } } } } return prot; } static void CleanupECNumber (CharPtr str) { size_t len; len = StringLen (str); if (len < 1) return; if (str [len - 1] == '.') { str [len - 1] = ' '; } if (StringNICmp (str, "EC ", 3) == 0) { str [0] = ' '; str [1] = ' '; } else if (StringNICmp (str, "EC:", 3) == 0) { str [0] = ' '; str [1] = ' '; str [2] = ' '; } TrimSpacesAroundString (str); } static Boolean HandledGBQualOnCDS (SeqFeatPtr sfp, GBQualPtr gbq, ValNodePtr PNTR afterMe) { Int2 choice = 0; CdRegionPtr crp; Uint1 frame; ValNodePtr gcp; ValNodePtr prev; SeqFeatPtr prot; ProtRefPtr prp = NULL; Char str [16]; Int4 transl_table; int val; ValNodePtr vnp; SeqFeatXrefPtr xref; if (StringICmp (gbq->qual, "product") == 0) { choice = 1; } else if (StringICmp (gbq->qual, "function") == 0) { choice = 2; } else if (StringICmp (gbq->qual, "EC_number") == 0) { choice = 3; } else if (StringICmp (gbq->qual, "prot_note") == 0) { choice = 4; } if (choice > 0) { prot = GetBestProteinFeatureUnindexed (sfp->product); if (prot != NULL) { prp = (ProtRefPtr) prot->data.value.ptrvalue; } if (prp == NULL) { /* otherwise make cross reference */ xref = sfp->xref; while (xref != NULL && xref->data.choice != SEQFEAT_PROT) { xref = xref->next; } if (xref == NULL) { prp = ProtRefNew (); if (prp == NULL) return FALSE; xref = SeqFeatXrefNew (); if (xref == NULL) return FALSE; xref->data.choice = SEQFEAT_PROT; xref->data.value.ptrvalue = (Pointer) prp; xref->next = sfp->xref; sfp->xref = xref; } if (xref != NULL) { prp = (ProtRefPtr) xref->data.value.ptrvalue; } } if (prp == NULL) return FALSE; switch (choice) { case 1 : if (prot != NULL && prot->data.value.ptrvalue != NULL) { if (*afterMe == NULL) { /* if protein product exists, product gbqual becomes first name */ vnp = ValNodeCopyStr (NULL, 0, gbq->val); if (vnp != NULL) { vnp->next = prp->name; prp->name = vnp; } *afterMe = vnp; } else { vnp = ValNodeCopyStr (NULL, 0, gbq->val); prev = *afterMe; if (vnp != NULL) { vnp->next = prev->next; prev->next = vnp; } *afterMe = vnp; } } else { /* if local xref, append to name */ ValNodeCopyStr (&(prp->name), 0, gbq->val); } break; case 2 : ValNodeCopyStr (&(prp->activity), 0, gbq->val); break; case 3 : ValNodeCopyStr (&(prp->ec), 0, gbq->val); break; case 4 : if (prot == NULL) { return FALSE; } else { prot->comment = StringSave (gbq->val); } break; default : break; } return TRUE; } if (StringICmp (gbq->qual, "transl_except") == 0) { return ParseCodeBreak (sfp, gbq->val, 0); } if (StringICmp (gbq->qual, "codon_start") == 0) { crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { frame = crp->frame; if (frame == 0) { StringNCpy_0 (str, gbq->val, sizeof (str)); if (sscanf (str, "%d", &val) == 1) { if (val > 0 && val < 4) { crp->frame = (Uint1) val; return TRUE; } } frame = 1; } sprintf (str, "%d", (int) frame); if (StringICmp (str, gbq->val) == 0) { return TRUE; } else if (sfp->pseudo && sfp->product == NULL) { StringNCpy_0 (str, gbq->val, sizeof (str)); if (sscanf (str, "%d", &val) == 1) { if (val > 0 && val < 4) { crp->frame = (Uint1) val; return TRUE; } } } } } if (StringICmp (gbq->qual, "transl_table") == 0) { crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { transl_table = 0; gcp = crp->genetic_code; if (gcp != NULL) { for (vnp = gcp->data.ptrvalue; vnp != NULL; vnp = vnp->next) { if (vnp->choice == 2 && vnp->data.intvalue != 0) { transl_table = vnp->data.intvalue; } } if (transl_table == 0) { transl_table = 1; } sprintf (str, "%ld", (long) transl_table); if (StringICmp (str, gbq->val) == 0) { return TRUE; } } else { StringNCpy_0 (str, gbq->val, sizeof (str)); if (sscanf (str, "%d", &val) == 1) { vnp = ValNodeNew (NULL); if (vnp != NULL) { vnp->choice = 2; vnp->data.intvalue = (Int4) val; gcp = GeneticCodeNew (); if (gcp != NULL) { gcp->data.ptrvalue = vnp; crp->genetic_code = gcp; return TRUE; } } } } } } if (StringICmp (gbq->qual, "translation") == 0) { return TRUE; } return FALSE; } static Boolean HandledGBQualOnRNA (SeqFeatPtr sfp, GBQualPtr gbq, Boolean isEmblOrDdbj) { Uint1 aa; BioseqPtr bsp; Uint1 codon [6]; Boolean emptyRNA; Int4 from; Boolean is_fMet = FALSE; Boolean is_std_name = FALSE; Int2 j; Boolean justTrnaText; size_t len; CharPtr name; CharPtr ptr; RnaRefPtr rrp; SeqIntPtr sintp; SeqIdPtr sip; CharPtr str; Char tmp [64]; Int4 to; tRNAPtr trp; long int val; is_std_name = (Boolean) (StringICmp (gbq->qual, "standard_name") == 0); if (StringICmp (gbq->qual, "product") == 0 || (is_std_name && (! isEmblOrDdbj) )) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp == NULL) return FALSE; if (rrp->type == 0) { rrp->type = 255; } if (rrp->type == 255 && is_std_name) return FALSE; if (rrp->ext.choice == 1) { name = (CharPtr) rrp->ext.value.ptrvalue; if (StringHasNoText (name)) { rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.choice = 0; } } if (rrp->ext.choice == 2) { trp = (tRNAPtr) rrp->ext.value.ptrvalue; if (trp != NULL) { if (trp->aatype == 0 && trp->aa == 0 && trp->anticodon == NULL) { emptyRNA = TRUE; for (j = 0; j < 6; j++) { if (trp->codon [j] != 255) { emptyRNA = FALSE; } } if (emptyRNA) { rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.choice = 0; } } } } if (rrp->type == 3 && rrp->ext.choice == 1) { name = (CharPtr) rrp->ext.value.ptrvalue; aa = ParseTRnaString (name, &justTrnaText, codon, FALSE); if (aa != 0) { is_fMet = (Boolean) (StringStr (name, "fMet") != NULL); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); trp = (tRNAPtr) MemNew (sizeof (tRNA)); if (trp != NULL) { trp->aatype = 2; for (j = 0; j < 6; j++) { trp->codon [j] = 255; } if (justTrnaText) { for (j = 0; j < 6; j++) { trp->codon [j] = codon [j]; } } trp->aa = aa; rrp->ext.choice = 2; rrp->ext.value.ptrvalue = (Pointer) trp; if (aa == 'M') { if (is_fMet) { if (sfp->comment == NULL) { sfp->comment = StringSave ("fMet"); } else { len = StringLen (sfp->comment) + StringLen ("fMet") + 5; str = MemNew (sizeof (Char) * len); StringCpy (str, sfp->comment); StringCat (str, "; "); StringCat (str, "fMet"); sfp->comment = MemFree (sfp->comment); sfp->comment = str; } } } CleanupTrna (sfp, trp); } } } if (rrp->type == 3 && rrp->ext.choice == 0) { AddQualifierToFeature (sfp, "product", gbq->val); return TRUE; } if (rrp->type == 3 && rrp->ext.choice == 2) { trp = (tRNAPtr) rrp->ext.value.ptrvalue; if (trp != NULL && trp->aatype == 2) { if (trp->aa == ParseTRnaString (gbq->val, NULL, NULL, FALSE)) { return TRUE; } } } if (rrp->ext.choice != 0 && rrp->ext.choice != 1) return FALSE; name = (CharPtr) rrp->ext.value.ptrvalue; if (! HasNoText (name)) { if (StringICmp (name, gbq->val) == 0) { return TRUE; } str = StringStr (gbq->val, "rDNA"); if (str != NULL) { str [1] = 'R'; if (StringICmp (name, gbq->val) == 0) { return TRUE; } } if (rrp->type == 255 || rrp->type == 8 || rrp->type == 9 || rrp->type == 10) { /* new convention follows ASN.1 spec comments, allows new RNA types */ return FALSE; } /* subsequent /product now added to comment */ if (sfp->comment == NULL) { sfp->comment = gbq->val; gbq->val = NULL; } else if (StringStr (gbq->val, sfp->comment) == NULL) { len = StringLen (sfp->comment) + StringLen (gbq->val) + 5; str = MemNew (sizeof (Char) * len); StringCpy (str, sfp->comment); StringCat (str, "; "); StringCat (str, gbq->val); sfp->comment = MemFree (sfp->comment); sfp->comment = str; } /* return FALSE; */ return TRUE; } if (rrp->type == 8 || rrp->type == 9 || rrp->type == 10) { /* new convention follows ASN.1 spec comments, allows new RNA types */ return FALSE; } if (rrp->ext.choice == 1 && rrp->ext.value.ptrvalue != NULL) { rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); } if (rrp->ext.choice == 0 || rrp->ext.choice == 1) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = StringSave (gbq->val); return TRUE; } } else if (StringICmp (gbq->qual, "anticodon") == 0) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp == NULL) return FALSE; if (rrp->type == 0) { rrp->type = 255; } if (rrp->type == 3 && rrp->ext.choice == 0) { trp = (tRNAPtr) MemNew (sizeof (tRNA)); if (trp != NULL) { rrp->ext.choice = 2; rrp->ext.value.ptrvalue = trp; for (j = 0; j < 6; j++) { trp->codon [j] = 255; } } } if (rrp->type == 3 && rrp->ext.choice == 2) { trp = (tRNAPtr) rrp->ext.value.ptrvalue; if (trp != NULL) { StringNCpy_0 (tmp, gbq->val, sizeof (tmp)); ptr = StringStr (tmp, "("); if (ptr != NULL) { ptr = StringStr (ptr + 1, "pos"); if (ptr != NULL) { ptr = StringStr (ptr + 3, ":"); } } if (ptr != NULL) { str = ptr + 1; ptr = StringStr (str, ".."); if (ptr != NULL) { *ptr = '\0'; if (sscanf (str, "%ld", &val) == 1) { from = val - 1; str = ptr + 2; ptr = StringStr (str, ","); if (ptr != NULL) { *ptr = '\0'; if (sscanf (str, "%ld", &val) == 1) { to = val - 1; sip = SeqLocId (sfp->location); if (sip != NULL) { bsp = BioseqFind (sip); if (bsp != NULL) { if (from >= 0 && from < bsp->length - 1) { if (to >= 0 && to < bsp->length - 1) { sintp = SeqIntNew (); if (sintp != NULL) { if (from > to) { sintp->from = to; sintp->to = from; sintp->strand = Seq_strand_minus; } else { sintp->from = from; sintp->to = to; sintp->strand = Seq_strand_plus; } sintp->id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); trp->anticodon = ValNodeAddPointer (NULL, SEQLOC_INT, (Pointer) sintp); if (trp->aatype == 0 && trp->aa == 0) { ptr = StringStr (ptr + 1, "aa:"); if (ptr != NULL) { str = ptr + 3; ptr = StringStr (str, ")"); if (ptr != NULL) { *ptr = '\0'; trp->aa = ParseTRnaString (str, NULL, NULL, FALSE); if (trp->aa != 0) { trp->aatype = 2; } } } } return TRUE; } } } } } } } } } } } } } return FALSE; } static Boolean HandledGBQualOnProt (SeqFeatPtr sfp, GBQualPtr gbq) { Int2 choice = 0; ProtRefPtr prp; ValNodePtr vnp; prp = (ProtRefPtr) sfp->data.value.ptrvalue; if (prp == NULL) return FALSE; if (StringICmp (gbq->qual, "product") == 0) { choice = 1; } else if (StringICmp (gbq->qual, "function") == 0) { choice = 2; } else if (StringICmp (gbq->qual, "EC_number") == 0) { choice = 3; } else if (StringICmp (gbq->qual, "standard_name") == 0) { choice = 4; } else if (StringICmp (gbq->qual, "label") == 0) { choice = 5; } else if (StringICmp (gbq->qual, "allele") == 0) { choice = 6; } if (choice == 1 || choice == 4) { vnp = prp->name; if (vnp != NULL && (! HasNoText (vnp->data.ptrvalue))) return FALSE; ValNodeCopyStr (&(prp->name), 0, gbq->val); vnp = prp->name; if (vnp != NULL && prp->desc != NULL) { if (StringICmp (vnp->data.ptrvalue, prp->desc) == 0) { prp->desc = MemFree (prp->desc); } } return TRUE; } else if (choice == 2) { ValNodeCopyStr (&(prp->activity), 0, gbq->val); return TRUE; } else if (choice == 3) { ValNodeCopyStr (&(prp->ec), 0, gbq->val); return TRUE; } else if (choice == 5) { return FALSE; /* keep label gbqual only */ } else if (choice == 6) { return FALSE; } if (StringICmp (gbq->qual, "experiment") == 0 || StringICmp (gbq->qual, "inference") == 0) { return FALSE; } if (StringICmp (gbq->qual, "UniProtKB_evidence") == 0) { return FALSE; } return TRUE; /* all other gbquals not appropriate on protein features */ } static Boolean HandledGBQualOnImp (SeqFeatPtr sfp, GBQualPtr gbq) { Char ch; ImpFeatPtr ifp; Int4 len; CharPtr ptr; if (StringICmp (gbq->qual, "rpt_unit") == 0) { if (HasNoText (gbq->val)) return FALSE; ifp = (ImpFeatPtr) sfp->data.value.ptrvalue; if (ifp == NULL) return FALSE; if (StringICmp (ifp->key, "repeat_region") != 0) return FALSE; len = SeqLocLen (sfp->location); if (len != (Int4) StringLen (gbq->val)) return FALSE; ptr = gbq->val; ch = *ptr; while (ch != '\0') { if (StringChr ("ACGTNacgtn", ch) == NULL) return FALSE; ptr++; ch = *ptr; } /* return TRUE; */ } return FALSE; } static void CleanupRptUnit (GBQualPtr gbq) { Char ch; size_t len; CharPtr ptr; CharPtr str; CharPtr tmp; if (gbq == NULL) return; if (StringHasNoText (gbq->val)) return; len = StringLen (gbq->val) * 2 + 1; str = MemNew (sizeof (Char) * len); if (str == NULL) return; ptr = str; tmp = gbq->val; ch = *tmp; while (ch != '\0') { while (ch == '(' || ch == ')' || ch == ',') { *ptr = ch; ptr++; tmp++; ch = *tmp; } while (IS_WHITESP (ch)) { tmp++; ch = *tmp; } while (IS_DIGIT (ch)) { *ptr = ch; ptr++; tmp++; ch = *tmp; } if (ch == '.' || ch == '-') { while (ch == '.' || ch == '-') { tmp++; ch = *tmp; } *ptr = '.'; ptr++; *ptr = '.'; ptr++; } while (IS_WHITESP (ch)) { tmp++; ch = *tmp; } while (IS_DIGIT (ch)) { *ptr = ch; ptr++; tmp++; ch = *tmp; } while (IS_WHITESP (ch)) { tmp++; ch = *tmp; } if (ch == '\0' || ch == '(' || ch == ')' || ch == ',' || ch == '.' || IS_WHITESP (ch) || IS_DIGIT (ch)) { } else { MemFree (str); /* lower case the contents */ ptr = gbq->val; ch = *ptr; while (ch != '\0') { if (IS_UPPER (ch)) { *ptr = TO_LOWER (ch); } ptr++; ch = *ptr; } return; } } *ptr = '\0'; gbq->val = MemFree (gbq->val); gbq->val = str; /* and lower case the contents */ ptr = str; ch = *ptr; while (ch != '\0') { if (IS_UPPER (ch)) { *ptr = TO_LOWER (ch); } ptr++; ch = *ptr; } } static void CleanupRptUnitSeq (GBQualPtr gbq) { Char ch; CharPtr ptr; if (gbq == NULL) return; if (StringHasNoText (gbq->val)) return; /* lower case, and convert U to T */ ptr = gbq->val; ch = *ptr; while (ch != '\0') { if (IS_UPPER (ch)) { ch = TO_LOWER (ch); if (ch == 'u') { ch = 't'; } *ptr = ch; } ptr++; ch = *ptr; } } static void CleanupRptUnitRange (GBQualPtr gbq) { Char ch; Int2 dashes = 0; Int2 dots = 0; size_t len; CharPtr ptr; CharPtr str; CharPtr tmp; if (gbq == NULL) return; if (StringHasNoText (gbq->val)) return; ptr = gbq->val; ch = *ptr; while (ch != '\0') { if (ch == '-') { dashes++; } else if (ch == '.') { dots++; } else if (IS_DIGIT (ch)) { /* okay */ } else return; ptr++; ch = *ptr; } if (dashes > 0 && dots == 0) { len = StringLen (gbq->val + dashes); str = (CharPtr) MemNew (sizeof (Char) * (len + 5)); tmp = str; ptr = gbq->val; ch = *ptr; while (ch != '\0') { if (ch == '-') { *tmp = '.'; tmp++; *tmp = '.'; tmp++; } else { *tmp = ch; tmp++; } ptr++; ch = *ptr; } gbq->val = MemFree (gbq->val); gbq->val = str; } } static void CleanupReplace (GBQualPtr gbq) { Char ch; CharPtr ptr; if (gbq == NULL) return; if (StringHasNoText (gbq->val)) return; ptr = gbq->val; ch = *ptr; while (ch != '\0') { if (StringChr ("ACGTUacgtu", ch) == NULL) return; ptr++; ch = *ptr; } /* lower case, and convert U to T */ ptr = gbq->val; ch = *ptr; while (ch != '\0') { if (IS_UPPER (ch)) { ch = TO_LOWER (ch); if (ch == 'u') { ch = 't'; } *ptr = ch; } ptr++; ch = *ptr; } } static CharPtr evCategoryPfx [] = { "", "COORDINATES: ", "DESCRIPTION: ", "EXISTENCE: ", NULL }; static void CleanupInference (GBQualPtr gbq) { Char ch; CharPtr colon; CharPtr dst; Int2 j; size_t len; CharPtr ptr; CharPtr skip; CharPtr space; CharPtr str; if (gbq == NULL) return; if (StringHasNoText (gbq->val)) return; str = gbq->val; space = NULL; colon = NULL; skip = NULL; for (j = 0; evCategoryPfx [j] != NULL; j++) { len = StringLen (evCategoryPfx [j]); if (StringNICmp (str, evCategoryPfx [j], len) != 0) continue; skip = str + len; } if (skip != NULL) { str = skip; } dst = str; ptr = str; ch = *ptr; while (ch != '\0') { *dst = ch; if (ch == ' ') { if (space == NULL) { space = dst; } } else if (ch == ':') { if (space != NULL) { dst = space; *dst = ch; } space = NULL; colon = dst; } else { if (space != NULL && colon != NULL) { colon++; dst = colon; *dst = ch; } space = NULL; colon = NULL; } dst++; ptr++; ch = *ptr; } *dst = '\0'; } static CharPtr evCategoryNoSpace [] = { "", "COORDINATES:", "DESCRIPTION:", "EXISTENCE:", NULL }; static void RepairInference (GBQualPtr gbq) { Int2 j; size_t len; CharPtr ptr; CharPtr skip; CharPtr str; if (gbq == NULL) return; if (StringHasNoText (gbq->val)) return; str = gbq->val; for (j = 0; evCategoryNoSpace [j] != NULL; j++) { len = StringLen (evCategoryNoSpace [j]); if (StringNICmp (str, evCategoryNoSpace [j], len) != 0) continue; if (StringNICmp (str, evCategoryPfx [j], len + 1) == 0) continue; /* need to repair */ skip = str + len; ptr = MemNew (StringLen (skip) + 20); if (ptr == NULL) return; StringCpy (ptr, evCategoryPfx [j]); StringCat (ptr, skip); gbq->val = MemFree (gbq->val); gbq->val = ptr; return; } } static void CleanupConsSplice (GBQualPtr gbq) { size_t len; CharPtr ptr; CharPtr str; if (StringNICmp (gbq->val, "(5'site:", 8) != 0) return; ptr = StringStr (gbq->val, ",3'site:"); if (ptr == NULL) return; len = StringLen (gbq->val) + 5; str = (CharPtr) MemNew (len); if (str == NULL) return; *ptr = '\0'; ptr++; StringCpy (str, gbq->val); StringCat (str, ", "); StringCat (str, ptr); gbq->val = MemFree (gbq->val); gbq->val = str; } static Boolean ExpandParenGroup (GBQualPtr headgbq) { Char ch; GBQualPtr lastgbq; size_t len; Int2 nesting; GBQualPtr newgbq; GBQualPtr nextqual; CharPtr ptr; CharPtr str; CharPtr tmp; nextqual = headgbq->next; lastgbq = headgbq; ptr = headgbq->val; tmp = StringSave (ptr + 1); len = StringLen (tmp); if (len > 0 && tmp [len - 1] == ')') { tmp [len - 1] = '\0'; } str = tmp; nesting = 0; ptr = str; ch = *ptr; while (ch != '\0') { if (ch == '(') { nesting++; } else if (ch == ')') { nesting--; if (nesting < 0) { MemFree (tmp); return FALSE; } } else if (ch == ',') { if (nesting < 0) { MemFree (tmp); return FALSE; } } ptr++; ch = *ptr; } while (! StringHasNoText (str)) { ptr = StringChr (str, ','); if (ptr == NULL) { ptr = StringRChr (str, ')'); } if (ptr != NULL) { *ptr = '\0'; ptr++; } TrimSpacesAroundString (str); newgbq = GBQualNew (); if (newgbq != NULL) { newgbq->qual = StringSave (headgbq->qual); newgbq->val = StringSave (str); newgbq->next = nextqual; lastgbq->next = newgbq; lastgbq = newgbq; } str = ptr; } MemFree (tmp); return TRUE; } static Boolean IsBaseRange (CharPtr str) { CharPtr ptr; Char tmp [32]; long int val; if (StringLen (str) > 25) return FALSE; StringNCpy_0 (tmp, str, sizeof (tmp)); ptr = StringStr (tmp, ".."); if (ptr == NULL) return FALSE; *ptr = '\0'; if (StringHasNoText (tmp)) return FALSE; if (sscanf (tmp, "%ld", &val) != 1 || val < 1) return FALSE; ptr += 2; if (StringHasNoText (ptr)) return FALSE; if (sscanf (ptr, "%ld", &val) != 1 || val < 1) return FALSE; return TRUE; } static void ModernizeFeatureGBQuals (SeqFeatPtr sfp) { GBQualPtr gbq; size_t len; GBQualPtr nextqual; GBQualPtr PNTR prevqual; CharPtr str; Boolean unlink; if (sfp == NULL) return; gbq = sfp->qual; prevqual = (GBQualPtr PNTR) &(sfp->qual); while (gbq != NULL) { CleanVisString (&(gbq->qual)); CleanVisString (&(gbq->val)); if (gbq->qual == NULL) { gbq->qual = StringSave (""); } if (StringIsJustQuotes (gbq->val)) { gbq->val = MemFree (gbq->val); } if (gbq->val == NULL) { gbq->val = StringSave (""); } nextqual = gbq->next; unlink = TRUE; if (StringICmp (gbq->qual, "rpt_unit_seq") == 0) { str = gbq->val; len = StringLen (str); if (len > 1 && *str == '{' && str [len - 1] == '}') { *str = '('; str [len - 1] = ')'; } if (len > 1 && *str == '(' && str [len - 1] == ')' /* && StringChr (str + 1, '(') == NULL */) { if (ExpandParenGroup (gbq)) { nextqual = gbq->next; /* individual parsed out (xxx,xxx) qualifiers will be processed next, now get rid of original */ unlink = TRUE; } else { unlink = FALSE; } } else { unlink = FALSE; } } else if (StringICmp (gbq->qual, "rpt_type") == 0 || StringICmp (gbq->qual, "rpt_unit") == 0 || StringICmp (gbq->qual, "rpt_unit_range") == 0 || StringICmp (gbq->qual, "rpt_unit_seq") == 0 || StringICmp (gbq->qual, "replace") == 0 || StringICmp (gbq->qual, "compare") == 0 || StringICmp (gbq->qual, "old_locus_tag") == 0 || StringICmp (gbq->qual, "usedin") == 0) { str = gbq->val; len = StringLen (str); if (len > 1 && *str == '{' && str [len - 1] == '}') { *str = '('; str [len - 1] = ')'; } if (len > 1 && *str == '(' && str [len - 1] == ')' && StringChr (str + 1, '(') == NULL) { if (ExpandParenGroup (gbq)) { nextqual = gbq->next; /* individual parsed out (xxx,xxx) qualifiers will be processed next, now get rid of original */ unlink = TRUE; } else { unlink = FALSE; } } else { unlink = FALSE; } } else { unlink = FALSE; } if (unlink) { *(prevqual) = gbq->next; gbq->next = NULL; gbq->qual = MemFree (gbq->qual); gbq->val = MemFree (gbq->val); GBQualFree (gbq); } else { prevqual = (GBQualPtr PNTR) &(gbq->next); } gbq = nextqual; } } static void MendSatelliteQualifier (CharPtr PNTR satellite) { Int4 microsatellite_len = StringLen ("microsatellite"); Int4 minisatellite_len = StringLen ("minisatellite"); Int4 satellite_len = StringLen ("satellite"); Int4 type_len = 0; CharPtr new_qual, colon, src, dst; if (satellite == NULL || StringHasNoText (*satellite)) { return; } if (StringNCmp (*satellite, "microsatellite", microsatellite_len) == 0) { type_len = microsatellite_len; } else if (StringNCmp (*satellite, "minisatellite", minisatellite_len) == 0) { type_len = minisatellite_len; } else if (StringNCmp (*satellite, "satellite", satellite_len) == 0) { type_len = satellite_len; } if (type_len == 0) { new_qual = (CharPtr) MemNew (sizeof (Char) * (StringLen (*satellite) + satellite_len + 3)); sprintf (new_qual, "satellite:%s", *satellite); *satellite = MemFree (*satellite); *satellite = new_qual; } else if (*(*satellite + type_len) == ' ') { *(*satellite + type_len) = ':'; } /* remove spaces after colon */ colon = StringChr (*satellite, ':'); if (colon != NULL) { src = colon + 1; dst = colon + 1; while (*src == ' ') { src++; } while (*src != 0) { *dst = *src; dst++; src++; } *dst = 0; } } static void CleanupFeatureGBQuals (SeqFeatPtr sfp, Boolean isEmblOrDdbj) { ValNodePtr afterMe = NULL; Boolean all_digits; Char ch; DbtagPtr db; GBQualPtr gbq; GeneRefPtr grp; ImpFeatPtr ifp; size_t len; GBQualPtr nextqual; ObjectIdPtr oip; GBQualPtr PNTR prevqual; CharPtr ptr; GBQualPtr rpt_unit_range = NULL; GBQualPtr rpt_unit_seq = NULL; CharPtr str; CharPtr tag; Boolean unlink; ValNodePtr vnp; SeqFeatXrefPtr xref; if (sfp == NULL) return; gbq = sfp->qual; prevqual = (GBQualPtr PNTR) &(sfp->qual); while (gbq != NULL) { CleanVisString (&(gbq->qual)); CleanVisString (&(gbq->val)); if (gbq->qual == NULL) { gbq->qual = StringSave (""); } if (StringIsJustQuotes (gbq->val)) { gbq->val = MemFree (gbq->val); } if (gbq->val == NULL) { gbq->val = StringSave (""); } if (StringICmp (gbq->qual, "replace") == 0) { if (sfp->data.choice == SEQFEAT_IMP) { ifp = (ImpFeatPtr) sfp->data.value.ptrvalue; if (ifp != NULL) { if (StringICmp (ifp->key, "variation") == 0 && gbq->val != NULL) { ptr = gbq->val; ch = *ptr; while (ch != '\0') { *ptr = TO_LOWER (ch); ptr++; ch = *ptr; } } } } } nextqual = gbq->next; unlink = TRUE; if (StringICmp (gbq->qual, "partial") == 0) { sfp->partial = TRUE; } else if (StringICmp (gbq->qual, "evidence") == 0) { /* if (StringICmp (gbq->val, "experimental") == 0) { if (sfp->exp_ev != 2) { sfp->exp_ev = 1; } } else if (StringICmp (gbq->val, "not_experimental") == 0) { sfp->exp_ev = 2; } */ } else if (StringICmp (gbq->qual, "exception") == 0) { sfp->excpt = TRUE; if (! HasNoText (gbq->val)) { if (StringICmp (gbq->val, "TRUE") != 0) { if (sfp->except_text == NULL) { sfp->except_text = StringSaveNoNull (gbq->val); } } } } else if (StringICmp (gbq->qual, "note") == 0 || StringICmp (gbq->qual, "notes") == 0 || StringICmp (gbq->qual, "comment") == 0) { if (sfp->comment == NULL) { sfp->comment = gbq->val; gbq->val = NULL; } else { len = StringLen (sfp->comment) + StringLen (gbq->val) + 5; str = MemNew (sizeof (Char) * len); StringCpy (str, sfp->comment); StringCat (str, "; "); StringCat (str, gbq->val); sfp->comment = MemFree (sfp->comment); sfp->comment = str; } } else if (StringICmp (gbq->qual, "label") == 0) { if (StringICmp (gbq->val, FindKeyFromFeatDefType (sfp->idx.subtype, FALSE)) == 0) { /* skip label that is simply the feature key */ } else if (sfp->comment == NULL || StringISearch (sfp->comment, gbq->qual) == NULL) { /* if label is not already in comment, append */ len = StringLen (sfp->comment) + StringLen (gbq->val) + StringLen ("label: ") + 5; str = MemNew (sizeof (Char) * len); if (sfp->comment == NULL) { StringCpy (str, "label: "); StringCat (str, gbq->val); sfp->comment = str; } else { StringCpy (str, sfp->comment); StringCat (str, "; "); StringCat (str, "label: "); StringCat (str, gbq->val); sfp->comment = MemFree (sfp->comment); sfp->comment = str; } } } else if (StringICmp (gbq->qual, "db_xref") == 0) { tag = gbq->val; ptr = StringChr (tag, ':'); if (ptr != NULL) { vnp = ValNodeNew (NULL); db = DbtagNew (); vnp->data.ptrvalue = db; *ptr = '\0'; ptr++; db->db = StringSave (tag); oip = ObjectIdNew (); oip->str = StringSave (ptr); db->tag = oip; vnp->next = sfp->dbxref; sfp->dbxref = vnp; } else { /* db->db = StringSave ("?"); oip = ObjectIdNew (); oip->str = StringSave (tag); db->tag = oip; vnp->next = sfp->dbxref; sfp->dbxref = vnp; */ unlink = FALSE; } } else if (StringICmp (gbq->qual, "gdb_xref") == 0) { vnp = ValNodeNew (NULL); db = DbtagNew (); vnp->data.ptrvalue = db; db->db = StringSave ("GDB"); oip = ObjectIdNew (); oip->str = StringSave (gbq->val); db->tag = oip; vnp->next = sfp->dbxref; sfp->dbxref = vnp; } else if (StringICmp (gbq->qual, "cons_splice") == 0) { /* CleanupConsSplice (gbq); unlink = FALSE; */ } else if (StringICmp (gbq->qual, "replace") == 0) { CleanupReplace (gbq); unlink = FALSE; } else if (StringICmp (gbq->qual, "rpt_unit_seq") == 0) { CleanupRptUnitSeq (gbq); unlink = FALSE; } else if (StringICmp (gbq->qual, "rpt_unit_range") == 0) { CleanupRptUnitRange (gbq); unlink = FALSE; } else if (sfp->data.choice == SEQFEAT_GENE && HandledGBQualOnGene (sfp, gbq)) { } else if (sfp->data.choice == SEQFEAT_CDREGION && HandledGBQualOnCDS (sfp, gbq, &afterMe)) { } else if (sfp->data.choice == SEQFEAT_RNA && HandledGBQualOnRNA (sfp, gbq, isEmblOrDdbj)) { } else if (sfp->data.choice == SEQFEAT_PROT && HandledGBQualOnProt (sfp, gbq)) { } else if (sfp->data.choice == SEQFEAT_IMP && HandledGBQualOnImp (sfp, gbq)) { } else if (StringICmp (gbq->qual, "rpt_unit") == 0) { if (IsBaseRange (gbq->val)) { gbq->qual = MemFree (gbq->qual); gbq->qual = StringSave ("rpt_unit_range"); unlink = FALSE; } else { gbq->qual = MemFree (gbq->qual); gbq->qual = StringSave ("rpt_unit_seq"); unlink = FALSE; } } else if (StringICmp (gbq->qual, "EC_number") == 0) { CleanupECNumber (gbq->val); unlink = FALSE; } else if (StringICmp (gbq->qual, "pseudo") == 0) { sfp->pseudo = TRUE; } else if (StringICmp (gbq->qual, "ribosomal_slippage") == 0 || StringICmp (gbq->qual, "ribosomal-slippage") == 0 || StringICmp (gbq->qual, "ribosomal slippage") == 0) { sfp->excpt = TRUE; if (HasNoText (gbq->val)) { if (sfp->except_text == NULL) { sfp->except_text = StringSaveNoNull ("ribosomal slippage"); } } } else if (StringICmp (gbq->qual, "trans_splicing") == 0 || StringICmp (gbq->qual, "trans-splicing") == 0 || StringICmp (gbq->qual, "trans splicing") == 0) { sfp->excpt = TRUE; if (HasNoText (gbq->val)) { if (sfp->except_text == NULL) { sfp->except_text = StringSaveNoNull ("trans-splicing"); } } } else if (StringICmp (gbq->qual, "artificial_location") == 0 || StringICmp (gbq->qual, "artificial-location") == 0 || StringICmp (gbq->qual, "artificial location") == 0) { sfp->excpt = TRUE; if (HasNoText (gbq->val)) { if (sfp->except_text == NULL) { sfp->except_text = StringSaveNoNull ("artificial location"); } } } else if (StringICmp (gbq->qual, "gene") == 0 && (! StringHasNoText (gbq->val))) { grp = GeneRefNew (); grp->locus = StringSave (gbq->val); xref = SeqFeatXrefNew (); xref->data.choice = SEQFEAT_GENE; xref->data.value.ptrvalue = (Pointer) grp; xref->specialCleanupFlag = TRUE; /* flag to test for overlapping gene later */ xref->next = sfp->xref; sfp->xref = xref; } else if (sfp->data.choice != SEQFEAT_CDREGION && StringICmp (gbq->qual, "codon_start") == 0) { /* not legal on anything but CDS, so remove it */ } else if (StringICmp (gbq->qual, "experiment") == 0 && StringICmp (gbq->val, "experimental evidence, no additional details recorded") == 0) { /* remove default experiment string if instantiated */ } else if (StringICmp (gbq->qual, "inference") == 0) { if (StringICmp (gbq->val, "non-experimental evidence, no additional details recorded") == 0) { /* remove default inference string if instantiated */ } else { CleanupInference (gbq); RepairInference (gbq); unlink = FALSE; } } else if (StringICmp (gbq->qual, "transposon") == 0) { if (StringICmp (gbq->val, "class I integron") == 0 || StringICmp (gbq->val, "class II integron") == 0 || StringICmp (gbq->val, "class III integron") == 0 || StringICmp (gbq->val, "class 1 integron") == 0 || StringICmp (gbq->val, "class 2 integron") == 0 || StringICmp (gbq->val, "class 3 integron") == 0) { len = StringLen ("integron") + StringLen (gbq->val) + 5; str = MemNew (sizeof (Char) * len); StringCpy (str, "integron"); StringCat (str, ":"); ptr = StringStr (gbq->val, " integron"); if (ptr != NULL) { *ptr = '\0'; } StringCat (str, gbq->val); gbq->val = MemFree (gbq->val); gbq->val = str; gbq->qual = MemFree (gbq->qual); gbq->qual = StringSave ("mobile_element"); unlink = FALSE; } else { len = StringLen ("transposon") + StringLen (gbq->val) + 5; str = MemNew (sizeof (Char) * len); StringCpy (str, "transposon"); StringCat (str, ":"); StringCat (str, gbq->val); gbq->val = MemFree (gbq->val); gbq->val = str; gbq->qual = MemFree (gbq->qual); gbq->qual = StringSave ("mobile_element"); unlink = FALSE; } } else if (StringICmp (gbq->qual, "insertion_seq") == 0) { len = StringLen ("insertion sequence") + StringLen (gbq->val) + 5; str = MemNew (sizeof (Char) * len); StringCpy (str, "insertion sequence"); StringCat (str, ":"); StringCat (str, gbq->val); gbq->val = MemFree (gbq->val); gbq->val = str; gbq->qual = MemFree (gbq->qual); gbq->qual = StringSave ("mobile_element"); unlink = FALSE; } else if (StringCmp (gbq->qual, "satellite") == 0) { MendSatelliteQualifier(&(gbq->val)); unlink = FALSE; } else { unlink = FALSE; } if (StringICmp (gbq->qual, "mobile_element") == 0) { if (StringStr (gbq->val, " :") == 0 || StringStr (gbq->val, ": ") == 0) { len = StringLen (gbq->val) + 5; ptr = StringChr (gbq->val, ':'); if (ptr != NULL) { *ptr = '\0'; ptr++; TrimSpacesAroundString (gbq->val); TrimSpacesAroundString (ptr); str = MemNew (sizeof (Char) * len); StringCpy (str, gbq->val); StringCat (str, ":"); StringCat (str, ptr); gbq->val = MemFree (gbq->val); gbq->val = str; } } } if (StringICmp (gbq->qual, "mobile_element") == 0) { if (sfp->data.choice == SEQFEAT_IMP) { ifp = (ImpFeatPtr) sfp->data.value.ptrvalue; if (ifp != NULL) { if (StringICmp (ifp->key, "repeat_region") == 0 && gbq->val != NULL) { gbq->qual = MemFree (gbq->qual); gbq->qual = StringSave ("mobile_element_type"); ifp->key = MemFree (ifp->key); ifp->key = StringSave ("mobile_element"); sfp->idx.subtype = FEATDEF_mobile_element; } } } } if (StringICmp (gbq->qual, "estimated_length") == 0) { all_digits = TRUE; ptr = gbq->val; ch = *ptr; while (ch != '\0') { if (! IS_DIGIT (ch)) { all_digits = FALSE; } ptr++; ch = *ptr; } if (! all_digits) { if (StringICmp (gbq->val, "unknown") != 0) { MemFree (gbq->val); gbq->val = StringSave ("unknown"); } } } if (sfp->data.choice == SEQFEAT_IMP) { ifp = (ImpFeatPtr) sfp->data.value.ptrvalue; if (ifp != NULL) { if (StringICmp (ifp->key, "conflict") == 0 ) { ifp->key = MemFree (ifp->key); ifp->key = StringSave ("misc_difference"); sfp->idx.subtype = FEATDEF_misc_difference; len = StringLen (sfp->comment) + StringLen ("conflict") + 5; str = MemNew (sizeof (Char) * len); if (sfp->comment == NULL) { StringCpy (str, "conflict"); sfp->comment = str; } else { StringCpy (str, "conflict; "); StringCat (str, sfp->comment); sfp->comment = MemFree (sfp->comment); sfp->comment = str; } } } } if (rpt_unit_seq != NULL) { CleanupRptUnit (rpt_unit_seq); } if (rpt_unit_range != NULL) { CleanupRptUnit (rpt_unit_range); } if (unlink) { *(prevqual) = gbq->next; gbq->next = NULL; gbq->qual = MemFree (gbq->qual); gbq->val = MemFree (gbq->val); GBQualFree (gbq); } else { prevqual = (GBQualPtr PNTR) &(gbq->next); } gbq = nextqual; } } static int LIBCALLBACK SortByGBQualKeyAndVal (VoidPtr ptr1, VoidPtr ptr2) { int compare; GBQualPtr gbq1; GBQualPtr gbq2; CharPtr str1; CharPtr str2; if (ptr1 == NULL || ptr2 == NULL) return 0; gbq1 = *((GBQualPtr PNTR) ptr1); gbq2 = *((GBQualPtr PNTR) ptr2); if (gbq1 == NULL || gbq2 == NULL) return 0; str1 = (CharPtr) gbq1->qual; str2 = (CharPtr) gbq2->qual; if (str1 == NULL || str2 == NULL) return 0; compare = StringICmp (str1, str2); if (compare != 0) return compare; str1 = (CharPtr) gbq1->val; str2 = (CharPtr) gbq2->val; if (str1 == NULL || str2 == NULL) return 0; compare = StringICmp (str1, str2); return compare; } static Boolean GBQualsAlreadyInOrder (GBQualPtr list) { int compare; GBQualPtr curr; GBQualPtr next; if (list == NULL || list->next == NULL) return TRUE; curr = list; next = curr->next; while (next != NULL) { compare = StringICmp (curr->qual, next->qual); if (compare > 0) return FALSE; if (compare == 0) { compare = StringICmp (curr->val, next->val); if (compare > 0) return FALSE; } curr = next; next = curr->next; } return TRUE; } static GBQualPtr SortFeatureGBQuals (GBQualPtr list) { size_t count, i; GBQualPtr gbq, PNTR head; if (list == NULL) return NULL; if (GBQualsAlreadyInOrder (list)) return list; for (gbq = list, count = 0; gbq != NULL; gbq = gbq->next, count++) continue; head = MemNew (sizeof (GBQualPtr) * (count + 1)); for (gbq = list, i = 0; gbq != NULL && i < count; i++) { head [i] = gbq; gbq = gbq->next; } StableMergeSort (head, count, sizeof (GBQualPtr), SortByGBQualKeyAndVal); for (i = 0; i < count; i++) { gbq = head [i]; gbq->next = head [i + 1]; } list = head [0]; MemFree (head); return list; } static void CleanupDuplicateGBQuals (GBQualPtr PNTR prevgbq) { GBQualPtr gbq; GBQualPtr last = NULL; GBQualPtr next; Boolean unlink; if (prevgbq == NULL) return; gbq = *prevgbq; while (gbq != NULL) { next = gbq->next; unlink = FALSE; if (last != NULL) { if (StringICmp (last->qual, gbq->qual) == 0 && StringICmp (last->val, gbq->val) == 0) { unlink = TRUE; } } else { last = gbq; } if (unlink) { *prevgbq = gbq->next; gbq->next = NULL; GBQualFree (gbq); } else { last = gbq; prevgbq = (GBQualPtr PNTR) &(gbq->next); } gbq = next; } } /* this identifies gbquals that should have been placed into special fields */ #define NUM_ILLEGAL_QUALS 14 /* StringICmp use of TO_UPPER means translation should go before transl_XXX */ static CharPtr illegalGbqualList [NUM_ILLEGAL_QUALS] = { "anticodon", "citation", "codon_start", "db_xref", "evidence", "exception", "gene", "note", "protein_id", "pseudo", "transcript_id", "transl_except", "transl_table", "translation", }; static Int2 QualifierIsIllegal (CharPtr qualname) { Int2 L, R, mid; if (qualname == NULL || *qualname == '\0') return FALSE; L = 0; R = NUM_ILLEGAL_QUALS - 1; while (L < R) { mid = (L + R) / 2; if (StringICmp (illegalGbqualList [mid], qualname) < 0) { L = mid + 1; } else { R = mid; } } if (StringICmp (illegalGbqualList [R], qualname) == 0) { return TRUE; } return FALSE; } static void GbqualLink (GBQualPtr PNTR head, GBQualPtr qual) { GBQualPtr gbq; if (head == NULL || qual == NULL) return; gbq = *head; if (gbq != NULL) { while (gbq->next != NULL) { gbq = gbq->next; } gbq->next = qual; } else { *head = qual; } } static GBQualPtr SortIllegalGBQuals (GBQualPtr list) { GBQualPtr gbq, next, legal = NULL, illegal = NULL; gbq = list; while (gbq != NULL) { next = gbq->next; gbq->next = NULL; if (QualifierIsIllegal (gbq->qual)) { GbqualLink (&illegal, gbq); } else { GbqualLink (&legal, gbq); } gbq = next; } GbqualLink (&legal, illegal); return legal; } static Boolean IsSubString (CharPtr str1, CharPtr str2) { Char ch; size_t len1, len2; len1 = StringLen (str1); len2 = StringLen (str2); if (len1 >= len2) return FALSE; if (StringNICmp (str1, str2, len1) != 0) return FALSE; ch = str2 [len1]; if (IS_ALPHANUM (ch)) return FALSE; return TRUE; } static int LIBCALLBACK SortByOrgModSubtype (VoidPtr ptr1, VoidPtr ptr2) { int compare; OrgModPtr omp1; OrgModPtr omp2; CharPtr str1; CharPtr str2; if (ptr1 == NULL || ptr2 == NULL) return 0; omp1 = *((OrgModPtr PNTR) ptr1); omp2 = *((OrgModPtr PNTR) ptr2); if (omp1 == NULL || omp2 == NULL) return 0; if (omp1->subtype > omp2->subtype) { return 1; } else if (omp1->subtype < omp2->subtype) { return -1; } str1 = (CharPtr) omp1->subname; str2 = (CharPtr) omp2->subname; if (str1 == NULL || str2 == NULL) return 0; compare = StringICmp (str1, str2); return compare; } static Boolean OrgModsAlreadyInOrder (OrgModPtr list) { int compare; OrgModPtr curr; OrgModPtr next; CharPtr str1; CharPtr str2; if (list == NULL || list->next == NULL) return TRUE; curr = list; next = curr->next; while (next != NULL) { if (curr->subtype > next->subtype) return FALSE; str1 = (CharPtr) curr->subname; str2 = (CharPtr) next->subname; compare = StringICmp (str1, str2); if (compare > 0) return FALSE; curr = next; next = curr->next; } return TRUE; } static OrgModPtr SortOrgModList (OrgModPtr list) { size_t count, i; OrgModPtr omp, PNTR head; if (list == NULL) return NULL; if (OrgModsAlreadyInOrder (list)) return list; for (omp = list, count = 0; omp != NULL; omp = omp->next, count++) continue; head = MemNew (sizeof (OrgModPtr) * (count + 1)); for (omp = list, i = 0; omp != NULL && i < count; i++) { head [i] = omp; omp = omp->next; } StableMergeSort (head, count, sizeof (OrgModPtr), SortByOrgModSubtype); for (i = 0; i < count; i++) { omp = head [i]; omp->next = head [i + 1]; } list = head [0]; MemFree (head); return list; } static void RemoveSpaceBeforeAndAfterColon (CharPtr str) { CharPtr pColon, cp, src, dst; if (StringHasNoText (str)) { return; } pColon = StringChr (str, ':'); while (pColon != NULL) { cp = pColon - 1; while (cp > str && isspace (*cp)) { cp--; } if (cp < str || !isspace (*cp)) { cp++; } *cp = ':'; dst = cp + 1; cp = pColon + 1; while (isspace (*cp)) { cp++; } src = cp; pColon = dst - 1; if (src != dst) { while (*src != 0) { *dst = *src; dst++; src++; } *dst = 0; } pColon = StringChr (pColon + 1, ':'); } } static void CleanOrgModListEx (OrgModPtr PNTR ompp, CharPtr orpcommon) { Char ch; OrgModPtr last = NULL; OrgModPtr next; OrgModPtr omp; OrgModPtr omp_anamorph, omp_gb_anamorph, omp_other; OrgModPtr PNTR prev; CharPtr ptr; Boolean redund; CharPtr str; CharPtr tmp; Boolean unlink; if (ompp == NULL) return; prev = ompp; omp = *ompp; while (omp != NULL) { next = omp->next; unlink= FALSE; CleanVisStringAndCompress (&(omp->subname)); TrimSpacesAndJunkFromEnds (omp->subname, FALSE); RemoveFlankingQuotes (&(omp->subname)); CleanVisStringAndCompress (&(omp->attrib)); if (omp->subtype == ORGMOD_common && StringICmp (omp->subname, orpcommon) == 0) { unlink = TRUE; } else if (last != NULL) { if (HasNoText (omp->subname)) { unlink = TRUE; } else if (last->subtype == omp->subtype && StringICmp (last->subname, omp->subname) == 0 || (last->subtype == omp->subtype && last->subtype == ORGMOD_other && StringStr (last->subname, omp->subname) != NULL)) { unlink = TRUE; } else if (last->subtype == omp->subtype && last->subtype == ORGMOD_other && IsSubString (last->subname, omp->subname)) { last->subname = MemFree (last->subname); last->subname = omp->subname; omp->subname = NULL; unlink = TRUE; } } else if (HasNoText (omp->subname) || StringCmp (omp->subname, ")") == 0 || StringCmp (omp->subname, "(") == 0) { unlink = TRUE; } else { last = omp; } if (unlink) { *prev = omp->next; omp->next = NULL; OrgModFree (omp); } else { last = omp; prev = &(omp->next); } omp = next; } for (omp = *ompp; omp != NULL; omp = omp->next) { if (omp->subtype != ORGMOD_specimen_voucher && omp->subtype != ORGMOD_culture_collection && omp->subtype != ORGMOD_bio_material) continue; if (StringHasNoText (omp->subname)) continue; RemoveSpaceBeforeAndAfterColon (omp->subname); ptr = StringStr (omp->subname, "::"); if (ptr == NULL) continue; ptr++; tmp = ptr; tmp++; ch = *tmp; while (ch != '\0') { *ptr = ch; ptr++; tmp++; ch = *tmp; } *ptr = '\0'; } omp_anamorph = NULL; omp_gb_anamorph = NULL; omp_other = NULL; redund = FALSE; for (omp = *ompp; omp != NULL; omp = omp->next) { if (omp->subtype == ORGMOD_anamorph) { omp_anamorph = omp; } else if (omp->subtype == ORGMOD_gb_anamorph) { omp_gb_anamorph = omp; } else if (omp->subtype == ORGMOD_other) { omp_other = omp; } } if (omp_other != NULL && StringNICmp (omp_other->subname, "anamorph:", 9) == 0) { ptr = omp_other->subname + 9; ch = *ptr; while (ch == ' ') { ptr++; ch = *ptr; } if (omp_anamorph != NULL) { str = omp_anamorph->subname; if (StringCmp (ptr, str) == 0) { redund = TRUE; } } else if (omp_gb_anamorph != NULL) { str = omp_gb_anamorph->subname; if (StringCmp (ptr, str) == 0) { redund = TRUE; } } } if (redund) { prev = ompp; omp = *ompp; while (omp != NULL) { next = omp->next; unlink= FALSE; if (omp == omp_other) { unlink= TRUE; } if (unlink) { *prev = omp->next; omp->next = NULL; OrgModFree (omp); } else { prev = &(omp->next); } omp = next; } } } NLM_EXTERN void CleanOrgModList (OrgModPtr PNTR ompp) { CleanOrgModListEx (ompp, NULL); } static Boolean IsNoNameSubSource (SubSourcePtr ssp) { if (ssp == NULL) return FALSE; return (Boolean) (ssp->subtype == SUBSRC_germline || ssp->subtype == SUBSRC_rearranged || ssp->subtype == SUBSRC_transgenic || ssp->subtype == SUBSRC_environmental_sample || ssp->subtype == SUBSRC_metagenomic); } static int LIBCALLBACK SortBySubSourceSubtype (VoidPtr ptr1, VoidPtr ptr2) { int compare; SubSourcePtr ssp1; SubSourcePtr ssp2; CharPtr str1; CharPtr str2; if (ptr1 == NULL || ptr2 == NULL) return 0; ssp1 = *((SubSourcePtr PNTR) ptr1); ssp2 = *((SubSourcePtr PNTR) ptr2); if (ssp1 == NULL || ssp2 == NULL) return 0; if (ssp1->subtype > ssp2->subtype) { return 1; } else if (ssp1->subtype < ssp2->subtype) { return -1; } if (IsNoNameSubSource (ssp1)) return 0; str1 = (CharPtr) ssp1->name; str2 = (CharPtr) ssp2->name; if (str1 == NULL || str2 == NULL) return 0; compare = StringICmp (str1, str2); return compare; } static Boolean SubSourceAlreadyInOrder (SubSourcePtr list) { int compare; SubSourcePtr curr; SubSourcePtr next; CharPtr str1; CharPtr str2; if (list == NULL || list->next == NULL) return TRUE; curr = list; next = curr->next; while (next != NULL) { if (curr->subtype > next->subtype) return FALSE; if (curr->subtype == next->subtype) { if (! IsNoNameSubSource (curr)) { str1 = (CharPtr) curr->name; str2 = (CharPtr) next->name; compare = StringICmp (str1, str2); if (compare > 0) return FALSE; } } curr = next; next = curr->next; } return TRUE; } static SubSourcePtr SortSubSourceList (SubSourcePtr list) { size_t count, i; SubSourcePtr ssp, PNTR head; if (list == NULL) return NULL; if (SubSourceAlreadyInOrder (list)) return list; for (ssp = list, count = 0; ssp != NULL; ssp = ssp->next, count++) continue; head = MemNew (sizeof (SubSourcePtr) * (count + 1)); for (ssp = list, i = 0; ssp != NULL && i < count; i++) { head [i] = ssp; ssp = ssp->next; } StableMergeSort (head, count, sizeof (SubSourcePtr), SortBySubSourceSubtype); for (i = 0; i < count; i++) { ssp = head [i]; ssp->next = head [i + 1]; } list = head [0]; MemFree (head); return list; } static CharPtr TrimParenthesesAndCommasAroundString (CharPtr str) { Uchar ch; /* to use 8bit characters in multibyte languages */ CharPtr dst; CharPtr ptr; if (str != NULL && str [0] != '\0') { dst = str; ptr = str; ch = *ptr; while (ch != '\0' && (ch < ' ' || ch == '(' || ch == ',')) { ptr++; ch = *ptr; } while (ch != '\0') { *dst = ch; dst++; ptr++; ch = *ptr; } *dst = '\0'; dst = NULL; ptr = str; ch = *ptr; while (ch != '\0') { if (ch != ')' && ch != ',') { dst = NULL; } else if (dst == NULL) { dst = ptr; } ptr++; ch = *ptr; } if (dst != NULL) { *dst = '\0'; } } return str; } static CharPtr CombineSplitQual (CharPtr origval, CharPtr newval) { size_t len; CharPtr str = NULL; if (StringStr (origval, newval) != NULL) return origval; len = StringLen (origval) + StringLen (newval) + 5; str = MemNew (sizeof (Char) * len); if (str == NULL) return origval; TrimParenthesesAndCommasAroundString (origval); TrimParenthesesAndCommasAroundString (newval); StringCpy (str, "("); StringCat (str, origval); StringCat (str, ","); StringCat (str, newval); StringCat (str, ")"); /* free original string, knowing return value will replace it */ MemFree (origval); return str; } static Uint1 LocationForPlastidText (CharPtr plastid_name) { if (StringICmp (plastid_name, "chloroplast") == 0) { return GENOME_chloroplast; } else if (StringICmp (plastid_name, "chromoplast") == 0) { return GENOME_chromoplast; } else if (StringICmp (plastid_name, "kinetoplast") == 0) { return GENOME_kinetoplast; } else if (StringICmp (plastid_name, "plastid") == 0) { return GENOME_plastid; } else if (StringICmp (plastid_name, "apicoplast") == 0) { return GENOME_apicoplast; } else if (StringICmp (plastid_name, "leucoplast") == 0) { return GENOME_leucoplast; } else if (StringICmp (plastid_name, "proplastid") == 0) { return GENOME_proplastid; } else if (StringICmp (plastid_name, "chromatophore") == 0) { return GENOME_chromatophore; } else { return 0; } } NLM_EXTERN void StringToLower (CharPtr str) { Char ch; if (str == NULL) return; ch = *str; while (ch != '\0') { *str = TO_LOWER (ch); str++; ch = *str; } } static void CleanPCRPrimerSeq (CharPtr seq) { CharPtr ptr, src, dst, tmp; Char ch; Boolean in_brackets = FALSE; Int4 i; if (StringHasNoText (seq)) { return; } /* upper case sequence */ ptr = seq; ch = *ptr; while (ch != '\0') { if (IS_UPPER (ch)) { *ptr = TO_LOWER (ch); } ptr++; ch = *ptr; } /* remove any spaces in sequence outisde of */ src = seq; dst = seq; ch = *src; while (ch != '\0') { if (ch == '<') { in_brackets = TRUE; *dst = ch; dst++; } else if (ch == '>') { in_brackets = FALSE; *dst = ch; dst++; } else if (ch != ' ') { *dst = ch; dst++; } else if (in_brackets) { *dst = ch; dst++; } src++; ch = *src; } *dst = '\0'; /* upper case modified base */ ptr = seq; tmp = StringStr (ptr, ""); while (tmp != NULL) { ptr = tmp + 7; for (i = 1; i < 6; i++) { ch = tmp [i]; tmp [i] = TO_UPPER (ch); } tmp = StringStr (ptr, ""); } } static void CleanupPCRPrimers (PCRPrimerPtr PNTR pppp) { PCRPrimerPtr next; PCRPrimerPtr PNTR prev; PCRPrimerPtr ppp; if (pppp == NULL) return; prev = pppp; ppp = *pppp; while (ppp != NULL) { next = ppp->next; CleanVisString (&(ppp->seq)); CleanPCRPrimerSeq (ppp->seq); CleanVisString (&(ppp->name)); if (ppp->seq == NULL && ppp->name == NULL) { *prev = next; ppp->next = NULL; PCRPrimerFree (ppp); } else { StringToLower (ppp->seq); prev = &(ppp->next); } ppp = next; } /* fix artifact caused by fwd/rev-primer-seq starting with colon, separating name and seq */ ppp = *pppp; if (ppp == NULL) return; next = ppp->next; if (next == NULL) return; if (next->next != NULL) return; if (ppp->name != NULL && ppp->seq == NULL && next->name == NULL && next->seq != NULL) { ppp->seq = next->seq; next->seq = NULL; ppp->next = NULL; PCRPrimerFree (next); } else if (ppp->seq != NULL && ppp->name == NULL && next->seq == NULL && next->name != NULL) { ppp->name = next->name; next->name = NULL; ppp->next = NULL; PCRPrimerFree (next); } } static void CleanupPCRReactionSet (PCRReactionSetPtr PNTR prpp) { PCRReactionSetPtr next; PCRReactionSetPtr PNTR prev; PCRReactionSetPtr prp; if (prpp == NULL) return; prev = prpp; prp = *prpp; while (prp != NULL) { next = prp->next; CleanupPCRPrimers (&(prp->forward)); CleanupPCRPrimers (&(prp->reverse)); if (prp->forward == NULL && prp->reverse == NULL) { *prev = next; prp->next = NULL; PCRReactionFree (prp); } else { prev = &(prp->next); } prp = next; } } extern void CleanSubSourceList (SubSourcePtr PNTR sspp, Uint1 location) { Char ch; CharPtr dst; Int2 i; Boolean in_brackets = FALSE; SubSourcePtr last = NULL; SubSourcePtr next; SubSourcePtr PNTR prev; CharPtr ptr; CharPtr src; SubSourcePtr ssp; CharPtr str; CharPtr tmp; Boolean unlink; /* SubSourcePtr fwd_seq = NULL, rev_seq = NULL, fwd_name = NULL, rev_name = NULL; size_t len; */ if (sspp == NULL) return; prev = sspp; ssp = *sspp; while (ssp != NULL) { next = ssp->next; unlink= FALSE; if (! IsNoNameSubSource (ssp)) { CleanVisStringAndCompress (&(ssp->name)); TrimSpacesAndJunkFromEnds (ssp->name, FALSE); RemoveFlankingQuotes (&(ssp->name)); } else /* if (StringICmp (ssp->name, "TRUE") == 0) */ { ssp->name = MemFree (ssp->name); ssp->name = StringSave (""); } if (ssp->subtype == SUBSRC_country) { CleanVisStringJunk (&(ssp->name)); if (StringICmp (ssp->name, "United States") == 0 || StringICmp (ssp->name, "United States of America") == 0 || StringICmp (ssp->name, "U.S.A.") == 0) { ssp->name = MemFree (ssp->name); ssp->name = StringSave ("USA"); } if (StringNICmp (ssp->name, "United States:", 14) == 0) { str = ssp->name; str [0] = ' '; str [1] = ' '; str [2] = ' '; str [3] = ' '; str [4] = ' '; str [5] = ' '; str [6] = ' '; str [7] = ' '; str [8] = ' '; str [9] = ' '; str [10] = 'U'; str [11] = 'S'; str [12] = 'A'; TrimSpacesAroundString (ssp->name); } } else if (ssp->subtype == SUBSRC_clone) { CleanVisStringJunk (&(ssp->name)); } if (ssp->subtype == SUBSRC_fwd_primer_seq || ssp->subtype == SUBSRC_rev_primer_seq) { if (ssp->name != NULL) { /* upper case sequence */ ptr = ssp->name; ch = *ptr; while (ch != '\0') { if (IS_UPPER (ch)) { *ptr = TO_LOWER (ch); } ptr++; ch = *ptr; } /* remove any spaces in sequence outisde of */ src = ssp->name; dst = ssp->name; ch = *src; while (ch != '\0') { if (ch == '<') { in_brackets = TRUE; *dst = ch; dst++; } else if (ch == '>') { in_brackets = FALSE; *dst = ch; dst++; } else if (ch != ' ') { *dst = ch; dst++; } else if (in_brackets) { *dst = ch; dst++; } src++; ch = *src; } *dst = '\0'; /* upper case modified base */ ptr = ssp->name; tmp = StringStr (ptr, ""); while (tmp != NULL) { ptr = tmp + 7; for (i = 1; i < 6; i++) { ch = tmp [i]; tmp [i] = TO_UPPER (ch); } tmp = StringStr (ptr, ""); } } } /* if (ssp->subtype == SUBSRC_fwd_primer_seq) { if (fwd_seq == NULL) { fwd_seq = ssp; } else { fwd_seq->name = CombineSplitQual (fwd_seq->name, ssp->name); unlink = TRUE; } } if (ssp->subtype == SUBSRC_rev_primer_seq) { if (rev_seq == NULL) { rev_seq = ssp; } else { rev_seq->name = CombineSplitQual (rev_seq->name, ssp->name); unlink = TRUE; } } if (ssp->subtype == SUBSRC_fwd_primer_name) { if (fwd_name == NULL) { fwd_name = ssp; } else { fwd_name->name = CombineSplitQual (fwd_name->name, ssp->name); unlink = TRUE; } } if (ssp->subtype == SUBSRC_rev_primer_name) { if (rev_name == NULL) { rev_name = ssp; } else { rev_name->name = CombineSplitQual (rev_name->name, ssp->name); unlink = TRUE; } } */ CleanVisString (&(ssp->attrib)); if (last != NULL) { if (HasNoText (ssp->name) && (! IsNoNameSubSource (ssp))) { unlink = TRUE; } else if (last->subtype == ssp->subtype && (IsNoNameSubSource (ssp) || StringICmp (last->name, ssp->name) == 0 || (last->subtype == SUBSRC_other && StringStr (last->name, ssp->name) != NULL))) { unlink = TRUE; } else if (last->subtype == ssp->subtype && last->subtype == SUBSRC_other && IsSubString (last->name, ssp->name)) { last->name = MemFree (last->name); last->name = ssp->name; ssp->name = NULL; unlink = TRUE; } else if (ssp->subtype == SUBSRC_plastid_name && location != 0 && location == LocationForPlastidText (ssp->name)) { unlink = TRUE; } } else if (HasNoText (ssp->name) && (! IsNoNameSubSource (ssp))) { unlink = TRUE; } else if (ssp->subtype == SUBSRC_plastid_name && location != 0 && location == LocationForPlastidText (ssp->name)) { unlink = TRUE; } else { last = ssp; } if (unlink) { *prev = ssp->next; ssp->next = NULL; SubSourceFree (ssp); } else { last = ssp; prev = &(ssp->next); } ssp = next; } /* if (fwd_seq != NULL) { if (StringChr (fwd_seq->name, ',') != NULL) { ptr = fwd_seq->name; len = StringLen (ptr); if (ptr [0] != '(' || ptr [len - 1] != ')') { TrimParenthesesAndCommasAroundString (fwd_seq->name); str = MemNew (sizeof (Char) * (len + 4)); if (str != NULL) { StringCpy (str, "("); StringCat (str, fwd_seq->name); StringCat (str, ")"); fwd_seq->name = MemFree (fwd_seq->name); fwd_seq->name = str; } } } } if (rev_seq != NULL) { if (StringChr (rev_seq->name, ',') != NULL) { ptr = rev_seq->name; len = StringLen (ptr); if (ptr [0] != '(' || ptr [len - 1] != ')') { TrimParenthesesAndCommasAroundString (rev_seq->name); str = MemNew (sizeof (Char) * (len + 4)); if (str != NULL) { StringCpy (str, "("); StringCat (str, rev_seq->name); StringCat (str, ")"); rev_seq->name = MemFree (rev_seq->name); rev_seq->name = str; } } } } if (fwd_name != NULL) { if (StringChr (fwd_name->name, ',') != NULL) { ptr = fwd_name->name; len = StringLen (ptr); if (ptr [0] != '(' || ptr [len - 1] != ')') { TrimParenthesesAndCommasAroundString (fwd_name->name); str = MemNew (sizeof (Char) * (len + 4)); if (str != NULL) { StringCpy (str, "("); StringCat (str, fwd_name->name); StringCat (str, ")"); fwd_name->name = MemFree (fwd_name->name); fwd_name->name = str; } } } } if (rev_name != NULL) { if (StringChr (rev_name->name, ',') != NULL) { ptr = rev_name->name; len = StringLen (ptr); if (ptr [0] != '(' || ptr [len - 1] != ')') { TrimParenthesesAndCommasAroundString (rev_name->name); str = MemNew (sizeof (Char) * (len + 4)); if (str != NULL) { StringCpy (str, "("); StringCat (str, rev_name->name); StringCat (str, ")"); rev_name->name = MemFree (rev_name->name); rev_name->name = str; } } } } */ } extern void CleanSubSourcePrimers (SubSourcePtr PNTR sspp) { SubSourcePtr fwd_seq = NULL, rev_seq = NULL, fwd_name = NULL, rev_name = NULL; size_t len; SubSourcePtr next; SubSourcePtr PNTR prev; CharPtr ptr; SubSourcePtr ssp; CharPtr str; Boolean unlink; if (sspp == NULL) return; prev = sspp; ssp = *sspp; while (ssp != NULL) { next = ssp->next; unlink= FALSE; if (ssp->subtype == SUBSRC_fwd_primer_seq) { if (fwd_seq == NULL) { fwd_seq = ssp; } else { fwd_seq->name = CombineSplitQual (fwd_seq->name, ssp->name); unlink = TRUE; } } if (ssp->subtype == SUBSRC_rev_primer_seq) { if (rev_seq == NULL) { rev_seq = ssp; } else { rev_seq->name = CombineSplitQual (rev_seq->name, ssp->name); unlink = TRUE; } } if (ssp->subtype == SUBSRC_fwd_primer_name) { if (fwd_name == NULL) { fwd_name = ssp; } else { fwd_name->name = CombineSplitQual (fwd_name->name, ssp->name); unlink = TRUE; } } if (ssp->subtype == SUBSRC_rev_primer_name) { if (rev_name == NULL) { rev_name = ssp; } else { rev_name->name = CombineSplitQual (rev_name->name, ssp->name); unlink = TRUE; } } if (unlink) { *prev = ssp->next; ssp->next = NULL; SubSourceFree (ssp); } else { prev = &(ssp->next); } ssp = next; } if (fwd_seq != NULL) { if (StringChr (fwd_seq->name, ',') != NULL) { ptr = fwd_seq->name; len = StringLen (ptr); if (ptr [0] != '(' || ptr [len - 1] != ')') { TrimParenthesesAndCommasAroundString (fwd_seq->name); str = MemNew (sizeof (Char) * (len + 4)); if (str != NULL) { StringCpy (str, "("); StringCat (str, fwd_seq->name); StringCat (str, ")"); fwd_seq->name = MemFree (fwd_seq->name); fwd_seq->name = str; } } } } if (rev_seq != NULL) { if (StringChr (rev_seq->name, ',') != NULL) { ptr = rev_seq->name; len = StringLen (ptr); if (ptr [0] != '(' || ptr [len - 1] != ')') { TrimParenthesesAndCommasAroundString (rev_seq->name); str = MemNew (sizeof (Char) * (len + 4)); if (str != NULL) { StringCpy (str, "("); StringCat (str, rev_seq->name); StringCat (str, ")"); rev_seq->name = MemFree (rev_seq->name); rev_seq->name = str; } } } } if (fwd_name != NULL) { if (StringChr (fwd_name->name, ',') != NULL) { ptr = fwd_name->name; len = StringLen (ptr); if (ptr [0] != '(' || ptr [len - 1] != ')') { TrimParenthesesAndCommasAroundString (fwd_name->name); str = MemNew (sizeof (Char) * (len + 4)); if (str != NULL) { StringCpy (str, "("); StringCat (str, fwd_name->name); StringCat (str, ")"); fwd_name->name = MemFree (fwd_name->name); fwd_name->name = str; } } } } if (rev_name != NULL) { if (StringChr (rev_name->name, ',') != NULL) { ptr = rev_name->name; len = StringLen (ptr); if (ptr [0] != '(' || ptr [len - 1] != ')') { TrimParenthesesAndCommasAroundString (rev_name->name); str = MemNew (sizeof (Char) * (len + 4)); if (str != NULL) { StringCpy (str, "("); StringCat (str, rev_name->name); StringCat (str, ")"); rev_name->name = MemFree (rev_name->name); rev_name->name = str; } } } } } /* if string starts with given prefix, return pointer to remaining text */ static CharPtr StringHasPrefix (CharPtr str, CharPtr pref, Boolean novalneeded, Boolean skippref) { Char ch; size_t len; Char tmp [64]; CharPtr val; if (StringHasNoText (str) || StringHasNoText (pref)) return NULL; len = StringLen (pref); StringNCpy_0 (tmp, pref, sizeof (tmp)); if (StringNICmp (str, tmp, len) != 0) { /* try after replacing dash with underscore */ val = tmp; ch = *val; while (ch != '\0') { if (ch == '-') { *val = '_'; } val++; ch = *val; } if (StringNICmp (str, tmp, len) != 0) return NULL; } if (skippref) { val = str + len; } else { val = str; } if (StringHasNoText (val)) { if (novalneeded) return " "; return NULL; } ch = *(str + len); if (ch != '=' && ch != ' ' && ch != ':' && ch != '\0') return NULL; ch = *val; while (ch == '=' || ch == ' ' || ch == ':') { val++; ch = *val; } if (StringHasNoText (val)) return NULL; return val; } Nlm_QualNameAssoc current_orgmod_subtype_alist[] = { {" ", 0}, {"Acronym", ORGMOD_acronym}, {"Anamorph", ORGMOD_anamorph}, {"Authority", ORGMOD_authority}, {"Bio-material", ORGMOD_bio_material}, {"Biotype", ORGMOD_biotype}, {"Biovar", ORGMOD_biovar}, {"Breed", ORGMOD_breed}, {"Chemovar", ORGMOD_chemovar}, {"Common", ORGMOD_common}, {"Cultivar", ORGMOD_cultivar}, {"Culture-collection", ORGMOD_culture_collection}, {"Ecotype", ORGMOD_ecotype}, {"Forma", ORGMOD_forma}, {"Forma-specialis", ORGMOD_forma_specialis}, {"Group", ORGMOD_group}, {"Host", ORGMOD_nat_host}, {"Isolate", ORGMOD_isolate}, {"Metagenome-source", ORGMOD_metagenome_source}, {"Pathovar", ORGMOD_pathovar}, {"Serogroup", ORGMOD_serogroup}, {"Serotype", ORGMOD_serotype}, {"Serovar", ORGMOD_serovar}, {"Specimen-voucher", ORGMOD_specimen_voucher}, {"Strain", ORGMOD_strain}, {"Subgroup", ORGMOD_subgroup}, {"Sub-species", ORGMOD_sub_species}, {"Substrain", ORGMOD_substrain}, {"Subtype", ORGMOD_subtype}, {"Synonym", ORGMOD_synonym}, {"Teleomorph", ORGMOD_teleomorph}, {"Type", ORGMOD_type}, {"Variety", ORGMOD_variety}, { NULL, 0 } }; Nlm_QualNameAssoc discouraged_orgmod_subtype_alist[] = { {"Old Lineage", ORGMOD_old_lineage}, {"Old Name", ORGMOD_old_name}, { NULL, 0 } }; Nlm_QualNameAssoc discontinued_orgmod_subtype_alist[] = { {"Dosage", ORGMOD_dosage}, { NULL, 0 } }; Nlm_NameNameAssoc orgmod_aliases[] = { {"Sub-species", "subspecies", ORGMOD_sub_species}, {"Host", "nat-host", ORGMOD_nat_host}, {"Host", "specific-host", ORGMOD_nat_host}, {"Substrain", "Sub_strain", ORGMOD_substrain}, { NULL, NULL, 0 } }; extern CharPtr GetOrgModQualName (Uint1 subtype) { Int4 i; if (subtype == ORGMOD_other) { return "Note"; } for (i = 0; current_orgmod_subtype_alist[i].name != NULL; i++) { if (current_orgmod_subtype_alist[i].value == subtype) { return current_orgmod_subtype_alist[i].name; } } for (i = 0; discouraged_orgmod_subtype_alist[i].name != NULL; i++) { if (discouraged_orgmod_subtype_alist[i].value == subtype) { return discouraged_orgmod_subtype_alist[i].name; } } for (i = 0; discontinued_orgmod_subtype_alist[i].name != NULL; i++) { if (discontinued_orgmod_subtype_alist[i].value == subtype) { return discontinued_orgmod_subtype_alist[i].name; } } return NULL; } extern void BioSourceHasOldOrgModQualifiers (BioSourcePtr biop, BoolPtr has_discouraged, BoolPtr has_discontinued) { OrgModPtr mod; Boolean discouraged = FALSE, discontinued = FALSE; Int4 i; if (biop != NULL && biop->org != NULL && biop->org->orgname != NULL) { mod = biop->org->orgname->mod; while (mod != NULL && (!discouraged || !discontinued)) { for (i = 0; discouraged_orgmod_subtype_alist[i].name != NULL && !discouraged; i++) { if (mod->subtype == discouraged_orgmod_subtype_alist[i].value) { discouraged = TRUE; } } for (i = 0; discontinued_orgmod_subtype_alist[i].name != NULL && !discontinued; i++) { if (mod->subtype == discontinued_orgmod_subtype_alist[i].value) { discontinued = TRUE; } } mod = mod->next; } } if (has_discouraged != NULL) { *has_discouraged = discouraged; } if (has_discontinued != NULL) { *has_discontinued = discontinued; } } static void StringHasOrgModPrefix (CharPtr str, CharPtr PNTR pval, Uint1Ptr p_subtypeval, Boolean skippref) { Int2 i; CharPtr val = NULL; Uint1 subtype_val = 0; for (i = 0; current_orgmod_subtype_alist[i].name != NULL && subtype_val == 0; i++) { if (current_orgmod_subtype_alist[i].value == ORGMOD_nat_host) continue; val = StringHasPrefix (str, current_orgmod_subtype_alist [i].name, FALSE, skippref); if (val != NULL) { subtype_val = current_orgmod_subtype_alist[i].value; } } if (subtype_val == 0) { for (i = 0; orgmod_aliases[i].name != NULL && subtype_val == 0; i++) { if (orgmod_aliases[i].value == ORGMOD_nat_host) continue; val = StringHasPrefix (str, orgmod_aliases [i].alias, FALSE, skippref); if (val != NULL) { subtype_val = orgmod_aliases[i].value; } } } if (pval != NULL) { *pval = val; } if (p_subtypeval != NULL) { *p_subtypeval = subtype_val; } } static void OrpModToOrgMod (ValNodePtr PNTR vnpp, OrgModPtr PNTR ompp) { Char ch; ValNodePtr next; Int2 numcommas; Int2 numspaces; OrgModPtr omp; CharPtr ptr; CharPtr str; CharPtr val; ValNodePtr vnp; Uint1 subtype; if (vnpp == NULL || ompp == NULL) return; vnp = *vnpp; while (vnp != NULL) { next = vnp->next; str = (CharPtr) vnp->data.ptrvalue; val = NULL; subtype = 0; StringHasOrgModPrefix (str, &val, &subtype, TRUE); if (val != NULL) { numspaces = 0; numcommas = 0; ptr = str; ch = *ptr; while (ch != '\0') { if (ch == ' ') { numspaces++; } else if (ch == ',') { numcommas++; } ptr++; ch = *ptr; } if (numspaces > 4 || numcommas > 0) { val = NULL; } } if (val != NULL) { omp = OrgModNew (); if (omp != NULL) { omp->subtype = (Uint1) subtype; omp->subname = StringSave (val); omp->next = *ompp; *ompp = omp; } *vnpp = vnp->next; vnp->next = NULL; ValNodeFreeData (vnp); } else { vnpp = &(vnp->next); } vnp = next; } } Nlm_QualNameAssoc current_subsource_subtype_alist[] = { {" ", 0}, {"Cell-line", SUBSRC_cell_line}, {"Cell-type", SUBSRC_cell_type}, {"Chromosome", SUBSRC_chromosome}, {"Clone", SUBSRC_clone}, {"Clone-lib", SUBSRC_clone_lib}, {"Collected-by", SUBSRC_collected_by}, {"Collection-date", SUBSRC_collection_date}, {"Country", SUBSRC_country}, {"Dev-stage", SUBSRC_dev_stage}, {"Endogenous-virus-name", SUBSRC_endogenous_virus_name}, {"Environmental-sample", SUBSRC_environmental_sample}, {"Frequency", SUBSRC_frequency}, {"Genotype", SUBSRC_genotype}, {"Germline", SUBSRC_germline}, {"Haplogroup", SUBSRC_haplogroup}, {"Haplotype", SUBSRC_haplotype}, {"Identified-by", SUBSRC_identified_by}, {"Isolation-source", SUBSRC_isolation_source}, {"Lab-host", SUBSRC_lab_host}, {"Lat-Lon", SUBSRC_lat_lon}, {"Linkage-group", SUBSRC_linkage_group}, {"Map", SUBSRC_map}, {"Mating-type", SUBSRC_mating_type}, {"Metagenomic", SUBSRC_metagenomic}, {"Plasmid-name", SUBSRC_plasmid_name}, {"Pop-variant", SUBSRC_pop_variant}, {"Rearranged", SUBSRC_rearranged}, {"Segment", SUBSRC_segment}, {"Sex", SUBSRC_sex}, {"Subclone", SUBSRC_subclone}, {"Tissue-lib", SUBSRC_tissue_lib}, {"Tissue-type", SUBSRC_tissue_type}, {"Transgenic", SUBSRC_transgenic}, { NULL, 0 } }; Nlm_QualNameAssoc discouraged_subsource_subtype_alist[] = { {"Plastid-name", SUBSRC_plastid_name}, { NULL, 0 } }; Nlm_QualNameAssoc discontinued_subsource_subtype_alist[] = { {"Ins-seq-name", SUBSRC_insertion_seq_name}, {"Transposon-name", SUBSRC_transposon_name}, {"Fwd-PCR-primer-name", SUBSRC_fwd_primer_name}, {"Fwd-PCR-primer-seq", SUBSRC_fwd_primer_seq}, {"Rev-PCR-primer-name", SUBSRC_rev_primer_name}, {"Rev-PCR-primer-seq", SUBSRC_rev_primer_seq}, { NULL, 0 } }; Nlm_NameNameAssoc subsource_aliases[] = { {"Fwd-PCR-primer-name", "fwd-primer-name", SUBSRC_fwd_primer_name}, {"Fwd-PCR-primer-seq", "fwd-primer-seq", SUBSRC_fwd_primer_seq}, {"Rev-PCR-primer-name", "rev-primer-name", SUBSRC_rev_primer_name}, {"Rev-PCR-primer-seq", "rev-primer-seq", SUBSRC_rev_primer_seq}, {"Subclone", "sub-clone", SUBSRC_subclone}, {"Lat-Lon", "Lat-long", SUBSRC_lat_lon}, {"Lat-Lon", "Latitude-Longitude", SUBSRC_lat_lon }, { NULL, NULL, 0 } }; extern CharPtr GetSubsourceQualName (Uint1 subtype) { Int4 i; if (subtype == SUBSRC_other) { return "Note"; } for (i = 0; current_subsource_subtype_alist[i].name != NULL; i++) { if (current_subsource_subtype_alist[i].value == subtype) { return current_subsource_subtype_alist[i].name; } } for (i = 0; discouraged_subsource_subtype_alist[i].name != NULL; i++) { if (discouraged_subsource_subtype_alist[i].value == subtype) { return discouraged_subsource_subtype_alist[i].name; } } for (i = 0; discontinued_subsource_subtype_alist[i].name != NULL; i++) { if (discontinued_subsource_subtype_alist[i].value == subtype) { return discontinued_subsource_subtype_alist[i].name; } } return NULL; } extern void BioSourceHasOldSubSourceQualifiers (BioSourcePtr biop, BoolPtr has_discouraged, BoolPtr has_discontinued) { SubSourcePtr ssp; Boolean discouraged = FALSE, discontinued = FALSE; Int4 i; if (biop != NULL) { ssp = biop->subtype; while (ssp != NULL && (!discouraged || !discontinued)) { for (i = 0; discouraged_subsource_subtype_alist[i].name != NULL && !discouraged; i++) { if (ssp->subtype == discouraged_subsource_subtype_alist[i].value) { discouraged = TRUE; } } for (i = 0; discontinued_subsource_subtype_alist[i].name != NULL && !discontinued; i++) { if (ssp->subtype == discontinued_subsource_subtype_alist[i].value) { discontinued = TRUE; } } ssp = ssp->next; } } if (has_discouraged != NULL) { *has_discouraged = discouraged; } if (has_discontinued != NULL) { *has_discontinued = discontinued; } } static void StringHasSubSourcePrefix (CharPtr str, CharPtr PNTR pval, Uint1Ptr p_subtypeval, Boolean skippref) { Int2 i; CharPtr val = NULL; Uint1 subtype_val = 0; for (i = 0; current_subsource_subtype_alist[i].name != NULL && subtype_val == 0; i++) { val = StringHasPrefix (str, current_subsource_subtype_alist [i].name, (Boolean) (current_subsource_subtype_alist[i].value == SUBSRC_germline || current_subsource_subtype_alist[i].value == SUBSRC_rearranged || current_subsource_subtype_alist[i].value == SUBSRC_transgenic || current_subsource_subtype_alist[i].value == SUBSRC_environmental_sample || current_subsource_subtype_alist[i].value == SUBSRC_metagenomic), skippref); if (val != NULL) { subtype_val = current_subsource_subtype_alist[i].value; } } if (subtype_val == 0) { for (i = 0; subsource_aliases[i].name != NULL && subtype_val == 0; i++) { val = StringHasPrefix (str, subsource_aliases [i].alias, (Boolean) (subsource_aliases[i].value == SUBSRC_germline || subsource_aliases[i].value == SUBSRC_rearranged || subsource_aliases[i].value == SUBSRC_transgenic || subsource_aliases[i].value == SUBSRC_environmental_sample || subsource_aliases[i].value == SUBSRC_metagenomic), skippref); if (val != NULL) { subtype_val = subsource_aliases[i].value; } } } if (pval != NULL) { *pval = val; } if (p_subtypeval != NULL) { *p_subtypeval = subtype_val; } } static void OrpModToSubSource (ValNodePtr PNTR vnpp, SubSourcePtr PNTR sspp) { Char ch; ValNodePtr next; Int2 numcommas; Int2 numspaces; CharPtr ptr; SubSourcePtr ssp; CharPtr str; CharPtr val; ValNodePtr vnp; Uint1 subtype_val = 0; if (vnpp == NULL || sspp == NULL) return; vnp = *vnpp; while (vnp != NULL) { next = vnp->next; str = (CharPtr) vnp->data.ptrvalue; val = NULL; subtype_val = 0; StringHasSubSourcePrefix (str, &val, &subtype_val, TRUE); if (val != NULL) { numspaces = 0; numcommas = 0; ptr = str; ch = *ptr; while (ch != '\0') { if (ch == ' ') { numspaces++; } else if (ch == ',') { numcommas++; } ptr++; ch = *ptr; } if (numspaces > 4 || numcommas > 0) { val = NULL; } } if (val != NULL) { ssp = SubSourceNew (); if (ssp != NULL) { ssp->subtype = subtype_val; ssp->name = StringSave (val); ssp->next = *sspp; *sspp = ssp; } *vnpp = vnp->next; vnp->next = NULL; ValNodeFreeData (vnp); } else { vnpp = &(vnp->next); } vnp = next; } } static void GbqualToOrpMod (GBQualPtr PNTR prevgbq, ValNodePtr PNTR vnpp) { GBQualPtr gbq; size_t len; GBQualPtr next; CharPtr str; Boolean unlink; CharPtr val; Uint1 subtype_val; if (prevgbq == NULL) return; gbq = *prevgbq; while (gbq != NULL) { next = gbq->next; unlink = FALSE; str = gbq->qual; if (str != NULL) { val = NULL; subtype_val = 0; StringHasOrgModPrefix (str, &val, &subtype_val, FALSE); if (val == NULL) { subtype_val = 0; StringHasSubSourcePrefix (str, &val, &subtype_val, FALSE); } if (val != NULL) { len = StringLen (gbq->val); str = MemNew (sizeof (Char) * (len + 64)); if (str != NULL) { StringCpy (str, val); StringCat (str, "="); StringCat (str, gbq->val); ValNodeAddStr (vnpp, 0, str); unlink = TRUE; } } } if (unlink) { *prevgbq = gbq->next; gbq->next = NULL; GBQualFree (gbq); } else { prevgbq = (GBQualPtr PNTR) &(gbq->next); } gbq = next; } } #define IS_WHITESP(c) (((c) == ' ') || ((c) == '\n') || ((c) == '\r') || ((c) == '\t')) static Boolean IsStringSingleToken (CharPtr str) { Char ch; if (StringHasNoText (str)) return FALSE; ch = *str; while (ch != '\0') { if (IS_WHITESP (ch)) return FALSE; str++; ch = *str; } return TRUE; } static CharPtr FindAnOrgMod (OrgNamePtr onp, Uint1 subtype) { OrgModPtr omp; if (onp == NULL || subtype == 0) return NULL; for (omp = onp->mod; omp != NULL; omp = omp->next) { if (omp->subtype != subtype) continue; if (StringHasNoText (omp->subname)) continue; return omp->subname; } return NULL; } static CharPtr FindASubSource (BioSourcePtr biop, Uint1 subtype) { SubSourcePtr ssp; if (biop == NULL || subtype == 0) return NULL; for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) { if (ssp->subtype != subtype) continue; if (StringHasNoText (ssp->name)) continue; return ssp->name; } return NULL; } static CharPtr FindNextSingleTilde (CharPtr str) { Char ch; if (StringHasNoText (str)) return NULL; ch = *str; while (ch != '\0') { if (ch == ' ') { if (str [1] == '~') { str++; ch = *str; while (ch == '~') { str++; ch = *str; } } else { str++; ch = *str; } } else if (ch == '~') { if (str [1] != '~') return str; str++; ch = *str; while (ch == '~') { str++; ch = *str; } } else { str++; ch = *str; } } return NULL; } static ValNodePtr SplitAtSingleTilde (CharPtr strs) { ValNodePtr head = NULL; CharPtr ptr, str, tmp; if (StringHasNoText (strs)) return NULL; tmp = StringSave (strs); str = tmp; while (StringDoesHaveText (str)) { ptr = FindNextSingleTilde (str); if (ptr != NULL) { *ptr = '\0'; ptr++; } TrimSpacesAroundString (str); ValNodeCopyStr (&head, 0, str); str = ptr; } MemFree (tmp); return head; } static CharPtr MergeTildeStrings (ValNodePtr head) { size_t len = 0; CharPtr prefix = "", ptr, str; ValNodePtr vnp; if (head == NULL) return NULL; for (vnp = head; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; len += StringLen (str) + 1; } if (len < 1) return NULL; ptr = MemNew (sizeof (Char) * (len + 2)); if (ptr == NULL) return NULL; for (vnp = head; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; StringCat (ptr, prefix); StringCat (ptr, str); prefix = "~"; } return ptr; } static void CleanupOrgModOther (BioSourcePtr biop, OrgNamePtr onp) { ValNodePtr head, vnp; OrgModPtr next; OrgModPtr omp; OrgModPtr PNTR prev; CharPtr str; Uint1 subtype_val; CharPtr tmp; Boolean unlink; CharPtr val; if (biop == NULL || onp == NULL) return; prev = &(onp->mod); omp = onp->mod; while (omp != NULL) { next = omp->next; unlink= FALSE; if (omp->subtype == ORGMOD_other) { str = omp->subname; head = SplitAtSingleTilde (str); for (vnp = head; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; val = NULL; subtype_val = 0; StringHasOrgModPrefix (str, &val, &subtype_val, TRUE); if (val != NULL) { tmp = FindAnOrgMod (onp, subtype_val); if (tmp != NULL && StringICmp (tmp, val) == 0) { vnp->data.ptrvalue = NULL; } } else { subtype_val = 0; StringHasSubSourcePrefix (str, &val, &subtype_val, TRUE); if (val != NULL) { tmp = FindASubSource (biop, subtype_val); if (tmp != NULL && StringICmp (tmp, val) == 0) { vnp->data.ptrvalue = NULL; } } } } str = MergeTildeStrings (head); ValNodeFreeData (head); omp->subname = MemFree (omp->subname); omp->subname = str; if (StringHasNoText (str)) { unlink = TRUE; } } if (unlink) { *prev = omp->next; omp->next = NULL; OrgModFree (omp); } else { prev = &(omp->next); } omp = next; } } static void CleanupSubSourceOther (BioSourcePtr biop, OrgNamePtr onp) { ValNodePtr head, vnp; SubSourcePtr next; SubSourcePtr PNTR prev; SubSourcePtr ssp; CharPtr str; Uint1 subtype_val; CharPtr tmp; Boolean unlink; CharPtr val; if (biop == NULL /* || onp == NULL */ ) return; prev = &(biop->subtype); ssp = biop->subtype; while (ssp != NULL) { next = ssp->next; unlink = FALSE; if (ssp->subtype == SUBSRC_other) { str = ssp->name; head = SplitAtSingleTilde (str); for (vnp = head; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; val = NULL; subtype_val = 0; StringHasOrgModPrefix (str, &val, &subtype_val, TRUE); if (val != NULL) { tmp = FindAnOrgMod (onp, subtype_val); if (tmp != NULL && StringICmp (tmp, val) == 0) { vnp->data.ptrvalue = NULL; } } else { subtype_val = 0; StringHasSubSourcePrefix (str, &val, &subtype_val, TRUE); if (val != NULL) { tmp = FindASubSource (biop, subtype_val); if (tmp != NULL && StringICmp (tmp, val) == 0) { vnp->data.ptrvalue = NULL; } } } } str = MergeTildeStrings (head); ValNodeFreeData (head); ssp->name = MemFree (ssp->name); ssp->name = str; if (StringHasNoText (str)) { unlink = TRUE; } } if (unlink) { *prev = ssp->next; ssp->next = NULL; SubSourceFree (ssp); } else { prev = &(ssp->next); } ssp = next; } } static int LIBCALLBACK SortDbxref (VoidPtr ptr1, VoidPtr ptr2) { int compare; DbtagPtr dbt1; DbtagPtr dbt2; ObjectIdPtr oip1; ObjectIdPtr oip2; CharPtr str1; CharPtr str2; ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; dbt1 = (DbtagPtr) vnp1->data.ptrvalue; dbt2 = (DbtagPtr) vnp2->data.ptrvalue; if (dbt1 == NULL || dbt2 == NULL) return 0; str1 = (CharPtr) dbt1->db; str2 = (CharPtr) dbt2->db; if (str1 == NULL || str2 == NULL) return 0; compare = StringICmp (str1, str2); if (compare != 0) return compare; oip1 = dbt1->tag; oip2 = dbt2->tag; if (oip1 == NULL || oip2 == NULL) return 0; str1 = oip1->str; str2 = oip2->str; if (str1 != NULL && str2 != NULL) { return StringICmp (str1, str2); } else if (str1 == NULL && str2 == NULL) { if (oip1->id > oip2->id) { return 1; } else if (oip1->id < oip2->id) { return -1; } } else if (str1 != NULL) { return 1; } else if (str2 != NULL) { return -1; } return 0; } static void FixNumericDbxrefs (ValNodePtr vnp) { Char ch; DbtagPtr dbt; Boolean isNum; Boolean leadingzero; Boolean notallzero; ObjectIdPtr oip; CharPtr ptr; long val; while (vnp != NULL) { dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt != NULL) { oip = dbt->tag; if (oip != NULL) { ptr = oip->str; if (ptr != NULL) { leadingzero = FALSE; notallzero = FALSE; isNum = TRUE; ch = *ptr; if (ch == '0') { leadingzero = TRUE; } while (ch != '\0') { if ((! IS_DIGIT (ch)) && (! IS_WHITESP (ch))) { isNum = FALSE; } else if ('1'<= ch && ch <='9') { notallzero = TRUE; } ptr++; ch = *ptr; } if (isNum) { if (leadingzero && notallzero) { /* suppress conversion */ } else if (sscanf (oip->str, "%ld", &val) == 1) { oip->id = (Int4) val; oip->str = MemFree (oip->str); } } } } } vnp = vnp->next; } } static void FixOldDbxrefs (ValNodePtr vnp) { Boolean all_digits; Char ch; DbtagPtr dbt; ObjectIdPtr oip; CharPtr ptr; CharPtr str; CharPtr tmp; ValNodePtr vp2; while (vnp != NULL) { dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt != NULL) { TrimSpacesAroundString (dbt->db); oip = dbt->tag; if (oip != NULL && oip->str != NULL) { /* TrimSpacesAroundString (oip->str); */ TrimSpacesSemicolonsAndCommasAndParens (oip->str); } if (StringICmp (dbt->db, "SWISS-PROT") == 0 && StringCmp (dbt->db, "Swiss-Prot") != 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("Swiss-Prot"); } else if (StringICmp (dbt->db, "SPTREMBL") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("TrEMBL"); } else if (StringICmp (dbt->db, "SUBTILIS") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("SubtiList"); } else if (StringICmp (dbt->db, "MGD") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("MGI"); } else if (StringCmp (dbt->db, "cdd") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("CDD"); } else if (StringCmp (dbt->db, "FlyBase") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("FLYBASE"); } else if (StringCmp (dbt->db, "GENEDB") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("GeneDB"); } else if (StringCmp (dbt->db, "GreengenesID") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("Greengenes"); } else if (StringCmp (dbt->db, "HMPID") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("HMP"); } if (StringICmp (dbt->db, "HPRD") == 0) { oip = dbt->tag; if (oip != NULL && StringDoesHaveText (oip->str)) { str = oip->str; if (StringNICmp (str, "HPRD_", 5) == 0) { str [0] = ' '; str [1] = ' '; str [2] = ' '; str [3] = ' '; str [4] = ' '; TrimSpacesAroundString (str); } } } else if (StringICmp (dbt->db, "MGI") == 0) { oip = dbt->tag; if (oip != NULL && StringDoesHaveText (oip->str)) { str = oip->str; if (StringNICmp (str, "MGI:", 4) == 0 || StringNICmp (str, "MGD:", 4) == 0) { str [0] = ' '; str [1] = ' '; str [2] = ' '; str [3] = ' '; TrimSpacesAroundString (str); } else if (StringNICmp (str, "J:", 2) == 0) { ptr = str + 2; ch = *ptr; all_digits = TRUE; while (ch != '\0') { if (! IS_DIGIT (ch)) { all_digits = FALSE; } ptr++; ch = *ptr; } if (all_digits) { oip->str = MemFree (oip->str); oip->str = StringSave (""); } } } } if (StringICmp (dbt->db, "Swiss-Prot") == 0 || StringICmp (dbt->db, "SWISSPROT") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("UniProt/Swiss-Prot"); } else if (StringICmp (dbt->db, "TrEMBL") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("UniProt/TrEMBL"); } else if (StringICmp (dbt->db, "LocusID") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("GeneID"); } else if (StringICmp (dbt->db, "MaizeDB") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("MaizeGDB"); } if (StringICmp (dbt->db, "UniProt/Swiss-Prot") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("UniProtKB/Swiss-Prot"); } else if (StringICmp (dbt->db, "UniProt/TrEMBL") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("UniProtKB/TrEMBL"); } else if (StringICmp (dbt->db, "Genew") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("HGNC"); } else if (StringICmp (dbt->db, "IFO") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("NBRC"); } else if (StringICmp (dbt->db, "BHB") == 0 || StringICmp (dbt->db, "BioHealthBase") == 0) { dbt->db = MemFree (dbt->db); dbt->db = StringSave ("IRD"); } /* expand db_xrefs with colons inside tags */ oip = dbt->tag; if (oip != NULL && oip->str != NULL) { ptr = StringChr (oip->str, ':'); if (ptr != NULL) { if (StringHasNoText (ptr + 1)) { *ptr = '\0'; } else { tmp = dbt->db; dbt = DbtagNew (); if (dbt != NULL) { oip = ObjectIdNew (); if (oip != NULL) { vp2 = ValNodeNew (NULL); if (vp2 != NULL) { *ptr = '\0'; ptr++; TrimSpacesAroundString (ptr); dbt->db = StringSave (tmp); oip->str = StringSave (ptr); dbt->tag = oip; vp2->data.ptrvalue = (Pointer) dbt; vp2->next = vnp->next; vnp->next = vp2; } } } } } } } vnp = vnp->next; } } static void CleanupDuplicateDbxrefs (ValNodePtr PNTR prevvnp) { DbtagPtr dbt; DbtagPtr last = NULL; ValNodePtr nextvnp; ObjectIdPtr oip1; ObjectIdPtr oip2; CharPtr str1; CharPtr str2; Boolean unlink; ValNodePtr vnp; if (prevvnp == NULL) return; vnp = *prevvnp; while (vnp != NULL) { nextvnp = vnp->next; dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt != NULL) { unlink = FALSE; if (last != NULL) { str1 = (CharPtr) dbt->db; str2 = (CharPtr) last->db; if (str1 != NULL && str2 != NULL && StringICmp (str1, str2) == 0) { oip1 = dbt->tag; oip2 = last->tag; if (oip1 != NULL && oip2 != NULL) { str1 = oip1->str; str2 = oip2->str; if (str1 != NULL && str2 != NULL) { if (StringICmp (str1, str2) == 0) { unlink = TRUE; } } else if (str1 == NULL && str2 == NULL) { if (oip1->id == oip2->id) { unlink = TRUE; } } } } } else { last = dbt; } if (unlink) { *prevvnp = vnp->next; vnp->next = NULL; DbtagFree (dbt); ValNodeFree (vnp); } else { last = dbt; prevvnp = (ValNodePtr PNTR) &(vnp->next); } } vnp = nextvnp; } } static void CleanupObsoleteDbxrefs (ValNodePtr PNTR prevvnp) { DbtagPtr dbt; ValNodePtr nextvnp; ObjectIdPtr oip; CharPtr str; Boolean unlink; ValNodePtr vnp; if (prevvnp == NULL) return; vnp = *prevvnp; while (vnp != NULL) { nextvnp = vnp->next; dbt = (DbtagPtr) vnp->data.ptrvalue; if (dbt != NULL) { unlink = FALSE; str = (CharPtr) dbt->db; if (StringHasNoText (str) || StringICmp (str, "PID") == 0 || StringICmp (str, "PIDg") == 0 || /* StringICmp (str, "PIDe") == 0 || StringICmp (str, "PIDd") == 0 || */ /* StringICmp (str, "GI") == 0 || */ StringICmp (str, "NID") == 0) { unlink = TRUE; } oip = dbt->tag; if (oip == NULL) { unlink = TRUE; } else if (oip->str != NULL) { if (StringHasNoText (oip->str)) { unlink = TRUE; } } else if (oip->id == 0) { unlink = TRUE; } if (unlink) { *prevvnp = vnp->next; vnp->next = NULL; DbtagFree (dbt); ValNodeFree (vnp); } else { prevvnp = (ValNodePtr PNTR) &(vnp->next); } } vnp = nextvnp; } } static int LIBCALLBACK SortCits (VoidPtr ptr1, VoidPtr ptr2) { int compare; Char label1 [128], label2 [128]; ValNodePtr ppr1, ppr2; if (ptr1 == NULL || ptr2 == NULL) return 0; ppr1 = *((ValNodePtr PNTR) ptr1); ppr2 = *((ValNodePtr PNTR) ptr2); if (ppr1 == NULL || ppr2 == NULL) return 0; PubLabel (ppr1, label1, 127, OM_LABEL_CONTENT); PubLabel (ppr2, label2, 127, OM_LABEL_CONTENT); compare = StringICmp (label1, label2); return compare; } static Boolean CitGenTitlesMatch (ValNodePtr pub1, ValNodePtr pub2) { CitGenPtr cgp1, cgp2; if (pub1->choice == PUB_Gen) { cgp1 = (CitGenPtr) pub1->data.ptrvalue; if (cgp1->serial_number != -1 && pub1->next != NULL) { pub1 = pub1->next; } } if (pub2->choice == PUB_Gen) { cgp2 = (CitGenPtr) pub2->data.ptrvalue; if (cgp2->serial_number != -1 && pub2->next != NULL) { pub2 = pub2->next; } } if (pub1->choice != PUB_Gen || pub2->choice != PUB_Gen) return TRUE; cgp1 = (CitGenPtr) pub1->data.ptrvalue; cgp2 = (CitGenPtr) pub2->data.ptrvalue; if (cgp1->title == NULL || cgp2->title == NULL) return TRUE; if (StringCmp (cgp1->title, cgp2->title) != 0) return FALSE; return TRUE; } static void CleanupDuplicateCits (ValNodePtr PNTR prevvnp) { Char label1 [128], label2 [128]; ValNodePtr last = NULL; ValNodePtr nextvnp; Boolean unlink; ValNodePtr vnp; if (prevvnp == NULL) return; vnp = *prevvnp; while (vnp != NULL) { nextvnp = vnp->next; unlink = FALSE; if (last != NULL) { PubLabelUnique (last, label1, 127, OM_LABEL_CONTENT, TRUE); PubLabelUnique (vnp, label2, 127, OM_LABEL_CONTENT, TRUE); if (StringCmp (label1, label2) == 0 && CitGenTitlesMatch (last, vnp)) { unlink = TRUE; } } else { last = vnp; } if (unlink) { *prevvnp = vnp->next; vnp->next = NULL; PubFree (vnp); } else { last = vnp; prevvnp = (ValNodePtr PNTR) &(vnp->next); } vnp = nextvnp; } } /* name processing code from Sequin editors */ NLM_EXTERN void FirstNameToInitials (CharPtr first, CharPtr inits, size_t maxsize) { Char ch; Uint2 i; if (inits != NULL && maxsize > 0) { inits [0] = '\0'; if (first != NULL) { i = 0; ch = *first; while (ch != '\0' && i < maxsize) { while (ch != '\0' && (ch <= ' ' || ch == '-')) { first++; ch = *first; } if (IS_ALPHA (ch)) { inits [i] = ch; i++; first++; ch = *first; } while (ch != '\0' && ch > ' ' && ch != '-') { first++; ch = *first; } if (ch == '-') { inits [i] = ch; i++; first++; ch = *first; } } inits [i] = '\0'; } } } static void StripPeriods (CharPtr str) { Char ch; CharPtr dst; if (str != NULL) { dst = str; ch = *str; while (ch != '\0') { if (ch != '.') { *dst = ch; dst++; } str++; ch = *str; } *dst = '\0'; } } static void TrimLeadingSpaces (CharPtr str) { Char ch; CharPtr dst; if (str != NULL && str [0] != '\0') { dst = str; ch = *str; while (ch != '\0' && ch <= ' ') { str++; ch = *str; } while (ch != '\0') { *dst = ch; dst++; str++; ch = *str; } *dst = '\0'; } } static void ExtractSuffixFromInitials (NameStdPtr nsp) { Char ch; Boolean has_period = FALSE; size_t len; CharPtr str; str = nsp->names [4]; ch = *str; while (ch != '\0') { if (ch == '.') { has_period = TRUE; } str++; ch = *str; } if (! has_period) return; str = nsp->names [4]; len = StringLen (str); if (len >= 4 && StringCmp (str + len - 3, "III") == 0) { str [len - 3] = '\0'; nsp->names [5] = StringSave ("III"); } else if (len >= 5 && StringCmp (str + len - 4, "III.") == 0) { str [len - 4] = '\0'; nsp->names [5] = StringSave ("III"); } else if (len >= 3 && StringCmp (str + len - 2, "Jr") == 0) { str [len - 2] = '\0'; nsp->names [5] = StringSave ("Jr"); } else if (len >= 4 && StringCmp (str + len - 3, "2nd") == 0) { str [len - 3] = '\0'; nsp->names [5] = StringSave ("II"); } else if (len >= 3 && StringCmp (str + len - 2, "IV") == 0) { str [len - 2] = '\0'; nsp->names [5] = StringSave ("IV"); } else if (len >= 4 && StringCmp (str + len - 3, "IV.") == 0) { str [len - 3] = '\0'; nsp->names [5] = StringSave ("IV"); } } static CharPtr NameStdPtrToTabbedString (NameStdPtr nsp, Boolean fixInitials) { Char first [256]; Char frstinits [64]; Char initials [64]; Int2 j; Char last [256]; Char middle [128]; Char str [512]; Char suffix [64]; if (nsp == NULL) return NULL; if (nsp->names [5] == NULL && nsp->names [4] != NULL) { ExtractSuffixFromInitials (nsp); } str [0] = '\0'; StringNCpy_0 (first, nsp->names [1], sizeof (first)); TrimSpacesAroundString (first); StringNCpy_0 (initials, nsp->names [4], sizeof (initials)); StripPeriods (initials); TrimLeadingSpaces (initials); StringNCpy_0 (last, nsp->names [0], sizeof (last)); TrimLeadingSpaces (last); StringNCpy_0 (middle, nsp->names [2], sizeof (middle)); TrimLeadingSpaces (middle); if (StringCmp (initials, "al") == 0 && StringCmp (last, "et") == 0 && first [0] == '\0') { initials [0] = '\0'; StringCpy (last, "et al."); } /* if (first [0] == '\0') { StringNCpy_0 (first, initials, sizeof (first)); if (IS_ALPHA (first [0])) { if (first [1] == '-') { first [3] = '\0'; } else { first [1] = '\0'; } } else { first [0] = '\0'; } } */ frstinits [0] = '\0'; FirstNameToInitials (first, frstinits, sizeof (frstinits) - 1); StripPeriods (first); TrimLeadingSpaces (first); if (first [0] != '\0') { StringCat (str, first); } else { /* StringCat (str, " "); */ } StringCat (str, "\t"); if (fixInitials) { j = 0; while (initials [j] != '\0' && TO_UPPER (initials [j]) == TO_UPPER (frstinits [j])) { j++; } if (initials [j] != '\0') { StringCat (str, initials + j); } else { /* StringCat (str, " "); */ } } else if (initials [0] != '\0') { StringCat (str, initials); } else if (frstinits [0] != '\0') { StringCat (str, frstinits); } StringCat (str, "\t"); StringCat (str, last); StringNCpy_0 (suffix, nsp->names [5], sizeof (suffix)); StringCat (str, "\t"); StripPeriods (suffix); TrimLeadingSpaces (suffix); if (suffix [0] != '\0') { StringCat (str, suffix); } else { /* StringCat (str, " "); */ } StringCat (str, "\t"); StringCat (str, middle); StringCat (str, "\n"); return StringSave (str); } static CharPtr XtractTagListColumn (CharPtr source, Int2 col) { Char ch; size_t count; CharPtr ptr; CharPtr str; if (source == NULL || source [0] == '\0' || col < 0) return NULL; ptr = source; ch = *ptr; while (col > 0 && ch != '\n' && ch != '\0') { while (ch != '\t' && ch != '\n' && ch != '\0') { ptr++; ch = *ptr; } if (ch == '\t') { ptr++; ch = *ptr; } col--; } count = 0; ch = ptr [count]; while (ch != '\t' && ch != '\n' && ch != '\0') { count++; ch = ptr [count]; } str = (CharPtr) MemNew(count + 1); if (str != NULL) { MemCpy (str, ptr, count); } return str; } static NameStdPtr TabbedStringToNameStdPtr (CharPtr txt, Boolean fixInitials) { Char ch; CharPtr first; Char initials [64]; Int2 j; Int2 k; Char last; Int2 len; NameStdPtr nsp; Char periods [128]; CharPtr str; Char str1 [64]; Char suffix [80]; if (txt == NULL) return NULL; nsp = NameStdNew (); if (nsp == NULL) return NULL; nsp->names [0] = XtractTagListColumn (txt, 2); TrimLeadingSpaces (nsp->names [0]); first = XtractTagListColumn (txt, 0); StripPeriods (first); nsp->names [1] = StringSave (first); TrimLeadingSpaces (nsp->names [1]); str1 [0] = '\0'; if (fixInitials) { FirstNameToInitials (first, str1, sizeof (str1) - 1); } str = XtractTagListColumn (txt, 1); StringNCat (str1, str, sizeof (str1) - 1); MemFree (str); j = 0; k = 0; ch = str1 [j]; while (ch != '\0') { if (ch != ' ') { initials [k] = ch; k++; } j++; ch = str1 [j]; } initials [k] = '\0'; periods [0] = '\0'; j = 0; ch = initials [j]; while (ch != '\0') { if (ch == ',') { initials [j] = '.'; } j++; ch = initials [j]; } str = StringStr (initials, ".ST."); if (str != NULL) { *(str + 2) = 't'; } j = 0; k = 0; ch = initials [j]; while (ch != '\0') { if (ch == '-') { periods [k] = ch; k++; j++; ch = initials [j]; } else if (ch == '.') { j++; ch = initials [j]; } else if (ch == ' ') { j++; ch = initials [j]; } else { periods [k] = ch; last = ch; k++; j++; ch = initials [j]; if (ch == '\0') { if (! (IS_LOWER (last))) { periods [k] = '.'; k++; } /* } else if (ch == '.' && initials [j + 1] == '\0') { */ } else if (! (IS_LOWER (ch))) { periods [k] = '.'; k++; } } } if (k > 0 && periods [k - 1] != '.') { periods [k] = '.'; k++; } periods [k] = '\0'; nsp->names [4] = StringSave (periods); TrimLeadingSpaces (nsp->names [4]); str = XtractTagListColumn (txt, 3); StringNCpy_0 (str1, str, sizeof (str1)); MemFree (str); j = 0; k = 0; ch = str1 [j]; while (ch != '\0') { if (ch != ' ') { suffix [k] = ch; k++; } j++; ch = str1 [j]; } suffix [k] = '\0'; if (suffix [0] != '\0') { len = StringLen (suffix); if (len > 0 && suffix [len - 1] == '.') { suffix [len - 1] = '\0'; } if (StringICmp (suffix, "1d") == 0) { StringCpy (suffix, "I"); } else if (StringICmp (suffix, "1st") == 0) { StringCpy (suffix, "I"); } else if (StringICmp (suffix, "2d") == 0) { StringCpy (suffix, "II"); } else if (StringICmp (suffix, "2nd") == 0) { StringCpy (suffix, "II"); } else if (StringICmp (suffix, "3d") == 0) { StringCpy (suffix, "III"); } else if (StringICmp (suffix, "3rd") == 0) { StringCpy (suffix, "III"); } else if (StringICmp (suffix, "4th") == 0) { StringCpy (suffix, "IV"); } else if (StringICmp (suffix, "5th") == 0) { StringCpy (suffix, "V"); } else if (StringICmp (suffix, "6th") == 0) { StringCpy (suffix, "VI"); } else if (StringICmp (suffix, "Sr") == 0) { StringCpy (suffix, "Sr."); } else if (StringICmp (suffix, "Jr") == 0) { StringCpy (suffix, "Jr."); } /* len = StringLen (suffix); if (len > 0 && suffix [len - 1] != '.') { StringCat (suffix, "."); } */ nsp->names [5] = StringSave (suffix); TrimLeadingSpaces (nsp->names [5]); } if (StringCmp (nsp->names [0], "et al") == 0) { nsp->names [0] = MemFree (nsp->names [0]); nsp->names [0] = StringSave ("et al."); } nsp->names [2] = XtractTagListColumn (txt, 4); TrimLeadingSpaces (nsp->names [2]); if (StringHasNoText (nsp->names [2])) { nsp->names [2] = MemFree (nsp->names [2]); } MemFree (first); return nsp; } static AffilPtr CleanAffil (AffilPtr afp) { if (afp == NULL) return NULL; CleanVisStringJunkAndCompress (&(afp->affil)); CleanVisStringJunkAndCompress (&(afp->div)); CleanVisStringJunkAndCompress (&(afp->city)); CleanVisStringJunkAndCompress (&(afp->sub)); CleanVisStringJunkAndCompress (&(afp->country)); CleanVisStringJunkAndCompress (&(afp->street)); CleanVisStringJunkAndCompress (&(afp->email)); CleanVisStringJunkAndCompress (&(afp->fax)); CleanVisStringJunkAndCompress (&(afp->phone)); CleanVisStringJunkAndCompress (&(afp->postal_code)); if (afp->choice == 2) { if (StringCmp (afp->country, "U.S.A.") == 0) { afp->country = MemFree (afp->country); afp->country = StringSave ("USA"); } } if (afp->affil == NULL && afp->div == NULL && afp->city == NULL && afp->sub == NULL && afp->country == NULL && afp->street == NULL && afp->email == NULL && afp->fax == NULL && afp->phone == NULL && afp->postal_code == NULL) { afp = MemFree (afp); } return afp; } static void NormalizeAuthors (AuthListPtr alp, Boolean fixInitials) { AuthorPtr ap; CharPtr initials; size_t len; ValNodePtr names; ValNodePtr next; NameStdPtr nsp; PersonIdPtr pid; ValNodePtr PNTR prev; CharPtr str; Boolean upcaseinits; ValNodePtr vnp; Boolean zap; if (alp == NULL) return; alp->affil = CleanAffil (alp->affil); if (alp->choice == 2 || alp->choice == 3) { for (vnp = alp->names; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; TrimSpacesAroundString (str); Asn2gnbkCompressSpaces (str); } } if (alp->choice != 1) return; prev = &(alp->names); names = alp->names; while (names != NULL) { next = names->next; zap = FALSE; ap = names->data.ptrvalue; if (ap != NULL) { pid = ap->name; if (pid == NULL) { /* continue */ } else if (pid->choice == 2) { nsp = pid->data; if (nsp != NULL /* && nsp->names [4] != NULL */) { upcaseinits = FALSE; initials = nsp->names [4]; if (StringLen (initials) > 0) { if (IS_UPPER (initials [0])) { upcaseinits = TRUE; } } str = NameStdPtrToTabbedString (nsp, fixInitials); pid->data = NameStdFree (nsp); nsp = TabbedStringToNameStdPtr (str, fixInitials); if (upcaseinits) { initials = nsp->names [4]; if (StringLen (initials) > 0) { if (IS_LOWER (initials [0])) { initials [0] = TO_UPPER (initials [0]); } } } pid->data = nsp; MemFree (str); CleanVisString (&(nsp->names [0])); CleanVisString (&(nsp->names [1])); CleanVisString (&(nsp->names [2])); CleanVisString (&(nsp->names [3])); CleanVisString (&(nsp->names [4])); CleanVisString (&(nsp->names [5])); CleanVisString (&(nsp->names [6])); if (StringCmp (nsp->names [0], "et") == 0 && (StringCmp (nsp->names [4], "al") == 0 || StringCmp (nsp->names [4], "al.") == 0 || StringCmp (nsp->names [4], "Al.") == 0) && (StringHasNoText (nsp->names [1]) || StringCmp (nsp->names [1], "a") == 0)) { nsp->names [4] = MemFree (nsp->names [4]); nsp->names [1] = MemFree (nsp->names [1]); nsp->names [0] = MemFree (nsp->names [0]); nsp->names [0] = StringSave ("et al."); } str = nsp->names [0]; len = StringLen (str); if (len > 4 && StringHasNoText (nsp->names [5])) { if (StringCmp (str + len - 4, " Jr.") == 0 || StringCmp (str + len - 4, " Sr.") == 0) { nsp->names [5] = StringSave (str + len - 3); str [len - 4] = '\0'; TrimSpacesAroundString (str); } } str = nsp->names [4]; len = StringLen (str); if (len > 4 && StringHasNoText (nsp->names [5])) { if (StringCmp (str + len - 4, ".Jr.") == 0 || StringCmp (str + len - 4, ".Sr.") == 0) { nsp->names [5] = StringSave (str + len - 3); str [len - 3] = '\0'; TrimSpacesAroundString (str); } } if (StringHasNoText (nsp->names [0]) && StringHasNoText (nsp->names [1]) && StringHasNoText (nsp->names [2]) && StringHasNoText (nsp->names [3]) && StringHasNoText (nsp->names [4]) && StringHasNoText (nsp->names [5]) && StringHasNoText (nsp->names [6])) { zap = TRUE; } /* last name is required, so zap if not present */ if (StringHasNoText (nsp->names [0])) { zap = TRUE; } } } else if (pid->choice == 3 || pid->choice == 4 || pid->choice == 5) { TrimSpacesAroundString ((CharPtr) pid->data); if (StringHasNoText ((CharPtr) pid->data)) { zap = TRUE; } } } if (zap) { /* remove empty authors */ *prev = names->next; names->next = NULL; AuthorFree (ap); ValNodeFree (names); } else { prev = &(names->next); } names = next; } /* if no remaining authors, put in default author for legal ASN.1 */ if (alp->names == NULL) { names = ValNodeNew (NULL); if (names != NULL) { /* ap = AuthorNew (); if (ap != NULL) { pid = PersonIdNew (); if (pid != NULL) { pid->choice = 4; pid->data = (Pointer) StringSave ("?"); ap->name = pid; names->choice = 1; names->data.ptrvalue = ap; alp->names = names; } } */ names->choice = 3; names->data.ptrvalue = StringSave ("?"); alp->names = names; alp->choice = 3; } } } static void StrStripSpaces ( CharPtr str ) { CharPtr new_str; if (str == NULL) return; new_str = str; while (*str != '\0') { *new_str++ = *str; if (*str == ' ' || *str == '\t' || *str == '(') { for (str++; *str == ' ' || *str == '\t'; str++) continue; if (*str == ')' || *str == ',') { new_str--; } } else { str++; } } *new_str = '\0'; } /* from utilpub.c */ static Boolean empty_citgen(CitGenPtr cit) { if (cit == NULL) return TRUE; if (cit->cit) return FALSE; if (cit->authors) return FALSE; if (cit->muid > 0) return FALSE; if (cit->journal) return FALSE; if (cit->volume) return FALSE; if (cit->issue) return FALSE; if (cit->pages) return FALSE; if (cit->date) return FALSE; if (cit->serial_number > 0) return FALSE; if (cit->title) return FALSE; if (cit->pmid > 0) return FALSE; return TRUE; } static void NormalizePubAuthors (ValNodePtr vnp, Boolean stripSerial, Boolean fixInitials) { CitArtPtr cap; CitBookPtr cbp; CitGenPtr cgp; CitPatPtr cpp; CitSubPtr csp; if (vnp == NULL) return; if (vnp->choice == PUB_PMid || vnp->choice == PUB_Muid) return; if (vnp->data.ptrvalue == NULL) return; switch (vnp->choice) { case PUB_Gen : cgp = (CitGenPtr) vnp->data.ptrvalue; NormalizeAuthors (cgp->authors, fixInitials); break; case PUB_Sub : csp = (CitSubPtr) vnp->data.ptrvalue; NormalizeAuthors (csp->authors, fixInitials); break; case PUB_Article : cap = (CitArtPtr) vnp->data.ptrvalue; NormalizeAuthors (cap->authors, fixInitials); if (cap->from == 2 || cap->from == 3) { cbp = (CitBookPtr) cap->fromptr; if (cbp != NULL) { NormalizeAuthors (cbp->authors, fixInitials); } } break; case PUB_Book : cbp = (CitBookPtr) vnp->data.ptrvalue; NormalizeAuthors (cbp->authors, fixInitials); break; case PUB_Man : cbp = (CitBookPtr) vnp->data.ptrvalue; if (cbp->othertype == 2 && cbp->let_type == 3) { NormalizeAuthors (cbp->authors, fixInitials); } break; case PUB_Patent : cpp = (CitPatPtr) vnp->data.ptrvalue; NormalizeAuthors (cpp->authors, fixInitials); NormalizeAuthors (cpp->applicants, fixInitials); NormalizeAuthors (cpp->assignees, fixInitials); break; default : break; } } static void NormalizeAPub (ValNodePtr vnp, Boolean stripSerial, Boolean fixInitials) { AffilPtr affil; AuthListPtr alp; CitArtPtr cap; CitBookPtr cbp; CitGenPtr cgp; CitJourPtr cjp; CitPatPtr cpp; CitSubPtr csp; ImprintPtr imp; CharPtr str; CharPtr tmp; ValNodePtr ttl; if (vnp == NULL) return; if (vnp->choice == PUB_PMid || vnp->choice == PUB_Muid) return; if (vnp->data.ptrvalue == NULL) return; imp = NULL; switch (vnp->choice) { case PUB_Gen : cgp = (CitGenPtr) vnp->data.ptrvalue; if (stripSerial) { cgp->serial_number = -1; /* but does not remove if empty */ } if (StringNICmp (cgp->cit, "unpublished", 11) == 0) { cgp->cit [0] = 'U'; /* cgp->date = DateFree (cgp->date); */ /* remove date if unpublished */ if (cgp->journal == NULL) { cgp->volume = MemFree (cgp->volume); cgp->issue = MemFree (cgp->issue); cgp->pages = MemFree (cgp->pages); } } TrimSpacesAroundString (cgp->cit); if (StringDoesHaveText (cgp->title)) { StrStripSpaces (cgp->title); } break; case PUB_Sub : csp = (CitSubPtr) vnp->data.ptrvalue; alp = csp->authors; imp = csp->imp; if (alp != NULL && alp->affil == NULL && imp != NULL && imp->pub != NULL) { alp->affil = imp->pub; imp->pub = NULL; } if (csp->date == NULL && imp != NULL && imp->date != NULL) { csp->date = imp->date; imp->date = NULL; } if (imp != NULL && imp->date == NULL) { csp->imp = ImprintFree (csp->imp); } if (alp != NULL && alp->affil != NULL) { affil = alp->affil; if (affil->choice == 1) { str = affil->affil; if (StringNICmp (str, "to the ", 7) == 0) { if (StringNICmp (str + 24, " databases", 10) == 0) { str += 34; if (*str == '.') { str++; } tmp = StringSaveNoNull (TrimSpacesAroundString (str)); affil->affil = MemFree (affil->affil); affil->affil = tmp; } } } alp->affil = CleanAffil (alp->affil); } imp = csp->imp; break; case PUB_Article : cap = (CitArtPtr) vnp->data.ptrvalue; if (cap != NULL) { if (cap->from == 1) { cjp = (CitJourPtr) cap->fromptr; if (cjp != NULL) { imp = cjp->imp; } } else if (cap->from == 2 || cap->from == 3) { cbp = (CitBookPtr) cap->fromptr; if (cbp != NULL) { imp = cbp->imp; } } for (ttl = cap->title; ttl != NULL; ttl = ttl->next) { if (ttl->choice == Cit_title_name) { str = (CharPtr) ttl->data.ptrvalue; if (StringHasNoText (str)) continue; StrStripSpaces (str); } } } break; case PUB_Patent : cpp = (CitPatPtr) vnp->data.ptrvalue; if (cpp != NULL) { if (StringCmp (cpp->country, "USA") == 0) { cpp->country = MemFree (cpp->country); cpp->country = StringSave ("US"); } } break; default : break; } if (imp != NULL) { CleanVisStringAndCompress (&(imp->volume)); CleanVisStringAndCompress (&(imp->issue)); CleanVisStringAndCompress (&(imp->pages)); CleanVisStringAndCompress (&(imp->section)); CleanVisStringAndCompress (&(imp->part_sup)); CleanVisStringAndCompress (&(imp->language)); CleanVisStringAndCompress (&(imp->part_supi)); } } NLM_EXTERN void CleanUpPubdescAuthors (PubdescPtr pdp) { Char buf1 [121]; Boolean fixInitials = TRUE; Boolean hasArt = FALSE; Boolean hasUid = FALSE; ValNodePtr next; ValNodePtr PNTR prev; ValNodePtr vnp; if (pdp == NULL) return; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { if (vnp->choice == PUB_Muid || vnp->choice == PUB_PMid) { if (vnp->data.intvalue > 0) { hasUid = TRUE; } } else if (vnp->choice == PUB_Article) { hasArt = TRUE; } } if (hasArt && hasUid) { fixInitials = FALSE; } prev = &(pdp->pub); vnp = pdp->pub; while (vnp != NULL) { next = vnp->next; PubLabelUnique (vnp, buf1, sizeof (buf1) - 1, OM_LABEL_CONTENT, TRUE); NormalizePubAuthors (vnp, TRUE, fixInitials); vnp = next; } } static void NormalizePubdesc (PubdescPtr pdp, Boolean stripSerial, Boolean doAuthors, ValNodePtr PNTR publist) { ArticleIdPtr aip; Int4 artpmid = 0; Char buf1 [121]; Char buf2 [121]; CitArtPtr cap = NULL; CitGenPtr cgp; CitJourPtr cjp; Boolean fixInitials = TRUE; Boolean hasArt = FALSE; Boolean hasUid = FALSE; ImprintPtr imp; ValNodePtr next; Int4 pmid = 0; ValNodePtr PNTR prev; ValNodePtr vnp; if (pdp == NULL) return; CleanVisString (&(pdp->comment)); for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { if (vnp->choice == PUB_Muid || vnp->choice == PUB_PMid) { if (vnp->data.intvalue > 0) { hasUid = TRUE; } } else if (vnp->choice == PUB_Article) { hasArt = TRUE; } } if (hasArt && hasUid) { fixInitials = FALSE; } prev = &(pdp->pub); vnp = pdp->pub; if (vnp != NULL && vnp->next == NULL && vnp->choice == PUB_Gen) { cgp = (CitGenPtr) vnp->data.ptrvalue; buf1 [0] = '\0'; PubLabelUnique (vnp, buf1, sizeof (buf1) - 1, OM_LABEL_CONTENT, TRUE); if (doAuthors) { NormalizeAuthors (cgp->authors, fixInitials); } if (stripSerial) { cgp->serial_number = -1; } if (StringNICmp (cgp->cit, "unpublished", 11) == 0) { cgp->cit [0] = 'U'; /* cgp->date = DateFree (cgp->date); */ /* remove date if unpublished */ if (cgp->journal == NULL) { cgp->volume = MemFree (cgp->volume); cgp->issue = MemFree (cgp->issue); cgp->pages = MemFree (cgp->pages); } } TrimSpacesAroundString (cgp->cit); if (StringDoesHaveText (cgp->title)) { StrStripSpaces (cgp->title); } buf2 [0] = '\0'; PubLabelUnique (vnp, buf2, sizeof (buf2) - 1, OM_LABEL_CONTENT, TRUE); if (StringCmp (buf1, buf2) != 0) { ValNodeCopyStr (publist, 1, buf1); ValNodeCopyStr (publist, 2, buf2); } return; /* but does not remove if empty and only element of Pub */ } while (vnp != NULL) { next = vnp->next; buf1 [0] = '\0'; PubLabelUnique (vnp, buf1, sizeof (buf1) - 1, OM_LABEL_CONTENT, TRUE); if (doAuthors) { NormalizePubAuthors (vnp, stripSerial, fixInitials); } NormalizeAPub (vnp, stripSerial, fixInitials); if (vnp->choice == PUB_Article) { cap = (CitArtPtr) vnp->data.ptrvalue; if (cap != NULL && cap->from == 1) { cjp = (CitJourPtr) cap->fromptr; if (cjp != NULL) { imp = cjp->imp; if (imp != NULL) { if (imp->pubstatus == PUBSTATUS_aheadofprint && imp->prepub != 2) { if (StringHasNoText (imp->volume) || StringHasNoText (imp->pages)) { imp->prepub = 2; } } if (imp->pubstatus == PUBSTATUS_aheadofprint && imp->prepub == 2) { if (StringDoesHaveText (imp->volume) && StringDoesHaveText (imp->pages)) { imp->prepub = 0; } } if (imp->pubstatus == PUBSTATUS_epublish && imp->prepub == 2) { imp->prepub = 0; } } } for (aip = cap->ids; aip != NULL; aip = aip->next) { if (aip->choice == ARTICLEID_PUBMED) { artpmid = aip->data.intvalue; } } } } else if (vnp->choice == PUB_PMid) { pmid = vnp->data.intvalue; } if (vnp->choice == PUB_Gen && empty_citgen ((CitGenPtr) vnp->data.ptrvalue)) { *prev = vnp->next; vnp->next = NULL; PubFree (vnp); } else { prev = &(vnp->next); buf2 [0] = '\0'; PubLabelUnique (vnp, buf2, sizeof (buf2) - 1, OM_LABEL_CONTENT, TRUE); if (StringCmp (buf1, buf2) != 0) { ValNodeCopyStr (publist, 1, buf1); ValNodeCopyStr (publist, 2, buf2); } } vnp = next; } if (pmid == 0 && artpmid > 0) { ValNodeAddInt (&(pdp->pub), PUB_PMid, artpmid); } else if (pmid > 0 && artpmid == 0 && cap != NULL) { ValNodeAddInt (&(cap->ids), ARTICLEID_PUBMED, pmid); } } NLM_EXTERN void CleanUpPubdescBody (PubdescPtr pdp, Boolean stripSerial) { if (pdp == NULL) return; NormalizePubdesc (pdp, stripSerial, FALSE, NULL); } static Boolean KeywordAlreadyInList (ValNodePtr head, CharPtr kwd) { ValNodePtr vnp; if (head == NULL || kwd == NULL) return FALSE; for (vnp = head; vnp != NULL; vnp = vnp->next) { if (StringICmp ((CharPtr) vnp->data.ptrvalue, kwd) == 0) return TRUE; } return FALSE; } static Boolean CopyGeneXrefToGeneFeat (GeneRefPtr grp, GeneRefPtr grx) { if (grp == NULL || grx == NULL) return FALSE; if (grx->db != NULL) { ValNodeLink (&(grp->db), grx->db); grx->db = NULL; } if (grx->locus == NULL && grx->allele == NULL && grx->desc == NULL && grx->maploc == NULL && grx->locus_tag == NULL && grx->db == NULL && grx->syn == NULL) return TRUE; return FALSE; } static void HandleXrefOnGene (SeqFeatPtr sfp) { GeneRefPtr grp; GeneRefPtr grx; SeqFeatXrefPtr next; SeqFeatXrefPtr PNTR prev; SeqFeatXrefPtr xref; if (sfp == NULL || sfp->data.choice != SEQFEAT_GENE) return; grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (grp == NULL) return; prev = &(sfp->xref); xref = sfp->xref; while (xref != NULL) { next = xref->next; if (xref->data.choice == SEQFEAT_GENE) { grx = (GeneRefPtr) xref->data.value.ptrvalue; if (CopyGeneXrefToGeneFeat (grp, grx)) { *(prev) = next; xref->next = NULL; SeqFeatXrefFree (xref); } else { prev = &(xref->next); } } else { prev = &(xref->next); } xref = next; } } static void CopyProtXrefToProtFeat (ProtRefPtr prp, ProtRefPtr prx) { ValNodePtr curr; size_t len; ValNodePtr next; ValNodePtr PNTR prev; CharPtr str; if (prp == NULL || prx == NULL) return; if (prx->db != NULL) { ValNodeLink (&(prp->db), prx->db); prx->db = NULL; } prev = &(prx->name); curr = prx->name; while (curr != NULL) { next = curr->next; str = (CharPtr) curr->data.ptrvalue; if (! KeywordAlreadyInList (prp->name, str)) { ValNodeCopyStr (&(prp->name), 0, str); *(prev) = next; curr->next = NULL; curr->data.ptrvalue = NULL; ValNodeFree (curr); } else { prev = &(curr->next); } curr = next; } if (prp->desc == NULL) { prp->desc = prx->desc; prx->desc = NULL; } else if (prx->desc != NULL) { if (StringCmp (prx->desc, prp->desc) != 0) { len = StringLen (prp->desc) + StringLen (prx->desc) + 6; str = MemNew (len); if (str != NULL) { StringCpy (str, prp->desc); StringCat (str, "; "); StringCat (str, prx->desc); prp->desc = MemFree (prp->desc); prp->desc = str; } } } prev = &(prx->ec); curr = prx->ec; while (curr != NULL) { next = curr->next; str = (CharPtr) curr->data.ptrvalue; if (! KeywordAlreadyInList (prp->ec, str)) { ValNodeCopyStr (&(prp->ec), 0, str); *(prev) = next; curr->next = NULL; curr->data.ptrvalue = NULL; ValNodeFree (curr); } else { prev = &(curr->next); } curr = next; } prev = &(prx->activity); curr = prx->activity; while (curr != NULL) { next = curr->next; str = (CharPtr) curr->data.ptrvalue; if (! KeywordAlreadyInList (prp->activity, str)) { ValNodeCopyStr (&(prp->activity), 0, str); curr->data.ptrvalue = NULL; } *(prev) = next; curr->next = NULL; curr->data.ptrvalue = NULL; ValNodeFree (curr); curr = next; } } static Boolean InGpsGenomic (SeqFeatPtr sfp) { BioseqPtr bsp; BioseqSetPtr bssp; if (sfp == NULL) return FALSE; bsp = BioseqFindFromSeqLoc (sfp->location); if (bsp == NULL) return FALSE; if (bsp->idx.parenttype == OBJ_BIOSEQSET) { bssp = (BioseqSetPtr) bsp->idx.parentptr; while (bssp != NULL) { if (bssp->_class == BioseqseqSet_class_nuc_prot) return FALSE; if (bssp->_class == BioseqseqSet_class_gen_prod_set) return TRUE; if (bssp->idx.parenttype != OBJ_BIOSEQSET) return FALSE; bssp = (BioseqSetPtr) bssp->idx.parentptr; } } return FALSE; } static void HandleXrefOnCDS (SeqFeatPtr sfp) { SeqFeatXrefPtr next; SeqFeatXrefPtr PNTR prev; SeqFeatPtr prot; ProtRefPtr prp; ProtRefPtr prx; SeqFeatXrefPtr xref; if (sfp != NULL && sfp->product != NULL) { if (InGpsGenomic (sfp)) return; prot = GetBestProteinFeatureUnindexed (sfp->product); if (prot != NULL) { prp = (ProtRefPtr) prot->data.value.ptrvalue; if (prp != NULL) { prev = &(sfp->xref); xref = sfp->xref; while (xref != NULL) { next = xref->next; if (xref->data.choice == SEQFEAT_PROT) { prx = (ProtRefPtr) xref->data.value.ptrvalue; CopyProtXrefToProtFeat (prp, prx); *(prev) = next; xref->next = NULL; SeqFeatXrefFree (xref); } else { prev = &(xref->next); } xref = next; } } } } } static void CleanUserStrings ( UserFieldPtr ufp, Pointer userdata ) { ObjectIdPtr oip; oip = ufp->label; if (oip != NULL && oip->str != NULL) { if (! StringHasNoText (oip->str)) { CleanVisString (&(oip->str)); } } if (ufp->choice == 1) { if (! StringHasNoText ((CharPtr) ufp->data.ptrvalue)) { CleanVisString ((CharPtr PNTR) &(ufp->data.ptrvalue)); } } } static void CleanUserFields ( UserFieldPtr ufp, Pointer userdata ) { ObjectIdPtr oip; oip = ufp->label; if (oip != NULL && oip->str != NULL) { if (! StringHasNoText (oip->str)) { CleanVisString (&(oip->str)); } } VisitUserFieldsInUfp (ufp, userdata, CleanUserStrings); } NLM_EXTERN void CleanStructuredComment ( UserObjectPtr uop ) { Boolean genome_assembly_data = FALSE; UserFieldPtr ufp; CharPtr str, core, new_str; if (uop == NULL || uop->type == NULL || StringCmp (uop->type->str, "StructuredComment") != 0) { return; } for (ufp = uop->data; ufp != NULL; ufp = ufp->next) { if (ufp->label != NULL && ufp->choice == 1 && (str = (CharPtr) ufp->data.ptrvalue) != NULL) { if (StringCmp (ufp->label->str, "StructuredCommentPrefix") == 0) { core = StructuredCommentDbnameFromString(str); new_str = (CharPtr) MemNew (sizeof (Char) * (StringLen (core) + 15)); sprintf (new_str, "##%s-START##", core); str = MemFree (str); ufp->data.ptrvalue = new_str; if (StringCmp (core, "Genome-Assembly-Data") == 0) { genome_assembly_data = TRUE; } core = MemFree (core); } else if (StringCmp (ufp->label->str, "StructuredCommentSuffix") == 0) { core = StructuredCommentDbnameFromString(str); new_str = (CharPtr) MemNew (sizeof (Char) * (StringLen (core) + 15)); sprintf (new_str, "##%s-END##", core); str = MemFree (str); ufp->data.ptrvalue = new_str; if (StringCmp (core, "Genome-Assembly-Data") == 0) { genome_assembly_data = TRUE; } core = MemFree (core); } } } if (genome_assembly_data) { for (ufp = uop->data; ufp != NULL; ufp = ufp->next) { if (ufp->label != NULL && ufp->choice == 1 && (str = (CharPtr) ufp->data.ptrvalue) != NULL) { if (StringCmp (ufp->label->str, "Finishing Goal") == 0 || StringCmp (ufp->label->str, "Current Finishing Status") == 0) { if (StringCmp (str, "High Quality Draft") == 0) { ufp->data.ptrvalue = StringSave ("High-Quality Draft"); str = MemFree (str); } else if (StringCmp (str, "Improved High Quality Draft") == 0) { ufp->data.ptrvalue = StringSave ("Improved High-Quality Draft"); str = MemFree (str); } else if (StringCmp (str, "Annotation Directed") == 0) { ufp->data.ptrvalue = StringSave ("Annotation-Directed Improvement"); str = MemFree (str); } else if (StringCmp (str, "Non-contiguous Finished") == 0) { ufp->data.ptrvalue = StringSave ("Noncontiguous Finished"); str = MemFree (str); } } } } } } static void CleanUserObject ( UserObjectPtr uop, Pointer userdata ) { ObjectIdPtr oip; oip = uop->type; if (oip != NULL && oip->str != NULL) { if (! StringHasNoText (oip->str)) { CleanVisString (&(oip->str)); } } VisitUserFieldsInUop (uop, userdata, CleanUserFields); CleanStructuredComment (uop); } static CharPtr bsecSiteList [] = { "", "active", "binding", "cleavage", "inhibit", "modifi", "glycosylation", "myristoylation", "mutagenized", "metal-binding", "phosphorylation", "acetylation", "amidation", "methylation", "hydroxylation", "sulfatation", "oxidative-deamination", "pyrrolidone-carboxylic-acid", "gamma-carboxyglutamic-acid", "blocked", "lipid-binding", "np-binding", "DNA-binding", "signal-peptide", "transit-peptide", "transmembrane-region", "nitrosylation", NULL }; static CharPtr uninfStrings [] = { "signal", "transit", "peptide", "signal peptide", "signal-peptide", "signal_peptide", "transit peptide", "transit-peptide", "transit_peptide", "unnamed", "unknown", "putative", NULL }; static Boolean InformativeString (CharPtr str) { Int2 i; if (StringHasNoText (str)) return FALSE; for (i = 0; uninfStrings [i] != NULL; i++) { if (StringICmp (str, uninfStrings [i]) == 0) return FALSE; } return TRUE; } static void CleanUpExceptText (SeqFeatPtr sfp) { ValNodePtr head, vnp; size_t len; CharPtr prefix, ptr, str, tmp; if (sfp == NULL || sfp->except_text == NULL) return; if (StringStr (sfp->except_text, "ribosome slippage") == NULL && StringStr (sfp->except_text, "trans splicing") == NULL && StringStr (sfp->except_text, "alternate processing") == NULL && StringStr (sfp->except_text, "non-consensus splice site") == NULL && StringStr (sfp->except_text, "adjusted for low quality genome") == NULL) return; head = NULL; str = sfp->except_text; tmp = str; while (! StringHasNoText (tmp)) { ptr = StringChr (tmp, ','); if (ptr != NULL) { *ptr = '\0'; ptr++; } TrimSpacesAroundString (tmp); ValNodeCopyStr (&head, 0, tmp); tmp = ptr; } for (vnp = head; vnp != NULL; vnp = vnp->next) { tmp = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (tmp)) continue; if (StringCmp (tmp, "ribosome slippage") == 0) { vnp->data.ptrvalue = MemFree (tmp); vnp->data.ptrvalue = StringSave ("ribosomal slippage"); } else if (StringCmp (tmp, "trans splicing") == 0) { vnp->data.ptrvalue = MemFree (tmp); vnp->data.ptrvalue = StringSave ("trans-splicing"); } else if (StringCmp (tmp, "alternate processing") == 0) { vnp->data.ptrvalue = MemFree (tmp); vnp->data.ptrvalue = StringSave ("alternative processing"); } else if (StringCmp (tmp, "non-consensus splice site") == 0) { vnp->data.ptrvalue = MemFree (tmp); vnp->data.ptrvalue = StringSave ("nonconsensus splice site"); } else if (StringCmp (tmp, "adjusted for low quality genome") == 0) { vnp->data.ptrvalue = MemFree (tmp); vnp->data.ptrvalue = StringSave ("adjusted for low-quality genome"); } } len = 0; for (vnp = head; vnp != NULL; vnp = vnp->next) { tmp = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (tmp)) continue; len += StringLen (tmp) + 2; } str = (CharPtr) MemNew (len + 2); if (str == NULL) return; prefix = ""; for (vnp = head; vnp != NULL; vnp = vnp->next) { tmp = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (tmp)) continue; StringCat (str, prefix); StringCat (str, tmp); prefix = ", "; } sfp->except_text = MemFree (sfp->except_text); sfp->except_text = str; ValNodeFreeData (head); } static Boolean ExpandGeneSynCom (ValNodePtr headsyn) { ValNodePtr lastsyn; ValNodePtr newsyn; ValNodePtr nextsyn; CharPtr ptr; CharPtr str; CharPtr tmp; str = (CharPtr) headsyn->data.ptrvalue; if (StringHasNoText (str)) return TRUE; if (StringChr (str, ',') == NULL) return FALSE; nextsyn = headsyn->next; lastsyn = headsyn; tmp = StringSave ((CharPtr) headsyn->data.ptrvalue); str = tmp; while (! StringHasNoText (str)) { ptr = StringChr (str, ','); if (ptr != NULL) { *ptr = '\0'; ptr++; } TrimSpacesAroundString (str); newsyn = ValNodeNew (NULL); if (newsyn != NULL) { newsyn->data.ptrvalue = StringSave (str); newsyn->next = nextsyn; lastsyn->next = newsyn; lastsyn = newsyn; } str = ptr; } MemFree (tmp); return TRUE; } static Boolean ExpandGeneSynSem (ValNodePtr headsyn) { ValNodePtr lastsyn; ValNodePtr newsyn; ValNodePtr nextsyn; CharPtr ptr; CharPtr str; CharPtr tmp; str = (CharPtr) headsyn->data.ptrvalue; if (StringHasNoText (str)) return TRUE; if (StringStr (str, "; ") == NULL) return FALSE; nextsyn = headsyn->next; lastsyn = headsyn; tmp = StringSave ((CharPtr) headsyn->data.ptrvalue); str = tmp; while (! StringHasNoText (str)) { ptr = StringStr (str, "; "); if (ptr != NULL) { ptr++; *ptr = '\0'; ptr++; } TrimSpacesAroundString (str); newsyn = ValNodeNew (NULL); if (newsyn != NULL) { newsyn->data.ptrvalue = StringSave (str); newsyn->next = nextsyn; lastsyn->next = newsyn; lastsyn = newsyn; } str = ptr; } MemFree (tmp); return TRUE; } static void ExpandGeneSynList (GeneRefPtr grp) { ValNodePtr currsyn; ValNodePtr nextsyn; ValNodePtr PNTR prevsyn; if (grp == NULL || grp->syn == NULL) return; currsyn = grp->syn; prevsyn = &(grp->syn); while (currsyn != NULL) { if (ExpandGeneSynCom (currsyn)) { nextsyn = currsyn->next; *(prevsyn) = currsyn->next; currsyn->next = NULL; ValNodeFreeData (currsyn); } else { nextsyn = currsyn->next; prevsyn = (ValNodePtr PNTR) &(currsyn->next); } currsyn = nextsyn; } currsyn = grp->syn; prevsyn = &(grp->syn); while (currsyn != NULL) { if (ExpandGeneSynSem (currsyn)) { nextsyn = currsyn->next; *(prevsyn) = currsyn->next; currsyn->next = NULL; ValNodeFreeData (currsyn); } else { nextsyn = currsyn->next; prevsyn = (ValNodePtr PNTR) &(currsyn->next); } currsyn = nextsyn; } } typedef struct gosstruc { CharPtr term; Char goid [32]; CharPtr evidence; Int4 pmid; CharPtr goref; UserFieldPtr ufp; } GosStruc, PNTR GosStrucPtr; static int LIBCALLBACK SortVnpByGssp (VoidPtr ptr1, VoidPtr ptr2) { int compare; GosStrucPtr gsp1, gsp2; ValNodePtr vnp1, vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; gsp1 = (GosStrucPtr) vnp1->data.ptrvalue; gsp2 = (GosStrucPtr) vnp2->data.ptrvalue; if (gsp1 == NULL || gsp2 == NULL) return 0; compare = StringICmp (gsp1->goid, gsp2->goid); if (compare > 0) { return 1; } else if (compare < 0) { return -1; } compare = StringICmp (gsp1->term, gsp2->term); if (compare > 0) { return 1; } else if (compare < 0) { return -1; } compare = StringICmp (gsp1->evidence, gsp2->evidence); if (compare > 0) { return 1; } else if (compare < 0) { return -1; } if (gsp1->pmid == 0) return 1; if (gsp2->pmid == 0) return -1; if (gsp1->pmid > gsp2->pmid) { return 1; } else if (gsp1->pmid < gsp2->pmid) { return -1; } return 0; } static CharPtr bsecGoQualType [] = { "", "Process", "Component", "Function", NULL }; static CharPtr bsecGoFieldType [] = { "", "text string", "go id", "pubmed id", "go ref", "evidence", NULL }; static UserFieldPtr SortGoTerms ( UserFieldPtr entryhead ) { UserFieldPtr entry, topufp, ufp, lastufp; CharPtr evidence, goid, goref, textstr; Char gid [32]; GosStrucPtr gsp, lastgsp; ValNodePtr head = NULL, vnp; Int2 j; ObjectIdPtr oip; Int4 pmid; if (entryhead == NULL) return entryhead; for (entry = entryhead; entry != NULL; entry = entry->next) { if (entry == NULL || entry->choice != 11) break; topufp = (UserFieldPtr) entry->data.ptrvalue; if (topufp == NULL) continue; textstr = NULL; evidence = NULL; goid = NULL; goref = NULL; pmid = 0; for (ufp = topufp; ufp != NULL; ufp = ufp->next) { oip = ufp->label; if (oip == NULL) continue; for (j = 0; bsecGoFieldType [j] != NULL; j++) { if (StringICmp (oip->str, bsecGoFieldType [j]) == 0) break; } if (bsecGoFieldType [j] == NULL) continue; switch (j) { case 1 : if (ufp->choice == 1) { textstr = (CharPtr) ufp->data.ptrvalue; } break; case 2 : if (ufp->choice == 1) { goid = (CharPtr) ufp->data.ptrvalue; } else if (ufp->choice == 2) { sprintf (gid, "%ld", (long) (Int4) ufp->data.intvalue); goid = (CharPtr) gid; } break; case 3 : if (ufp->choice == 2) { pmid = (Int4) ufp->data.intvalue; } break; case 4 : if (ufp->choice == 1) { goref = (CharPtr) ufp->data.ptrvalue; } break; case 5 : if (ufp->choice == 1) { evidence = (CharPtr) ufp->data.ptrvalue; } break; default : break; } } if (StringDoesHaveText (textstr)) { gsp = (GosStrucPtr) MemNew (sizeof (GosStruc)); if (gsp != NULL) { gsp->term = textstr; StringNCpy_0 (gsp->goid, goid, sizeof (gsp->goid)); gsp->evidence = evidence; gsp->pmid = pmid; gsp->goref = goref; gsp->ufp = entry; ValNodeAddPointer (&head, 0, (Pointer) gsp); } } } if (head == NULL) return entryhead; head = ValNodeSort (head, SortVnpByGssp); entryhead = NULL; lastgsp = NULL; lastufp = NULL; for (vnp = head; vnp != NULL; vnp = vnp->next) { gsp = (GosStrucPtr) vnp->data.ptrvalue; if (gsp == NULL || gsp->ufp == NULL) continue; if (lastgsp != NULL && (StringICmp (gsp->term, lastgsp->term) == 0 || StringICmp (gsp->goid, lastgsp->goid) == 0) && (gsp->pmid == lastgsp->pmid && StringICmp (gsp->goref, lastgsp->goref) == 0 && StringICmp (gsp->evidence, lastgsp->evidence) == 0)) { gsp->ufp->next = NULL; UserFieldFree (gsp->ufp); } else { if (lastufp != NULL) { lastufp->next = gsp->ufp; } else { entryhead = gsp->ufp; } lastufp = gsp->ufp; lastufp->next = NULL; } lastgsp = gsp; } ValNodeFreeData (head); return entryhead; } static void SortGoTermsUfp ( UserFieldPtr ufp, Pointer userdata ) { UserFieldPtr entry; Int2 i; ObjectIdPtr oip; if (ufp == NULL || ufp->choice != 11) return; oip = ufp->label; if (oip == NULL) return; for (i = 0; bsecGoQualType [i] != NULL; i++) { if (StringICmp (oip->str, bsecGoQualType [i]) == 0) break; } if (bsecGoQualType [i] == NULL) return; entry = ufp->data.ptrvalue; if (entry == NULL || entry->choice != 11) return; ufp->data.ptrvalue = SortGoTerms (entry); } static void SortGoTermsSfp ( UserObjectPtr uop, Pointer userdata ) { ObjectIdPtr oip; if (uop == NULL) return; oip = uop->type; if (oip == NULL) return; if (StringCmp (oip->str, "GeneOntology") == 0) { VisitUserFieldsInUop (uop, userdata, SortGoTermsUfp); } } static void CleanupGoTerms ( UserFieldPtr entryhead ) { UserFieldPtr entry, topufp, ufp; CharPtr goid, goref, str; Int2 j; ObjectIdPtr oip; if (entryhead == NULL) return; for (entry = entryhead; entry != NULL; entry = entry->next) { if (entry == NULL || entry->choice != 11) break; topufp = (UserFieldPtr) entry->data.ptrvalue; if (topufp == NULL) continue; goid = NULL; goref = NULL; for (ufp = topufp; ufp != NULL; ufp = ufp->next) { oip = ufp->label; if (oip == NULL) continue; for (j = 0; bsecGoFieldType [j] != NULL; j++) { if (StringICmp (oip->str, bsecGoFieldType [j]) == 0) break; } if (bsecGoFieldType [j] == NULL) continue; switch (j) { case 2 : if (ufp->choice == 1) { goid = (CharPtr) ufp->data.ptrvalue; if (goid != NULL && *goid != '\0') { if (StringNICmp (goid, "GO:", 3) == 0) { str = StringSave (goid + 3); ufp->data.ptrvalue = (Pointer) str; MemFree (goid); } } } break; case 4 : if (ufp->choice == 1) { goref = (CharPtr) ufp->data.ptrvalue; if (goref != NULL && *goref != '\0') { if (StringNICmp (goref, "GO_REF:", 7) == 0) { str = StringSave (goref + 7); ufp->data.ptrvalue = (Pointer) str; MemFree (goref); } } } break; default : break; } } } } static void CleanupGoTermsUfp ( UserFieldPtr ufp, Pointer userdata ) { UserFieldPtr entry; Int2 i; ObjectIdPtr oip; if (ufp == NULL || ufp->choice != 11) return; oip = ufp->label; if (oip == NULL) return; for (i = 0; bsecGoQualType [i] != NULL; i++) { if (StringICmp (oip->str, bsecGoQualType [i]) == 0) break; } if (bsecGoQualType [i] == NULL) return; entry = ufp->data.ptrvalue; if (entry == NULL || entry->choice != 11) return; CleanupGoTerms (entry); } static void CleanupGoTermsSfp ( UserObjectPtr uop, Pointer userdata ) { ObjectIdPtr oip; if (uop == NULL) return; oip = uop->type; if (oip == NULL) return; if (StringCmp (oip->str, "GeneOntology") == 0) { VisitUserFieldsInUop (uop, userdata, CleanupGoTermsUfp); } } static CharPtr CleanUpSgml ( CharPtr str ) { Int2 ascii_len; Char buf [256]; CharPtr ptr; if (StringHasNoText (str)) return NULL; if (StringChr (str, '&') == NULL) return NULL; ascii_len = Sgml2AsciiLen (str); if (ascii_len + 2 >= sizeof (buf)) return NULL; buf [0] = '\0'; Sgml2Ascii (str, buf, ascii_len + 1); if (StringHasNoText (buf)) return NULL; if (StringCmp (str, buf) == 0) return NULL; ptr = StringChr (buf, '<'); if (ptr != NULL) { *ptr = ' '; } ptr = StringChr (buf, '>'); if (ptr != NULL) { *ptr = ' '; } TrimSpacesAroundString (buf); Asn2gnbkCompressSpaces (buf); return StringSave (buf); } /* special exception for genome pipeline rRNA names */ static Boolean NotExceptedRibosomalName ( CharPtr name ) { Char ch; CharPtr str; str = StringStr (name, " ribosomal"); if (str == NULL) return FALSE; str += 10; ch = *str; while (ch != '\0') { if (ch == ' ' || IS_DIGIT (ch)) { /* okay */ } else { return TRUE; } str++; ch = *str; } return FALSE; } NLM_EXTERN void CleanupSubSourceOrgModOtherFeat ( SeqFeatPtr sfp, Pointer userdata ) { BioSourcePtr biop; OrgNamePtr onp = NULL; OrgRefPtr orp; if (sfp == NULL) return; if (sfp->data.choice != SEQFEAT_BIOSRC) return; biop = (BioSourcePtr) sfp->data.value.ptrvalue; if (biop == NULL) return; orp = biop->org; if (orp != NULL) { onp = orp->orgname; if (orp != NULL) { CleanupOrgModOther (biop, onp); } } CleanupSubSourceOther (biop, onp); } NLM_EXTERN void CleanupSubSourceOrgModOtherDesc ( SeqDescrPtr sdp, Pointer userdata ) { BioSourcePtr biop; OrgNamePtr onp = NULL; OrgRefPtr orp; if (sdp == NULL) return; if (sdp->choice != Seq_descr_source) return; biop = (BioSourcePtr) sdp->data.ptrvalue; if (biop == NULL) return; orp = biop->org; if (orp != NULL) { onp = orp->orgname; if (orp != NULL) { CleanupOrgModOther (biop, onp); } } CleanupSubSourceOther (biop, onp); } typedef struct xmltable { CharPtr code; size_t len; CharPtr letter; } XmlTable, PNTR XmlTablePtr; static XmlTable xmlunicodes [] = { { "&", 4, "&"}, { "&apos", 5, "\'"}, { ">", 3, ">"}, { "<", 3, "<"}, { """, 5, "\""}, { " ", 8, ""}, { "Δ", 5, "Delta"}, { "α", 5, "alpha"}, { "β", 5, "beta"}, { "γ", 5, "gamma"}, { "θ", 5, "theta"}, { "λ", 5, "lambda"}, { "μ", 5, "mu"}, { "ν", 5, "nu"}, { " ", 6, " "}, { "‎", 6, ""}, { "′", 6, "'"}, { "→", 6, "->"}, { "−", 6, "-"}, { "∆", 6, "delta"}, { "fi", 7, "fi"}, { "fl", 7, "fl"}, { "，", 7, ","}, { NULL, 0, ""} }; static CharPtr BSECDecodeXml ( CharPtr str ) { Char ch, nxt; CharPtr dst, ptr, src; Int2 i; size_t len; XmlTablePtr xtp; if (StringHasNoText (str)) return str; src = str; dst = str; ch = *src; while (ch != '\0') { if (ch == '&') { xtp = NULL; len = 1; for (i = 0; xmlunicodes [i].code != NULL; i++) { if (StringNICmp (src, xmlunicodes [i].code, xmlunicodes [i].len) == 0) { nxt = *(src +xmlunicodes [i].len); if (nxt == ';') { xtp = &(xmlunicodes [i]); len = xtp->len + 1; break; } else if (nxt == ' ' || nxt == '\0') { xtp = &(xmlunicodes [i]); len = xtp->len; break; } } } if (xtp != NULL) { if (StringLen (xtp->letter) > 0) { ptr = xtp->letter; ch = *ptr; while (ch != '\0') { *dst = ch; dst++; ptr++; ch = *ptr; } } src += len; } else { *dst = ch; dst++; src++; } } else { *dst = ch; dst++; src++; } ch = *src; } *dst = '\0'; return str; } static void CleanupFeatureStrings ( SeqFeatPtr sfp, Boolean isJscan, Boolean stripSerial, Boolean modernizeFeats, ValNodePtr PNTR publist ) { Uint1 aa; BioSourcePtr biop; Char ch; Uint1 codon [6]; GeneRefPtr grp; ImpFeatPtr ifp; Boolean is_fMet = FALSE; Int2 j; Boolean justTrnaText; size_t len; CharPtr name; OrgNamePtr onp = NULL; OrgRefPtr orp; PubdescPtr pdp; ProtRefPtr prp; CharPtr ptr; RnaRefPtr rrp; SubSourcePtr ssp; CharPtr str; CharPtr suff; CharPtr temp; Char tmp [64]; Boolean trimming_junk; tRNAPtr trp; CharPtr val; ValNodePtr vnp; RNAGenPtr rgp; RNAQualPtr rqp; SeqFeatXrefPtr xref; if (sfp == NULL) return; BSECDecodeXml (sfp->comment); CleanVisString (&(sfp->comment)); len = StringLen (sfp->comment); if (len > 4) { if (StringCmp (sfp->comment + len - 3, ",..") == 0 || StringCmp (sfp->comment + len - 3, ".,.") == 0 || StringCmp (sfp->comment + len - 3, "..,") == 0 || StringCmp (sfp->comment + len - 3, ",.,") == 0) { sfp->comment [len - 3] = '.'; sfp->comment [len - 2] = '.'; sfp->comment [len - 1] = '.'; } } BSECDecodeXml (sfp->title); CleanVisString (&(sfp->title)); CleanVisString (&(sfp->except_text)); if (StringDoesHaveText (sfp->except_text)) { CleanUpExceptText (sfp); } CleanDoubleQuote (sfp->comment); if (StringCmp (sfp->comment, ".") == 0) { sfp->comment = MemFree (sfp->comment); } /* if (sfp->ext != NULL) { VisitUserObjectsInUop (sfp->ext, NULL, SortGoTermsSfp); } */ if (sfp->ext != NULL) { VisitUserObjectsInUop (sfp->ext, NULL, CleanupGoTermsSfp); } for (xref = sfp->xref; xref != NULL; xref = xref->next) { if (xref->data.choice != SEQFEAT_PROT) continue; prp = (ProtRefPtr) xref->data.value.ptrvalue; if (prp == NULL) continue; RemoveFlankingQuotes (&(prp->desc)); RemoveFlankingQuotesList (&(prp->name)); } switch (sfp->data.choice) { case SEQFEAT_BOND : case SEQFEAT_PSEC_STR : case SEQFEAT_COMMENT: return; case SEQFEAT_SITE : for (j = 0; bsecSiteList [j] != NULL; j++) { StringNCpy_0 (tmp, bsecSiteList [j], sizeof (tmp)); len = StringLen (tmp); if (StringNICmp (sfp->comment, tmp, len) == 0) { if (sfp->data.value.intvalue == 0 || sfp->data.value.intvalue == 255) { sfp->data.value.intvalue = j; if (StringHasNoText (sfp->comment + len) || StringICmp (sfp->comment + len, " site") == 0) { sfp->comment = MemFree (sfp->comment); } } } else { val = tmp; ch = *val; while (ch != '\0') { if (ch == '-') { *val = ' '; } val++; ch = *val; } if (StringNICmp (sfp->comment, tmp, len) == 0) { if (sfp->data.value.intvalue == 0 || sfp->data.value.intvalue == 255) { sfp->data.value.intvalue = j; if (StringHasNoText (sfp->comment + len) || StringICmp (sfp->comment + len, " site") == 0) { sfp->comment = MemFree (sfp->comment); } } } } } break; default : break; } if (sfp->data.value.ptrvalue == NULL) return; biop = NULL; orp = NULL; switch (sfp->data.choice) { case SEQFEAT_ORG : orp = (OrgRefPtr) sfp->data.value.ptrvalue; break; case SEQFEAT_BIOSRC : biop = (BioSourcePtr) sfp->data.value.ptrvalue; if (biop != NULL) { orp = biop->org; } default : break; } if (orp != NULL && sfp->qual != NULL) { GbqualToOrpMod (&(sfp->qual), &(orp->mod)); } biop = NULL; orp = NULL; switch (sfp->data.choice) { case SEQFEAT_GENE : grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (sfp->xref != NULL) { HandleXrefOnGene (sfp); } BSECDecodeXml (grp->locus); CleanVisString (&(grp->locus)); /* if (isJscan && StringDoesHaveText (grp->locus)) { ptr = CleanUpSgml (grp->locus); if (ptr != NULL) { grp->locus = MemFree (grp->locus); grp->locus = StringSave (ptr); } } */ CleanVisString (&(grp->allele)); CleanVisString (&(grp->desc)); CleanVisString (&(grp->maploc)); CleanVisString (&(grp->locus_tag)); ExpandGeneSynList (grp); /* if (isJscan && grp->syn != NULL) { for (vnp = grp->syn; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; ptr = CleanUpSgml (str); if (ptr != NULL) { vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = StringSave (ptr); } } } */ for (vnp = grp->syn; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; BSECDecodeXml (str); } CleanVisStringListCaseSensitive (&(grp->syn)); grp->syn = ValNodeSort (grp->syn, SortVnpByStringCS); grp->syn = UniqueStringValNodeCS (grp->syn); grp->syn = ValNodeSort (grp->syn, SortVnpByStringCILCFirst); CleanDoubleQuote (grp->locus); CleanDoubleQuote (grp->allele); CleanDoubleQuote (grp->desc); /* if (isJscan && StringDoesHaveText (grp->desc)) { ptr = CleanUpSgml (grp->desc); if (ptr != NULL) { grp->desc = MemFree (grp->desc); grp->desc = StringSave (ptr); } } */ CleanDoubleQuote (grp->maploc); CleanDoubleQuote (grp->locus_tag); CleanDoubleQuoteList (grp->syn); FixOldDbxrefs (grp->db); FixNumericDbxrefs (grp->db); grp->db = ValNodeSort (grp->db, SortDbxref); CleanupDuplicateDbxrefs (&(grp->db)); CleanupObsoleteDbxrefs (&(grp->db)); /* now move grp->dbxref to sfp->dbxref */ vnp = grp->db; grp->db = NULL; ValNodeLink ((&sfp->dbxref), vnp); if (grp->locus != NULL && grp->syn != NULL) { vnp = grp->syn; str = (CharPtr) vnp->data.ptrvalue; if (StringCmp (grp->locus, str) == 0) { grp->syn = vnp->next; vnp->next = NULL; ValNodeFreeData (vnp); } } /* if (grp->locus != NULL && sfp->comment != NULL) { if (StringCmp (grp->locus, sfp->comment) == 0) { sfp->comment = MemFree (sfp->comment); } } */ break; case SEQFEAT_ORG : orp = (OrgRefPtr) sfp->data.value.ptrvalue; break; case SEQFEAT_CDREGION : if (sfp->xref != NULL && sfp->product != NULL) { HandleXrefOnCDS (sfp); } break; case SEQFEAT_PROT : prp = (ProtRefPtr) sfp->data.value.ptrvalue; for (vnp = prp->ec; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; CleanupECNumber (str); } for (vnp = prp->name; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; BSECDecodeXml (str); } BSECDecodeXml (prp->desc); CleanVisStringAndCompress (&(prp->desc)); CleanVisStringListAndCompress (&(prp->name)); CleanVisStringList (&(prp->ec)); CleanVisStringList (&(prp->activity)); CleanDoubleQuote (prp->desc); CleanDoubleQuoteList (prp->name); CleanDoubleQuoteList (prp->ec); CleanDoubleQuoteList (prp->activity); RemoveFlankingQuotes (&(prp->desc)); RemoveFlankingQuotesList (&(prp->name)); FixOldDbxrefs (prp->db); FixNumericDbxrefs (prp->db); prp->db = ValNodeSort (prp->db, SortDbxref); CleanupDuplicateDbxrefs (&(prp->db)); CleanupObsoleteDbxrefs (&(prp->db)); /* now move prp->dbxref to sfp->dbxref */ vnp = prp->db; prp->db = NULL; ValNodeLink ((&sfp->dbxref), vnp); if (prp->processed != 3 && prp->processed != 4 && prp->name == NULL && sfp->comment != NULL) { if (StringICmp (sfp->comment, "putative") != 0) { ValNodeAddStr (&(prp->name), 0, sfp->comment); sfp->comment = NULL; } } if (prp->processed == 3 || prp->processed == 4) { if (prp->name != NULL) { str = (CharPtr) prp->name->data.ptrvalue; if ((StringStr (str, "putative") != NULL || StringStr (str, "put. ") != NULL) && sfp->comment == NULL) { sfp->comment = StringSave ("putative"); } if (! InformativeString (str)) { prp->name = ValNodeFreeData (prp->name); } } } if ((prp->processed == 1 || prp->processed == 2) && prp->name == NULL) { ValNodeCopyStr (&(prp->name), 0, "unnamed"); } for (vnp = prp->name; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringICmp (str, "RbcL") == 0 || StringICmp (str, "rubisco large subunit") == 0) { vnp->data.ptrvalue = StringSave ("ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit"); MemFree (str); } else if (StringICmp (str, "RbcS") == 0 || StringICmp (str, "rubisco small subunit") == 0) { vnp->data.ptrvalue = StringSave ("ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit"); MemFree (str); } } if (StringDoesHaveText (prp->desc)) { for (vnp = prp->name; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; if (StringCmp (prp->desc, str) == 0) { prp->desc = MemFree (prp->desc); } } } break; case SEQFEAT_RNA : rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp->ext.choice == 1) { BSECDecodeXml ((CharPtr) rrp->ext.value.ptrvalue); CleanVisStringAndCompress ((CharPtr PNTR) &(rrp->ext.value.ptrvalue)); CleanDoubleQuote ((CharPtr) rrp->ext.value.ptrvalue); RemoveFlankingQuotes ((CharPtr PNTR) &(rrp->ext.value.ptrvalue)); if (rrp->ext.value.ptrvalue == NULL) { rrp->ext.choice = 0; } else if (rrp->type == 4) { name = (CharPtr) rrp->ext.value.ptrvalue; len = StringLen (name); if (len > 5) { if (len > 14 && StringNICmp (name + len - 14, " ribosomal rRNA", 14) == 0) { } else if (StringNICmp (name + len - 5, " rRNA", 5) == 0) { str = MemNew (len + 10); if (str != NULL) { StringNCpy (str, name, len - 5); StringCat (str, " ribosomal RNA"); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = (Pointer) str; } } else if (StringNICmp (name + len - 5, "_rRNA", 5) == 0) { str = MemNew (len + 10); if (str != NULL) { StringNCpy (str, name, len - 5); StringCat (str, " ribosomal RNA"); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = (Pointer) str; } } } } else if (rrp->type == 3) { name = (CharPtr) rrp->ext.value.ptrvalue; aa = ParseTRnaString (name, &justTrnaText, codon, FALSE); if (aa != 0) { is_fMet = (Boolean) (StringStr (name, "fMet") != NULL); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); trp = (tRNAPtr) MemNew (sizeof (tRNA)); if (trp != NULL) { trp->aatype = 2; for (j = 0; j < 6; j++) { trp->codon [j] = 255; } if (justTrnaText) { for (j = 0; j < 6; j++) { trp->codon [j] = codon [j]; } } trp->aa = aa; rrp->ext.choice = 2; rrp->ext.value.ptrvalue = (Pointer) trp; CleanupTrna (sfp, trp); } if (is_fMet) { if (sfp->comment == NULL) { sfp->comment = StringSave ("fMet"); } else { len = StringLen (sfp->comment) + StringLen ("fMet") + 5; str = MemNew (sizeof (Char) * len); StringCpy (str, sfp->comment); StringCat (str, "; "); StringCat (str, "fMet"); sfp->comment = MemFree (sfp->comment); sfp->comment = str; } } } } } else if (rrp->ext.choice == 2) { trp = (tRNAPtr) rrp->ext.value.ptrvalue; CleanupTrna (sfp, trp); } else if (rrp->type == 3 && (! StringHasNoText (sfp->comment))) { aa = ParseTRnaString (sfp->comment, &justTrnaText, codon, TRUE); if (aa != 0) { trp = (tRNAPtr) MemNew (sizeof (tRNA)); if (trp != NULL) { trp->aatype = 2; for (j = 0; j < 6; j++) { trp->codon [j] = 255; } if (justTrnaText) { for (j = 0; j < 6; j++) { trp->codon [j] = codon [j]; } } trp->aa = aa; rrp->ext.choice = 2; rrp->ext.value.ptrvalue = (Pointer) trp; if (justTrnaText) { if (StringCmp (sfp->comment, "fMet") != 0 && StringCmp (sfp->comment, "fMet tRNA") != 0 && StringCmp (sfp->comment, "fMet-tRNA") != 0) { sfp->comment = MemFree (sfp->comment); } else { sfp->comment = MemFree (sfp->comment); sfp->comment = StringSave ("fMet"); } } } } } if (rrp->ext.choice == 3) { rgp = (RNAGenPtr) rrp->ext.value.ptrvalue; if (rgp != NULL) { CleanVisStringAndCompress (&(rgp->product)); CleanDoubleQuote (rgp->product); RemoveFlankingQuotes (&(rgp->product)); CleanVisStringAndCompress (&(rgp->_class)); CleanDoubleQuote (rgp->_class); for (rqp = rgp->quals; rqp != NULL; rqp = rqp->next) { CleanVisStringAndCompress (&(rqp->qual)); CleanDoubleQuote (rqp->qual); CleanVisStringAndCompress (&(rqp->val)); CleanDoubleQuote (rqp->val); } } } if (rrp->ext.choice == 0 && sfp->comment != NULL && rrp->type == 4) { len = StringLen (sfp->comment); if (len > 15 && len < 20) { if (StringNICmp (sfp->comment + len - 15, "S ribosomal RNA", 15) == 0) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = sfp->comment; sfp->comment = NULL; } } else if (len > 6 && len < 20) { if (StringNICmp (sfp->comment + len - 6, "S rRNA", 6) == 0) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = sfp->comment; sfp->comment = NULL; } } } /* * This section has been commented out based on a request by DeAnne Cravaritis. * If left in, this causes unexpected results when RNA comments are copied to * the product name or vice versa. if (rrp->ext.choice == 1 && rrp->ext.value.ptrvalue != NULL) { if (StringICmp ((CharPtr) rrp->ext.value.ptrvalue, sfp->comment) == 0) { sfp->comment = MemFree (sfp->comment); } } */ if (rrp->type == 4 && rrp->ext.choice == 1 ) { name = (CharPtr) rrp->ext.value.ptrvalue; len = StringLen (name); if (len > 5 && NotExceptedRibosomalName (name)) { suff = NULL; str = StringStr (name, " ribosomal"); if (str != NULL) { suff = str + 10; ch = *suff; if (ch != '\0' && ch != ' ') { suff = NULL; str = NULL; } } if (str == NULL) { str = StringStr (name, " rRNA"); if (str != NULL) { suff = str + 5; ch = *suff; if (ch != '\0' && ch != ' ') { suff = NULL; str = NULL; } } } if (suff != NULL && StringNICmp (suff, " RNA", 4) == 0) { suff += 4; } if (suff != NULL && StringNICmp (suff, " DNA", 4) == 0) { suff += 4; } if (suff != NULL && StringNICmp (suff, " ribosomal", 10) == 0) { suff += 10; } TrimSpacesAroundString (suff); if (str != NULL) { *str = '\0'; len = StringLen (name); if (StringHasNoText (suff)) { suff = NULL; } if (suff != NULL) { len += StringLen (suff) + 2; } str = MemNew (len + 15); if (str != NULL) { StringCpy (str, name); StringCat (str, " ribosomal RNA"); if (suff != NULL) { ch = *suff; if (ch != ',' && ch != ';') { StringCat (str, " "); } StringCat (str, suff); } rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = (Pointer) str; } } } name = (CharPtr) rrp->ext.value.ptrvalue; len = StringLen (name); if (len > 5) { ch = *name; while (ch != '\0' && (ch == '.' || (IS_DIGIT (ch)))) { name++; ch = *name; } /* if (ch == 's' && StringCmp (name, "s ribosomal RNA") == 0) { *name = 'S'; } */ if (ch == 's' && name [1] == ' ') { *name = 'S'; } } StrStripSpaces ((CharPtr) rrp->ext.value.ptrvalue); name = (CharPtr) rrp->ext.value.ptrvalue; len = StringLen (name); if (len > 17) { if (StringNICmp (name + len - 17, "ribosomal RNA RNA", 17) == 0) { *(name + len - 4) = '\0'; } } trimming_junk = TRUE; while (trimming_junk) { StrStripSpaces ((CharPtr) rrp->ext.value.ptrvalue); name = (CharPtr) rrp->ext.value.ptrvalue; ptr = StringStr (name, "ribosomal ribosomal"); if (ptr != NULL) { suff = ptr + 19; *(ptr + 10) = '\0'; temp = MemNew (StringLen (name) + StringLen (suff) + 2); TrimSpacesAroundString (suff); StringCpy (temp, name); if (suff [0] != ' ' && suff [0] != '\0') { StringCat (temp, " "); } StringCat (temp, suff); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = (Pointer) temp; } else { ptr = StringStr (name, "RNA RNA"); if (ptr != NULL) { suff = ptr + 7; *(ptr + 4) = '\0'; temp = MemNew (StringLen (name) + StringLen (suff) + 2); TrimSpacesAroundString (suff); StringCpy (temp, name); if (suff [0] != ' ' && suff [0] != '\0') { StringCat (temp, " "); } StringCat (temp, suff); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = (Pointer) temp; } else { ptr = StringStr (name, "ribosomal RNA ribosomal"); if (ptr != NULL) { suff = ptr + 23; *(ptr + 14) = '\0'; temp = MemNew (StringLen (name) + StringLen (suff) + 2); TrimSpacesAroundString (suff); StringCpy (temp, name); if (suff [0] != ' ' && suff [0] != '\0') { StringCat (temp, " "); } StringCat (temp, suff); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = (Pointer) temp; } else { ptr = StringStr (name, "ribosomal rRNA"); if (ptr != NULL) { suff = ptr + 14; *(ptr + 10) = '\0'; temp = MemNew (StringLen (name) + StringLen (" RNA") + StringLen (suff) + 2); TrimSpacesAroundString (suff); StringCpy (temp, name); StringCat (temp, " RNA"); if (suff [0] != ' ' && suff [0] != '\0') { StringCat (temp, " "); } StringCat (temp, suff); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = (Pointer) temp; } else { ptr = StringStr (name, "RNA rRNA"); if (ptr != NULL) { suff = ptr + 8; *(ptr + 3) = '\0'; temp = MemNew (StringLen (name) + StringLen (suff) + 2); TrimSpacesAroundString (suff); StringCpy (temp, name); if (suff [0] != ' ' && suff [0] != '\0') { StringCat (temp, " "); } StringCat (temp, suff); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = (Pointer) temp; } else { trimming_junk = FALSE; } } } } } } TrimSpacesAroundString ((CharPtr) rrp->ext.value.ptrvalue); } /* if (rrp->type == 2 && rrp->ext.choice == 0 && sfp->comment != NULL) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = sfp->comment; sfp->comment = NULL; } */ if (rrp->type == 2 && rrp->ext.choice == 0 && sfp->comment != NULL) { len = StringLen (sfp->comment); if (len > 5) { if (StringNICmp (sfp->comment + len - 4, " RNA", 4) == 0 || StringNICmp (sfp->comment + len - 5, " mRNA", 5) == 0) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = sfp->comment; sfp->comment = NULL; } } } if (rrp->type == 255 || rrp->type == 10) { name = GetRNARefProductString (rrp, NULL); if (StringICmp (name, "its1") == 0 || StringICmp (name, "its 1") == 0) { SetRNARefProductString (rrp, NULL, "internal transcribed spacer 1", ExistingTextOption_replace_old); } else if (StringICmp (name, "its2") == 0 || StringICmp (name, "its 2") == 0) { SetRNARefProductString (rrp, NULL, "internal transcribed spacer 2", ExistingTextOption_replace_old); } else if (StringICmp (name, "its3") == 0 || StringICmp (name, "its 3") == 0) { SetRNARefProductString (rrp, NULL, "internal transcribed spacer 3", ExistingTextOption_replace_old); } name = MemFree (name); } if ((rrp->type == 255 || rrp->type == 10) && rrp->ext.choice == 0 && sfp->comment != NULL) { if (StringICmp (sfp->comment, "internal transcribed spacer 1") == 0 || StringICmp (sfp->comment, "internal transcribed spacer 2") == 0 || StringICmp (sfp->comment, "internal transcribed spacer 3") == 0) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = sfp->comment; sfp->comment = NULL; } } break; case SEQFEAT_PUB : pdp = (PubdescPtr) sfp->data.value.ptrvalue; CleanDoubleQuote (pdp->comment); NormalizePubdesc (pdp, stripSerial, TRUE, publist); break; case SEQFEAT_SEQ : break; case SEQFEAT_IMP : ifp = (ImpFeatPtr) sfp->data.value.ptrvalue; CleanVisString (&(ifp->key)); CleanVisString (&(ifp->loc)); CleanVisString (&(ifp->descr)); break; case SEQFEAT_REGION : CleanVisStringAndCompress ((CharPtr PNTR) &(sfp->data.value.ptrvalue)); CleanDoubleQuote ((CharPtr) sfp->data.value.ptrvalue); if (sfp->data.value.ptrvalue == NULL) { sfp->data.choice = SEQFEAT_COMMENT; } break; case SEQFEAT_COMMENT : break; case SEQFEAT_BOND : break; case SEQFEAT_SITE : break; case SEQFEAT_RSITE : break; case SEQFEAT_USER : VisitAllUserObjectsInUop ((UserObjectPtr) sfp->data.value.ptrvalue, NULL, CleanUserObject); break; case SEQFEAT_TXINIT : break; case SEQFEAT_NUM : break; case SEQFEAT_PSEC_STR : break; case SEQFEAT_NON_STD_RESIDUE : break; case SEQFEAT_HET : break; case SEQFEAT_BIOSRC : biop = (BioSourcePtr) sfp->data.value.ptrvalue; if (biop != NULL) { if (biop->genome == GENOME_virion) { biop->genome = GENOME_unknown; } orp = biop->org; if (orp != NULL) { CleanVisStringListAndCompress (&(orp->mod)); OrpModToSubSource (&(orp->mod), &(biop->subtype)); onp = orp->orgname; if (onp != NULL) { CleanupOrgModOther (biop, onp); } } biop->subtype = SortSubSourceList (biop->subtype); CleanSubSourceList (&(biop->subtype), biop->genome); CleanupSubSourceOther (biop, onp); biop->subtype = SortSubSourceList (biop->subtype); if (modernizeFeats) { ModernizePCRPrimers (biop); } CleanupPCRReactionSet (&(biop->pcr_primers)); if (biop->genome == GENOME_unknown || biop->genome == GENOME_genomic) { for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) { if (ssp->subtype == SUBSRC_plasmid_name) { biop->genome = GENOME_plasmid; } } } } break; default : break; } if (orp != NULL) { CleanVisStringAndCompress (&(orp->taxname)); CleanVisStringAndCompress (&(orp->common)); CleanVisStringList (&(orp->mod)); CleanVisStringList (&(orp->syn)); FixOldDbxrefs (orp->db); FixNumericDbxrefs (orp->db); orp->db = ValNodeSort (orp->db, SortDbxref); CleanupDuplicateDbxrefs (&(orp->db)); CleanupObsoleteDbxrefs (&(orp->db)); onp = orp->orgname; while (onp != NULL) { CleanVisString (&(onp->attrib)); CleanVisString (&(onp->lineage)); CleanVisString (&(onp->div)); OrpModToOrgMod (&(orp->mod), &(onp->mod)); onp->mod = SortOrgModList (onp->mod); CleanOrgModListEx (&(onp->mod), orp->common); onp->mod = SortOrgModList (onp->mod); onp = onp->next; } } } static void CleanupDescriptorStrings ( ValNodePtr sdp, Boolean stripSerial, Boolean modernizeFeats, ValNodePtr PNTR publist, Boolean isEmblOrDdbj ) { BioSourcePtr biop; EMBLBlockPtr ebp; GBBlockPtr gbp; OrgNamePtr onp = NULL; OrgRefPtr orp; PubdescPtr pdp; SubSourcePtr ssp; if (sdp == NULL) return; switch (sdp->choice) { case Seq_descr_mol_type : case Seq_descr_method : return; default : break; } if (sdp->data.ptrvalue == NULL) return; biop = NULL; orp = NULL; switch (sdp->choice) { case Seq_descr_mol_type : break; case Seq_descr_modif : break; case Seq_descr_method : break; case Seq_descr_name : CleanVisString ((CharPtr PNTR) &sdp->data.ptrvalue); if (sdp->data.ptrvalue == NULL) { sdp->data.ptrvalue = StringSave (""); } break; case Seq_descr_title : BSECDecodeXml ((CharPtr) sdp->data.ptrvalue); CleanVisStringAndCompress ((CharPtr PNTR) &sdp->data.ptrvalue); if (sdp->data.ptrvalue == NULL) { sdp->data.ptrvalue = StringSave (""); } break; case Seq_descr_org : orp = (OrgRefPtr) sdp->data.ptrvalue; break; case Seq_descr_comment : BSECDecodeXml ((CharPtr) sdp->data.ptrvalue); CleanVisStringJunk ((CharPtr PNTR) &sdp->data.ptrvalue); RemoveSpacesBetweenTildes ((CharPtr) sdp->data.ptrvalue); if (sdp->data.ptrvalue == NULL) { sdp->data.ptrvalue = StringSave (""); } break; case Seq_descr_num : break; case Seq_descr_maploc : break; case Seq_descr_pir : break; case Seq_descr_genbank : gbp = (GBBlockPtr) sdp->data.ptrvalue; CleanVisStringList (&(gbp->extra_accessions)); gbp->extra_accessions = ValNodeSort (gbp->extra_accessions, SortVnpByString); gbp->extra_accessions = UniqueValNode (gbp->extra_accessions); if (isEmblOrDdbj) { CleanVisStringListCaseSensitive (&(gbp->keywords)); } else { CleanVisStringList (&(gbp->keywords)); } CleanVisStringJunk (&(gbp->source)); if (StringCmp (gbp->source, ".") == 0) { gbp->source = MemFree (gbp->source); } CleanVisStringJunk (&(gbp->origin)); if (StringCmp (gbp->origin, ".") == 0) { gbp->origin = MemFree (gbp->origin); } CleanVisString (&(gbp->date)); CleanVisString (&(gbp->div)); CleanVisString (&(gbp->taxonomy)); break; case Seq_descr_pub : pdp = (PubdescPtr) sdp->data.ptrvalue; CleanDoubleQuote (pdp->comment); NormalizePubdesc (pdp, stripSerial, TRUE, publist); break; case Seq_descr_region : CleanVisString ((CharPtr PNTR) &sdp->data.ptrvalue); if (sdp->data.ptrvalue == NULL) { sdp->data.ptrvalue = StringSave (""); } break; case Seq_descr_user : VisitAllUserObjectsInUop ((UserObjectPtr) sdp->data.ptrvalue, NULL, CleanUserObject); break; case Seq_descr_sp : break; case Seq_descr_dbxref : break; case Seq_descr_embl : ebp = (EMBLBlockPtr) sdp->data.ptrvalue; CleanVisStringList (&(ebp->extra_acc)); ebp->extra_acc = ValNodeSort (ebp->extra_acc, SortVnpByString); CleanVisStringListCaseSensitive (&(ebp->keywords)); break; case Seq_descr_create_date : break; case Seq_descr_update_date : break; case Seq_descr_prf : break; case Seq_descr_pdb : break; case Seq_descr_het : break; case Seq_descr_source : biop = (BioSourcePtr) sdp->data.ptrvalue; if (biop != NULL) { if (biop->genome == GENOME_virion) { biop->genome = GENOME_unknown; } orp = biop->org; if (orp != NULL) { CleanVisStringList (&(orp->mod)); OrpModToSubSource (&(orp->mod), &(biop->subtype)); onp = orp->orgname; if (onp != NULL) { CleanupOrgModOther (biop, onp); } } biop->subtype = SortSubSourceList (biop->subtype); CleanSubSourceList (&(biop->subtype), biop->genome); CleanupSubSourceOther (biop, onp); biop->subtype = SortSubSourceList (biop->subtype); if (modernizeFeats) { ModernizePCRPrimers (biop); } CleanupPCRReactionSet (&(biop->pcr_primers)); if (biop->genome == GENOME_unknown || biop->genome == GENOME_genomic) { for (ssp = biop->subtype; ssp != NULL; ssp = ssp->next) { if (ssp->subtype == SUBSRC_plasmid_name) { biop->genome = GENOME_plasmid; } } } } break; case Seq_descr_molinfo : break; default : break; } if (orp != NULL) { CleanVisStringAndCompress (&(orp->taxname)); CleanVisStringAndCompress (&(orp->common)); CleanVisStringList (&(orp->mod)); CleanVisStringList (&(orp->syn)); FixOldDbxrefs (orp->db); FixNumericDbxrefs (orp->db); orp->db = ValNodeSort (orp->db, SortDbxref); CleanupDuplicateDbxrefs (&(orp->db)); CleanupObsoleteDbxrefs (&(orp->db)); onp = orp->orgname; while (onp != NULL) { CleanVisString (&(onp->attrib)); CleanVisString (&(onp->lineage)); CleanVisString (&(onp->div)); OrpModToOrgMod (&(orp->mod), &(onp->mod)); onp->mod = SortOrgModList (onp->mod); CleanOrgModListEx (&(onp->mod), orp->common); onp->mod = SortOrgModList (onp->mod); onp = onp->next; } } } static Int2 CheckForQual (GBQualPtr gbqual, CharPtr string_q, CharPtr string_v) { GBQualPtr curq; for (curq = gbqual; curq; curq = curq->next) { if (StringCmp (string_q, curq->qual) == 0) { if (curq->val == NULL) { curq->val = StringSave (string_v); return 1; } if (StringCmp (string_v, curq->val) == 0) return 1; } } return 0; } static GBQualPtr AddGBQual (GBQualPtr gbqual, CharPtr qual, CharPtr val) { GBQualPtr curq; if (StringCmp (qual, "translation") == 0) { if (val == NULL) return gbqual; if (*val == '\0') return gbqual; } if (gbqual) { if (CheckForQual (gbqual, qual, val) == 1) return gbqual; for (curq = gbqual; curq->next != NULL; curq = curq->next) continue; curq->next = GBQualNew (); curq = curq->next; if (val) curq->val = StringSave (val); curq->qual = StringSave (qual); } else { gbqual = GBQualNew (); gbqual->next = NULL; if (val) gbqual->val = StringSave (val); gbqual->qual = StringSave (qual); } return gbqual; } static void AddReplaceQual (SeqFeatPtr sfp, CharPtr p) { CharPtr s, val; val = StringChr (p, '\"'); if (val == NULL) return; val++; s = p + StringLen (p) - 1; if (*s != ')') return; for (s--; s > val && *s != '\"'; s--) continue; if (*s != '\"') return; *s = '\0'; sfp->qual = (GBQualPtr) AddGBQual (sfp->qual, "replace", val); *s = '\"'; } NLM_EXTERN Boolean SerialNumberInString (CharPtr str) { Char ch; Boolean hasdigits; CharPtr ptr; Boolean suspicious = FALSE; if (str == NULL || StringHasNoText (str)) return FALSE; ptr = StringChr (str, '['); while ((! suspicious) && ptr != NULL) { hasdigits = FALSE; ptr++; ch = *ptr; while (IS_DIGIT (ch)) { hasdigits = TRUE; ptr++; ch = *ptr; } if (ch == ']' && hasdigits) { suspicious = TRUE; } if (! suspicious) { ptr = StringChr (ptr, '['); } } return suspicious; } /* now only strips serials for local, general, refseq, and 2+6 genbank ids */ static void CheckForSwissProtID (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; SeqIdPtr sip; BoolPtr stripSerial; TextSeqIdPtr tsip; if (sep == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp == NULL) return; stripSerial = (BoolPtr) mydata; if (stripSerial == NULL) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { switch (sip->choice) { case SEQID_GIBBSQ : case SEQID_GIBBMT : *stripSerial = FALSE; break; case SEQID_EMBL : case SEQID_PIR : case SEQID_SWISSPROT : case SEQID_PATENT : case SEQID_DDBJ : case SEQID_PRF : case SEQID_PDB : case SEQID_TPE: case SEQID_TPD: case SEQID_GPIPE: *stripSerial = FALSE; break; case SEQID_GENBANK : case SEQID_TPG: tsip = (TextSeqIdPtr) sip->data.ptrvalue; if (tsip != NULL) { if (StringLen (tsip->accession) == 6) { *stripSerial = FALSE; } } break; case SEQID_NOT_SET : case SEQID_LOCAL : case SEQID_OTHER : case SEQID_GENERAL : break; default : break; } } } } static void CheckForEmblDdbjID (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BoolPtr isEmblOrDdbj; SeqIdPtr sip; if (sep == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp == NULL) return; isEmblOrDdbj = (BoolPtr) mydata; if (isEmblOrDdbj == NULL) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { switch (sip->choice) { case SEQID_EMBL : case SEQID_DDBJ : *isEmblOrDdbj = TRUE; break; default : break; } } } } static void CheckForJournalScanID (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BoolPtr isJScan; SeqIdPtr sip; if (sep == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp == NULL) return; isJScan = (BoolPtr) mydata; if (isJScan == NULL) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { switch (sip->choice) { case SEQID_GIBBSQ : case SEQID_GIBBMT : case SEQID_GIIM : *isJScan = TRUE; break; default : break; } } } } NLM_EXTERN void CleanUpSeqLoc (SeqLocPtr slp) { BioseqPtr bsp; SeqLocPtr curr; SeqLocPtr head; SeqLocPtr last; SeqLocPtr loc; SeqLocPtr next; SeqIdPtr sip; SeqIntPtr sintp; SeqPntPtr spp; Int4 swp; SeqLocPtr tail; if (slp == NULL) return; if (slp->choice == SEQLOC_WHOLE) { sip = (SeqIdPtr) slp->data.ptrvalue; if (sip != NULL) { bsp = BioseqFind (sip); if (bsp != NULL) { sintp = SeqIntNew (); if (sintp != NULL) { sintp->from = 0; sintp->to = bsp->length - 1; sintp->id = sip; /* reuse existing slp->data.ptrvalue, no need to free */ slp->choice = SEQLOC_INT; slp->data.ptrvalue = (Pointer) sintp; } } } } /* from < to for all intervals */ loc = SeqLocFindNext (slp, NULL); while (loc != NULL) { if (loc->choice == SEQLOC_INT) { sintp = (SeqIntPtr) loc->data.ptrvalue; if (sintp != NULL) { if (sintp->from > sintp->to) { swp = sintp->from; sintp->from = sintp->to; sintp->to = swp; } if (sintp->strand == Seq_strand_both) { sintp->strand = Seq_strand_plus; } else if (sintp->strand == Seq_strand_both_rev) { sintp->strand = Seq_strand_minus; } } } else if (loc->choice == SEQLOC_PNT) { spp = (SeqPntPtr) loc->data.ptrvalue; if (spp != NULL) { if (spp->strand == Seq_strand_both) { spp->strand = Seq_strand_plus; } else if (spp->strand == Seq_strand_both_rev) { spp->strand = Seq_strand_minus; } } } loc = SeqLocFindNext (slp, loc); } if (slp->choice == SEQLOC_PACKED_INT) { loc = (SeqLocPtr) slp->data.ptrvalue; if (loc == NULL || loc->next != NULL) return; /* here seqloc_packed_int points to a single location element, so no need for seqloc_packed_int parent */ slp->choice = loc->choice; slp->data.ptrvalue = (Pointer) loc->data.ptrvalue; MemFree (loc); return; } if (slp->choice != SEQLOC_MIX) return; loc = (SeqLocPtr) slp->data.ptrvalue; if (loc == NULL) return; if (loc->next != NULL) { /* check for null NULL at beginning */ if (loc->choice == SEQLOC_NULL) { slp->data.ptrvalue = (Pointer) loc->next; loc->next = NULL; ValNodeFree (loc); } /* check for null NULL at end */ loc = (SeqLocPtr) slp->data.ptrvalue; last = NULL; while (loc->next != NULL) { last = loc; loc = loc->next; } if (loc->choice == SEQLOC_NULL && last != NULL) { last->next = NULL; ValNodeFree (loc); } } loc = (SeqLocPtr) slp->data.ptrvalue; if (loc == NULL) return; if (loc->next == NULL) { /* here seqloc_mix points to a single location element, so no need for seqloc_mix parent */ slp->choice = loc->choice; slp->data.ptrvalue = (Pointer) loc->data.ptrvalue; MemFree (loc); return; } /* check for nested seqloc_mix, remove nesting */ curr = loc; last = NULL; while (curr != NULL) { next = curr->next; if (curr->choice == SEQLOC_MIX) { head = (SeqLocPtr) curr->data.ptrvalue; if (head != NULL) { tail = head; while (tail->next != NULL) { tail = tail->next; } if (last != NULL) { last->next = head; } tail->next = curr->next; curr->next = NULL; curr = MemFree (curr); } } else { last = curr; } curr = next; } } typedef struct cbloc { CodeBreakPtr cbp; Int4 pos; } CbLoc, PNTR CbLocPtr; static int LIBCALLBACK SortByCodeBreakLoc (VoidPtr ptr1, VoidPtr ptr2) { CbLocPtr clp1; CbLocPtr clp2; clp1 = (CbLocPtr) ptr1; clp2 = (CbLocPtr) ptr2; if (clp1 == NULL || clp2 == NULL) return 0; if (clp1->pos < clp2->pos) { return -1; } else if (clp1->pos > clp2->pos) { return 1; } return 0; } static CodeBreakPtr SortCodeBreaks (SeqFeatPtr sfp, CodeBreakPtr list) { BioseqPtr bsp; CodeBreakPtr cbp; CbLocPtr head; size_t count, i; Boolean out_of_order = FALSE; Int4 pos; SeqLocPtr slp; if (sfp == NULL || list == NULL) return list; bsp = BioseqFindFromSeqLoc (sfp->product); if (bsp == NULL) return list; for (cbp = list, count = 0; cbp != NULL; cbp = cbp->next, count++) continue; if (count < 2) return list; head = (CbLocPtr) MemNew (sizeof (CbLoc) * (count + 1)); if (head == NULL) return list; for (cbp = list, i = 0; cbp != NULL && i < count; i++) { head [i].cbp = cbp; slp = dnaLoc_to_aaLoc (sfp, cbp->loc, TRUE, NULL, TRUE); head [i].pos = GetOffsetInBioseq (slp, bsp, SEQLOC_START) + 1; SeqLocFree (slp); cbp = cbp->next; } pos = head [0].pos; for (i = 1; i < count; i++) { if (head [i].pos < pos) { out_of_order = TRUE; } pos = head [i].pos; } if (out_of_order) { StableMergeSort (head, count, sizeof (CbLoc), SortByCodeBreakLoc); for (i = 0; i < count; i++) { cbp = head [i].cbp; cbp->next = head [i + 1].cbp; } list = head [0].cbp; } MemFree (head); return list; } static void CleanupDuplicatedCodeBreaks (CodeBreakPtr PNTR prevcbp) { CodeBreakPtr cbp; CodeBreakPtr last = NULL; CodeBreakPtr next; Boolean unlink; if (prevcbp == NULL) return; cbp = *prevcbp; while (cbp != NULL) { next = cbp->next; unlink = FALSE; if (last != NULL) { if (SeqLocCompare (cbp->loc, last->loc) == SLC_A_EQ_B && cbp->aa.choice == last->aa.choice && cbp->aa.value.intvalue == last->aa.value.intvalue) { unlink = TRUE; } } else { last = cbp; } if (unlink) { *prevcbp = cbp->next; cbp->next = NULL; CodeBreakFree (cbp); } else { last = cbp; prevcbp = (CodeBreakPtr PNTR) &(cbp->next); } cbp = next; } } CharPtr ncrnaClassList[] = { "antisense_RNA", "autocatalytically_spliced_intron", "hammerhead_ribozyme", "ribozyme", "RNase_P_RNA", "RNase_MRP_RNA", "telomerase_RNA", "guide_RNA", "rasiRNA", "scRNA", "siRNA", "miRNA", "piRNA", "snoRNA", "snRNA", "SRP_RNA", "vault_RNA", "Y_RNA", "other", NULL}; Int4 NcrnaOTHER = sizeof (ncrnaClassList) / sizeof (CharPtr) - 1; extern Boolean IsStringInNcRNAClassList (CharPtr str) { CharPtr PNTR p; if (StringHasNoText (str)) return FALSE; for (p = ncrnaClassList; *p != NULL; p++) { if (StringICmp (str, *p) == 0) { return TRUE; } } return FALSE; } static void AddNonCopiedQual (SeqFeatPtr sfp, CharPtr qual, CharPtr class_val) { GBQualPtr gbq; if (sfp == NULL || StringHasNoText (qual) || StringHasNoText (class_val)) { return; } gbq = sfp->qual; while (gbq != NULL && (StringCmp (gbq->qual, qual) != 0 || StringCmp (gbq->val, class_val) != 0)) { gbq = gbq->next; } if (gbq == NULL) { gbq = GBQualNew (); gbq->qual = StringSave (qual); gbq->val = StringSave (class_val); gbq->next = sfp->qual; sfp->qual = gbq; } } static CharPtr GetMiRNAProduct (CharPtr str) { Int4 len; CharPtr product = NULL; if (StringHasNoText (str)) return NULL; if (StringNCmp (str, "miRNA ", 6) == 0) { product = StringSave (str + 6); } else if (StringNCmp (str, "microRNA ", 9) == 0) { product = StringSave (str + 9); } else { len = StringLen (str); if (len > 6 && StringCmp (str + len - 6, " miRNA") == 0 && (len < 15 || StringCmp (str + len - 15, "precursor miRNA") != 0)) { product = (CharPtr) MemNew (sizeof (Char) * (len - 5)); StringNCpy (product, str, len - 6); product[len - 6] = 0; } else if (len > 9 && StringCmp (str + len - 9, " microRNA") == 0 && (len < 18 || StringCmp (str + len - 18, "precursor microRNA") != 0)) { product = (CharPtr) MemNew (sizeof (Char) * (len - 8)); StringNCpy (product, str, len - 9); product[len - 9] = 0; } } return product; } static Boolean ConvertToNcRNA (SeqFeatPtr sfp) { GBQualPtr gbq; RnaRefPtr rrp; Boolean was_converted = FALSE; CharPtr miRNAproduct = NULL; if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA || sfp->data.value.ptrvalue == NULL) { return FALSE; } rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp->type == 5 || rrp->type == 6 || rrp->type == 7) { if (rrp->type == 5) { AddNonCopiedQual (sfp, "ncRNA_class", "snRNA"); } else if (rrp->type == 6) { AddNonCopiedQual (sfp, "ncRNA_class", "scRNA"); } else if (rrp->type == 7) { AddNonCopiedQual (sfp, "ncRNA_class", "snoRNA"); } if (rrp->ext.choice == 1) { AddNonCopiedQual (sfp, "product", rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); } rrp->ext.choice = 1; rrp->ext.value.ptrvalue = StringSave ("ncRNA"); rrp->type = 255; was_converted = TRUE; } else if (rrp->type == 255 && rrp->ext.choice == 1) { if (IsStringInNcRNAClassList (rrp->ext.value.ptrvalue)) { AddNonCopiedQual (sfp, "ncRNA_class", rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = StringSave ("ncRNA"); was_converted = TRUE; } else if ((miRNAproduct = GetMiRNAProduct (rrp->ext.value.ptrvalue)) != NULL) { AddNonCopiedQual (sfp, "ncRNA_class", "miRNA"); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = StringSave ("ncRNA"); AddNonCopiedQual (sfp, "product", miRNAproduct); miRNAproduct = MemFree (miRNAproduct); was_converted = TRUE; } else if (StringCmp (rrp->ext.value.ptrvalue, "ncRNA") != 0 && StringCmp (rrp->ext.value.ptrvalue, "tmRNA") != 0 && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") != 0) { AddNonCopiedQual (sfp, "product", rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = StringSave ("misc_RNA"); was_converted = TRUE; } } if (rrp->type == 255 && rrp->ext.choice == 0) { rrp->ext.choice = 1; rrp->ext.value.ptrvalue = StringSave ("misc_RNA"); } if (rrp->type == 255 && rrp->ext.choice == 1 && StringCmp (rrp->ext.value.ptrvalue, "misc_RNA") == 0) { for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) { if (StringCmp (gbq->qual, "ncRNA_class") == 0) { rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = StringSave ("ncRNA"); was_converted = TRUE; } else if (StringCmp (gbq->qual, "tag_peptide") == 0) { rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.value.ptrvalue = StringSave ("tmRNA"); was_converted = TRUE; } } } return was_converted; } static void ModernizeFeatureStrings (SeqFeatPtr sfp, Boolean isEmblOrDdbj) { CharPtr desc; GBQualPtr gbq; CharPtr name; ProtRefPtr prp; RnaRefPtr rrp; CharPtr str; ValNodePtr vnp; if (sfp == NULL) return; /* skip feature types that do not use data.value.ptrvalue */ switch (sfp->data.choice) { case SEQFEAT_COMMENT: case SEQFEAT_BOND: case SEQFEAT_SITE: case SEQFEAT_PSEC_STR: return; default: break; } if (sfp->data.value.ptrvalue == NULL) return; switch (sfp->data.choice) { case SEQFEAT_PROT: prp = (ProtRefPtr) sfp->data.value.ptrvalue; desc = prp->desc; if (! isEmblOrDdbj) { CleanVisStringList (&(prp->name)); break; } for (vnp = prp->name; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; if (StringICmp (str, "RbcL") == 0 || StringICmp (str, "rubisco large subunit") == 0) { vnp->data.ptrvalue = StringSave ("ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit"); str = MemFree (str); if (StringICmp (desc, "RbcL") == 0 || StringICmp (desc, "rubisco large subunit") == 0) { prp->desc = MemFree (prp->desc); } } else if (StringICmp (str, "RbcS") == 0 || StringICmp (str, "rubisco small subunit") == 0) { vnp->data.ptrvalue = StringSave ("ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit"); str = MemFree (str); if (StringICmp (desc, "RbcS") == 0 || StringICmp (desc, "rubisco small subunit") == 0) { prp->desc = MemFree (prp->desc); } } else if (StringCmp (desc, str) == 0) { prp->desc = MemFree (prp->desc); } if (StringStr (str, "ribulose") != NULL && StringStr (str, "bisphosphate") != NULL && StringStr (str, "methyltransferase") == NULL && StringICmp (str, "ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit") != 0 && StringICmp (str, "ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit") != 0) { if (StringICmp (str, "ribulose 1,5-bisphosphate carboxylase/oxygenase large subunit") == 0 || StringICmp (str, "ribulose 1,5-bisphosphate carboxylase large subunit") == 0 || StringICmp (str, "ribulose bisphosphate carboxylase large subunit") == 0 || StringICmp (str, "ribulose-bisphosphate carboxylase large subunit") == 0 || StringICmp (str, "ribulose-1,5-bisphosphate carboxylase large subunit") == 0 || StringICmp (str, "ribulose-1,5-bisphosphate carboxylase, large subunit") == 0 || StringICmp (str, "large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase") == 0 || StringICmp (str, "ribulose-1,5-bisphosphate carboxylase oxygenase large subunit") == 0 || StringICmp (str, "ribulose bisphosphate carboxylase large chain") == 0 || StringICmp (str, "ribulose 1,5-bisphosphate carboxylase-oxygenase large subunit") == 0 || StringICmp (str, "ribulose bisphosphate carboxylase oxygenase large subunit") == 0 || StringICmp (str, "ribulose 1,5 bisphosphate carboxylase large subunit") == 0 || StringICmp (str, "ribulose-1,5-bisphosphate carboxylase/oxygenase, large subunit") == 0 || StringICmp (str, "large subunit of ribulose-1,5-bisphosphate carboxylase/oxgenase") == 0 || StringICmp (str, "ribulose bisphosphate carboxylase/oxygenase large subunit") == 0 || StringICmp (str, "ribulose-1,5-bisphosphate carboxylase oxygenase, large subunit") == 0 || StringICmp (str, "ribulose 5-bisphosphate carboxylase, large subunit") == 0 || StringICmp (str, "ribulosebisphosphate carboxylase large subunit") == 0 || StringICmp (str, "ribulose bisphosphate large subunit") == 0 || StringICmp (str, "ribulose 1,5 bisphosphate carboxylase/oxygenase large subunit") == 0 || StringICmp (str, "ribulose 1,5-bisphosphate carboxylase/oxygenase large chain") == 0 || StringICmp (str, "large subunit ribulose-1,5-bisphosphate carboxylase/oxygenase") == 0 || StringICmp (str, "ribulose-bisphosphate carboxylase, large subunit") == 0 || StringICmp (str, "ribulose-1, 5-bisphosphate carboxylase/oxygenase large-subunit") == 0) { vnp->data.ptrvalue = StringSave ("ribulose-1,5-bisphosphate carboxylase/oxygenase large subunit"); str = MemFree (str); } } } CleanVisStringList (&(prp->name)); break; case SEQFEAT_RNA : rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp->type == 255 && rrp->ext.choice == 1) { name = (CharPtr) rrp->ext.value.ptrvalue; if (StringCmp (name, "misc_RNA") == 0) { for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) { if (StringCmp (gbq->qual, "product") != 0) continue; name = gbq->val; if (StringHasNoText (name)) continue; if (StringICmp (name, "its1") == 0 || StringICmp (name, "its 1") == 0) { gbq->val = MemFree (gbq->val); gbq->val = StringSave ("internal transcribed spacer 1"); } else if (StringICmp (name, "its2") == 0 || StringICmp (name, "its 2") == 0) { gbq->val = MemFree (gbq->val); gbq->val = StringSave ("internal transcribed spacer 2"); } else if (StringICmp (name, "its3") == 0 || StringICmp (name, "its 3") == 0) { gbq->val = MemFree (gbq->val); gbq->val = StringSave ("internal transcribed spacer 3"); } else if (StringICmp (name, "Ribosomal DNA internal transcribed spacer 1") == 0) { gbq->val = MemFree (gbq->val); gbq->val = StringSave ("internal transcribed spacer 1"); } else if (StringICmp (name, "Ribosomal DNA internal transcribed spacer 2") == 0) { gbq->val = MemFree (gbq->val); gbq->val = StringSave ("internal transcribed spacer 2"); } else if (StringICmp (name, "Ribosomal DNA internal transcribed spacer 3") == 0) { gbq->val = MemFree (gbq->val); gbq->val = StringSave ("internal transcribed spacer 3"); } else if (StringICmp (name, "internal transcribed spacer 1 (ITS1)") == 0) { gbq->val = MemFree (gbq->val); gbq->val = StringSave ("internal transcribed spacer 1"); } else if (StringICmp (name, "internal transcribed spacer 2 (ITS2)") == 0) { gbq->val = MemFree (gbq->val); gbq->val = StringSave ("internal transcribed spacer 2"); } else if (StringICmp (name, "internal transcribed spacer 3 (ITS3)") == 0) { gbq->val = MemFree (gbq->val); gbq->val = StringSave ("internal transcribed spacer 3"); } } } } break; default: break; } } static Boolean IsFeatureCommentRedundant (SeqFeatPtr sfp) { Uint1 aa; Choice cbaa; CodeBreakPtr cbp; CharPtr comment; CdRegionPtr crp; SeqFeatPtr feat; Uint1 from; GBQualPtr gbq; GeneRefPtr grp; CharPtr name; BioseqPtr prod; ProtRefPtr prp; Uint1 residue; RNAGenPtr rgp; RNAQualPtr rqp; RnaRefPtr rrp; SeqAnnotPtr sap; SeqCodeTablePtr sctp; Uint1 seqcode; SeqIdPtr sip; SeqMapTablePtr smtp; CharPtr str; tRNAPtr trp; ValNodePtr vnp; if (sfp == NULL) return FALSE; comment = sfp->comment; if (StringHasNoText (comment)) return FALSE; if (sfp->excpt && StringDoesHaveText (sfp->except_text)) { if (StringCmp (comment, sfp->except_text) == 0) return TRUE; } /* skip feature types that do not use data.value.ptrvalue */ switch (sfp->data.choice) { case SEQFEAT_COMMENT: case SEQFEAT_BOND: case SEQFEAT_SITE: case SEQFEAT_PSEC_STR: return FALSE; default: break; } if (sfp->data.value.ptrvalue == NULL) return FALSE; switch (sfp->data.choice) { case SEQFEAT_GENE: grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (StringCmp (comment, grp->locus) == 0) return TRUE; if (StringCmp (comment, grp->desc) == 0) return TRUE; if (StringCmp (comment, grp->locus_tag) == 0) return TRUE; for (vnp = grp->syn; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; if (StringCmp (comment, str) == 0) return TRUE; } break; case SEQFEAT_CDREGION: crp = (CdRegionPtr) sfp->data.value.ptrvalue; for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) { seqcode = 0; sctp = NULL; cbaa = cbp->aa; switch (cbaa.choice) { case 1 : seqcode = Seq_code_ncbieaa; break; case 2 : seqcode = Seq_code_ncbi8aa; break; case 3 : seqcode = Seq_code_ncbistdaa; break; default : break; } if (seqcode != 0) { sctp = SeqCodeTableFind (seqcode); if (sctp != NULL) { residue = cbaa.value.intvalue; if (residue != 42) { if (seqcode != Seq_code_ncbieaa) { smtp = SeqMapTableFind (seqcode, Seq_code_ncbieaa); residue = SeqMapTableConvert (smtp, residue); } if (residue == 'U') { if (StringCmp (comment, "selenocysteine") == 0) return TRUE; } else if (residue == 'O') { if (StringCmp (comment, "pyrrolysine") == 0) return TRUE; } } } } } if (sfp->product != NULL) { sip = SeqLocId (sfp->product); if (sip != NULL) { prod = BioseqFind (sip); if (prod != NULL) { for (sap = prod->annot; sap != NULL; sap = sap->next) { if (sap->type != 1) continue; for (feat = (SeqFeatPtr) sap->data; feat != NULL; feat = feat->next) { if (feat->data.choice != SEQFEAT_PROT) continue; prp = (ProtRefPtr) feat->data.value.ptrvalue; if (prp == NULL) continue; for (vnp = prp->ec; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; if (StringCmp (comment, str) == 0) return TRUE; } } } } } } break; case SEQFEAT_PROT: prp = (ProtRefPtr) sfp->data.value.ptrvalue; for (vnp = prp->name; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; if (StringCmp (comment, str) == 0) return TRUE; } if (StringDoesHaveText (prp->desc)) { if (StringCmp (comment, prp->desc) == 0) return TRUE; } for (vnp = prp->ec; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; if (StringCmp (comment, str) == 0) return TRUE; } break; case SEQFEAT_RNA : rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp->type == 255 && rrp->ext.choice == 1) { name = (CharPtr) rrp->ext.value.ptrvalue; if (StringCmp (name, "misc_RNA") == 0) { for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) { if (StringCmp (gbq->qual, "product") != 0) continue; name = gbq->val; if (StringHasNoText (name)) continue; /* if (StringICmp (name, "internal transcribed spacer 1") == 0) { if (StringICmp (comment, "its1") == 0 || StringICmp (comment, "its 1") == 0) return TRUE; } else if (StringICmp (name, "internal transcribed spacer 2") == 0) { if (StringICmp (comment, "its2") == 0 || StringICmp (comment, "its 2") == 0) return TRUE; } else if (StringICmp (name, "internal transcribed spacer 3") == 0) { if (StringICmp (comment, "its3") == 0 || StringICmp (comment, "its 3") == 0) return TRUE; } */ } } } else if (rrp->type == 3 && rrp->ext.choice == 2) { trp = (tRNAPtr) rrp->ext.value.ptrvalue; if (trp != NULL) { aa = 0; if (trp->aatype == 2) { aa = trp->aa; } else { from = 0; switch (trp->aatype) { case 0 : from = 0; break; case 1 : from = Seq_code_iupacaa; break; case 2 : from = Seq_code_ncbieaa; break; case 3 : from = Seq_code_ncbi8aa; break; case 4 : from = Seq_code_ncbistdaa; break; default: break; } seqcode = Seq_code_ncbieaa; smtp = SeqMapTableFind (seqcode, from); if (smtp != NULL) { aa = SeqMapTableConvert (smtp, trp->aa); if (aa == 255 && from == Seq_code_iupacaa) { if (trp->aa == 'U') { aa = 'U'; } else if (trp->aa == 'O') { aa = 'O'; } } } } if (aa > 0 && aa != 255) { if (StringNCmp (comment, "aa: ", 4) == 0) { comment += 4; } residue = FindTrnaAA3 (comment); if (residue == aa) { if (aa == 'M' && StringICmp ("fMet", comment) == 0) return FALSE; return TRUE; } residue = FindTrnaAA (comment); if (residue == aa) return TRUE; } } } else if (rrp->ext.choice == 3) { rgp = (RNAGenPtr) rrp->ext.value.ptrvalue; if (rgp != NULL) { if (StringCmp (comment, rgp->product) == 0) return TRUE; if (StringCmp (comment, rgp->_class) == 0) return TRUE; for (rqp = rgp->quals; rqp != NULL; rqp = rqp->next) { if (StringCmp (comment, rqp->val) == 0) return TRUE; } } } break; default: break; } return FALSE; } static CharPtr ExtractSatelliteFromComment (CharPtr comment) { CharPtr satellite_type = NULL, satellite_start = NULL; CharPtr satellite_qual = NULL; Int4 satellite_len, i; if (StringHasNoText (comment)) { return NULL; } if (StringNCmp (comment, "microsatellite", 14) == 0) { satellite_type = "microsatellite"; satellite_start = comment; } else if (StringNCmp (comment, "minisatellite", 13) == 0) { satellite_type = "minisatellite"; satellite_start = comment; } else if (StringNCmp (comment, "satellite", 9) == 0) { satellite_type = "satellite"; satellite_start = comment; } if (satellite_start == NULL) { return NULL; } satellite_len = StringLen (satellite_type); if (comment[satellite_len] == '\0') { satellite_qual = StringSave (satellite_type); *comment = 0; } else if (comment[satellite_len] == ';') { satellite_qual = StringSave (satellite_type); for (i = 0; i <= satellite_len; i++) { comment [i] = ' '; } TrimSpacesAroundString (comment); } if (comment != NULL && comment [0] == '~' && comment [1] != '~') { comment [0] = ' '; TrimSpacesAroundString (comment); } return satellite_qual; } static void DoModernizeRNAFields (SeqFeatPtr sfp) { RNAQualSetPtr nextrqp; RNAQualSetPtr PNTR prevrqp; RNAGenPtr rgp; RNAQualSetPtr rqp; RnaRefPtr rrp; CharPtr str; Boolean unlink; Int2 i; size_t len; CharPtr ncclass; CharPtr product; CharPtr tmp; if (sfp == NULL || sfp->data.choice != SEQFEAT_RNA) return; ModernizeRNAFields (sfp); rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp == NULL) return; if (rrp->ext.choice == 1 && rrp->type == 10) { str = rrp->ext.value.ptrvalue; if (StringHasNoText (str)) return; rgp = (RNAGenPtr) MemNew (sizeof (RNAGen)); if (rgp == NULL) return; rrp->ext.choice = 3; rrp->ext.value.ptrvalue = (Pointer) rgp; rgp->product = str; } if (rrp->ext.choice != 3) return; rgp = (RNAGenPtr) rrp->ext.value.ptrvalue; if (rgp == NULL) return; rqp = rgp->quals; prevrqp = (RNAQualSetPtr PNTR) &(rgp->quals); while (rqp != NULL) { nextrqp = rqp->next; unlink = FALSE; if (StringHasNoText (rqp->qual) || StringHasNoText (rqp->val)) { unlink = TRUE; } if (unlink) { *(prevrqp) = rqp->next; rqp->next = NULL; RNAQualFree (rqp); } else { prevrqp = (RNAQualSetPtr PNTR) &(rqp->next); } rqp = nextrqp; } if (rrp->type == 10 && StringDoesHaveText (rgp->product) && rgp->_class == NULL) { ncclass = rgp->product; for (i = 0; ncrnaClassList [i] != NULL; i++) { str = ncrnaClassList [i]; if (StringHasNoText (str)) continue; len = StringLen (str); if (len < 1) continue; if (StringNICmp (ncclass, str, len) != 0) continue; if (ncclass [len] != ' ') continue; tmp = ncclass + len + 1; if (StringHasNoText (tmp)) continue; ncclass [len] = '\0'; rgp->_class = StringSave (ncclass); product = StringSave (tmp); rgp->product = MemFree (rgp->product); rgp->product = product; TrimSpacesAroundString (rgp->_class); TrimSpacesAroundString (rgp->product); rrp->type = 8; sfp->idx.subtype = FEATDEF_ncRNA; } } if (rgp->quals != NULL) return; if (StringDoesHaveText (rgp->_class) || StringDoesHaveText (rgp->product)) return; rrp->ext.value.ptrvalue = NULL; rrp->ext.choice = 0; RNAGenFree (rgp); } static void FixncRNAClass (SeqFeatPtr sfp) { RnaRefPtr rrp; RNAGenPtr rgp; if (sfp == NULL || sfp->idx.subtype != FEATDEF_ncRNA || (rrp = (RnaRefPtr) sfp->data.value.ptrvalue) == NULL || rrp->ext.choice != 3 || (rgp = (RNAGenPtr) rrp->ext.value.ptrvalue) == NULL) { return; } if (StringICmp (rgp->_class, "antisense") == 0) { rgp->_class = MemFree (rgp->_class); rgp->_class = StringSave ("antisense_RNA"); } } NLM_EXTERN void CleanUpSeqFeat ( SeqFeatPtr sfp, Boolean isEmblOrDdbj, Boolean isJscan, Boolean stripSerial, Boolean modernizeFeats, ValNodePtr PNTR publist ) { BioseqPtr bsp; CodeBreakPtr cbp; CdRegionPtr crp; GBQualPtr gbq; Boolean emptyRNA; GeneRefPtr grp; Boolean hasNulls; SeqIdPtr id; ImpFeatPtr ifp; Int2 j; CharPtr name; Boolean partial5; Boolean partial3; Uint1 processed; ProtRefPtr prp; ValNodePtr psp; RNAGenPtr rgp; RNAQualPtr rqp; RnaRefPtr rrp; Uint1 rrptype; CharPtr satellite_type; SeqIntPtr sintp; SeqPntPtr pntp; SeqIdPtr sip; SeqLocPtr slp; CharPtr str; Uint1 strand; tRNAPtr trp; SeqFeatXrefPtr xref, next, PNTR prevlink; if (sfp == NULL) return; crp = NULL; if (sfp->data.choice == SEQFEAT_IMP) { ifp = (ImpFeatPtr) sfp->data.value.ptrvalue; if (ifp != NULL) { if (ifp->loc != NULL) { str = StringStr (ifp->loc, "replace"); if (str != NULL) { AddReplaceQual (sfp, str); ifp->loc = MemFree (ifp->loc); } } if (StringCmp (ifp->key, "CDS") == 0) { if (! isEmblOrDdbj) { sfp->data.value.ptrvalue = ImpFeatFree (ifp); sfp->data.choice = SEQFEAT_CDREGION; crp = CdRegionNew (); sfp->data.value.ptrvalue = crp; sfp->idx.subtype = FEATDEF_CDS; } } else if (StringCmp (ifp->key, "allele") == 0 || StringCmp (ifp->key, "mutation") == 0) { ifp->key = MemFree (ifp->key); ifp->key = StringSave ("variation"); sfp->idx.subtype = FEATDEF_variation; } else if (StringCmp (ifp->key, "Import") == 0 || StringCmp (ifp->key, "virion") == 0) { ifp->key = MemFree (ifp->key); ifp->key = StringSave ("misc_feature"); sfp->idx.subtype = FEATDEF_misc_feature; } else if (StringCmp (ifp->key, "repeat_unit") == 0 ) { ifp->key = MemFree (ifp->key); ifp->key = StringSave ("repeat_region"); sfp->idx.subtype = FEATDEF_repeat_region; } else if (StringCmp (ifp->key, "misc_bind") == 0) { ifp->key = MemFree (ifp->key); ifp->key = StringSave ("misc_binding"); sfp->idx.subtype = FEATDEF_misc_binding; } else if (StringCmp (ifp->key, "satellite") == 0 && (! isEmblOrDdbj)) { ifp->key = MemFree (ifp->key); ifp->key = StringSave ("repeat_region"); sfp->idx.subtype = FEATDEF_repeat_region; gbq = GBQualNew (); if (gbq != NULL) { gbq->qual = StringSave ("satellite"); gbq->val = ExtractSatelliteFromComment (sfp->comment); if (gbq->val == NULL) { gbq->val = StringSave ("satellite"); } gbq->next = sfp->qual; sfp->qual = gbq; } } else if (StringHasNoText (ifp->loc)) { rrptype = 0; if (StringCmp (ifp->key, "precursor_RNA") == 0) { rrptype = 1; } else if (StringCmp (ifp->key, "mRNA") == 0) { rrptype = 2; } else if (StringCmp (ifp->key, "tRNA") == 0) { rrptype = 3; } else if (StringCmp (ifp->key, "rRNA") == 0) { rrptype = 4; } else if (StringCmp (ifp->key, "snRNA") == 0) { rrptype = 5; } else if (StringCmp (ifp->key, "scRNA") == 0) { rrptype = 6; } else if (StringCmp (ifp->key, "snoRNA") == 0) { rrptype = 7; } else if (StringCmp (ifp->key, "misc_RNA") == 0) { rrptype = 255; } if (rrptype != 0) { sfp->data.value.ptrvalue = ImpFeatFree (ifp); sfp->data.choice = SEQFEAT_RNA; rrp = RnaRefNew (); sfp->data.value.ptrvalue = rrp; rrp->type = rrptype; sfp->idx.subtype = FindFeatDefType (sfp); } else { processed = 0; if (StringCmp (ifp->key, "proprotein") == 0 || StringCmp (ifp->key, "preprotein") == 0) { processed = 1; } else if (StringCmp (ifp->key, "mat_peptide") == 0) { processed = 2; } else if (StringCmp (ifp->key, "sig_peptide") == 0) { processed = 3; } else if (StringCmp (ifp->key, "transit_peptide") == 0) { processed = 4; } if (processed != 0 || StringCmp (ifp->key, "Protein") == 0) { bsp = BioseqFind (SeqLocId (sfp->location)); if (bsp != NULL && ISA_aa (bsp->mol)) { sfp->data.value.ptrvalue = ImpFeatFree (ifp); sfp->data.choice = SEQFEAT_PROT; prp = ProtRefNew (); sfp->data.value.ptrvalue = prp; prp->processed = processed; sfp->idx.subtype = FindFeatDefType (sfp); } } } } if (sfp->data.choice == SEQFEAT_IMP && StringCmp (ifp->key, "repeat_region") == 0 && (! isEmblOrDdbj)) { satellite_type = ExtractSatelliteFromComment (sfp->comment); if (satellite_type != NULL) { gbq = GBQualNew (); if (gbq != NULL) { gbq->qual = StringSave ("satellite"); gbq->val = satellite_type; gbq->next = sfp->qual; sfp->qual = gbq; } } } } } if (crp != NULL && crp->frame == 0 && (! sfp->pseudo)) { crp->frame = GetFrameFromLoc (sfp->location); } if (sfp->data.choice == SEQFEAT_RNA) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp != NULL) { if (rrp->ext.choice == 1) { name = (CharPtr) rrp->ext.value.ptrvalue; if (StringHasNoText (name)) { rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.choice = 0; } } else if (rrp->ext.choice == 2) { trp = (tRNAPtr) rrp->ext.value.ptrvalue; if (trp != NULL) { if (trp->aatype == 0 && trp->aa == 0 && trp->anticodon == NULL) { emptyRNA = TRUE; for (j = 0; j < 6; j++) { if (trp->codon [j] != 255) { emptyRNA = FALSE; } } if (emptyRNA) { rrp->ext.value.ptrvalue = MemFree (rrp->ext.value.ptrvalue); rrp->ext.choice = 0; } } } } else if (rrp->ext.choice == 3) { rgp = (RNAGenPtr) rrp->ext.value.ptrvalue; if (rgp != NULL) { if (StringHasNoText (rgp->_class) && StringHasNoText (rgp->product)) { emptyRNA = TRUE; for (rqp = rgp->quals; rqp != NULL; rqp = rqp->next) { if (StringDoesHaveText (rqp->qual) && StringDoesHaveText (rqp->val)) { emptyRNA = FALSE; } } if (emptyRNA) { rrp->ext.value.ptrvalue = RNAGenFree (rrp->ext.value.ptrvalue); rrp->ext.choice = 0; } } } } } } ModernizeFeatureGBQuals (sfp); sfp->qual = SortFeatureGBQuals (sfp->qual); CleanupDuplicateGBQuals (&(sfp->qual)); CleanupFeatureGBQuals (sfp, isEmblOrDdbj); sfp->qual = SortIllegalGBQuals (sfp->qual); CleanupFeatureStrings (sfp, isJscan, stripSerial, modernizeFeats, publist); FixOldDbxrefs (sfp->dbxref); FixNumericDbxrefs (sfp->dbxref); sfp->dbxref = ValNodeSort (sfp->dbxref, SortDbxref); CleanupDuplicateDbxrefs (&(sfp->dbxref)); CleanupObsoleteDbxrefs (&(sfp->dbxref)); psp = sfp->cit; if (psp != NULL && psp->data.ptrvalue) { psp->data.ptrvalue = ValNodeSort ((ValNodePtr) psp->data.ptrvalue, SortCits); CleanupDuplicateCits ((ValNodePtr PNTR) &(psp->data.ptrvalue)); } CleanUpSeqLoc (sfp->location); strand = SeqLocStrand (sfp->location); id = SeqLocId (sfp->location); if (sfp->data.choice == SEQFEAT_GENE) { grp = (GeneRefPtr) sfp->data.value.ptrvalue; if (grp != NULL) { if (grp->pseudo) { sfp->pseudo = TRUE; grp->pseudo = FALSE; } } } else if (sfp->data.choice == SEQFEAT_CDREGION) { crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { crp->code_break = SortCodeBreaks (sfp, crp->code_break); CleanupDuplicatedCodeBreaks (&(crp->code_break)); for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) { CleanUpSeqLoc (cbp->loc); if (strand == Seq_strand_minus && id != NULL) { slp = cbp->loc; if (slp != NULL && slp->choice == SEQLOC_INT) { sip = SeqLocId (slp); if (sip != NULL && SeqIdComp (id, sip) == SIC_YES) { sintp = (SeqIntPtr) slp->data.ptrvalue; if (sintp != NULL) { sintp->strand = Seq_strand_minus; } } } } } } } else if (sfp->data.choice == SEQFEAT_RNA) { rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp != NULL) { if (rrp->pseudo) { sfp->pseudo = TRUE; rrp->pseudo = FALSE; } } if (rrp != NULL && rrp->ext.choice == 2) { trp = (tRNAPtr) rrp->ext.value.ptrvalue; if (trp != NULL && trp->anticodon != NULL) { CleanUpSeqLoc (trp->anticodon); if (strand == Seq_strand_minus && id != NULL) { slp = trp->anticodon; if (slp != NULL && slp->choice == SEQLOC_INT) { sip = SeqLocId (slp); if (sip != NULL && SeqIdComp (id, sip) == SIC_YES) { sintp = (SeqIntPtr) slp->data.ptrvalue; if (sintp != NULL) { sintp->strand = Seq_strand_minus; } } } } } } if (ConvertToNcRNA (sfp)) { sfp->idx.subtype = FindFeatDefType (sfp); } if (sfp->idx.subtype == FEATDEF_ncRNA) { FixncRNAClass (sfp); } } else if (sfp->data.choice == SEQFEAT_REGION || sfp->data.choice == SEQFEAT_SITE || sfp->data.choice == SEQFEAT_BOND || sfp->data.choice == SEQFEAT_PROT) { bsp = BioseqFind (SeqLocId (sfp->location)); if (bsp != NULL && ISA_aa (bsp->mol)) { slp = SeqLocFindNext (sfp->location, NULL); while (slp != NULL) { if (slp->choice == SEQLOC_INT) { sintp = (SeqIntPtr) slp->data.ptrvalue; if (sintp != NULL) { if (sintp->strand != Seq_strand_unknown) { sintp->strand = Seq_strand_unknown; } } } else if (slp->choice == SEQLOC_PNT) { pntp = (SeqPntPtr) slp->data.ptrvalue; if (pntp->strand != Seq_strand_unknown) { pntp->strand = Seq_strand_unknown; } } slp = SeqLocFindNext (sfp->location, slp); } } } ModernizeFeatureStrings (sfp, isEmblOrDdbj); if (sfp->data.choice == SEQFEAT_GENE) { if (modernizeFeats) { ModernizeGeneFields (sfp); } } if (sfp->data.choice == SEQFEAT_RNA) { if (modernizeFeats) { DoModernizeRNAFields (sfp); } } if (IsFeatureCommentRedundant (sfp)) { sfp->comment = MemFree (sfp->comment); } /* sort and unique gbquals again after recent processing */ sfp->qual = SortFeatureGBQuals (sfp->qual); CleanupDuplicateGBQuals (&(sfp->qual)); sfp->qual = SortIllegalGBQuals (sfp->qual); CheckSeqLocForPartial (sfp->location, &partial5, &partial3); hasNulls = LocationHasNullsBetween (sfp->location); sfp->partial = (sfp->partial || partial5 || partial3 || (hasNulls && ! isEmblOrDdbj)); prevlink = (SeqFeatXrefPtr PNTR) &(sfp->xref); xref = sfp->xref; while (xref != NULL) { next = xref->next; if (xref->id.choice == 0 && xref->data.choice == 0) { *prevlink = xref->next; xref->next = NULL; MemFree (xref); } else { prevlink = (SeqFeatXrefPtr PNTR) &(xref->next); } xref = next; } } static void CleanUpSeqGraph (SeqGraphPtr sgp) { if (sgp == NULL) return; if (sgp->loc != NULL) { CleanUpSeqLoc (sgp->loc); } } static void RemoveZeroLengthSeqLits (BioseqPtr bsp) { DeltaSeqPtr dsp, prev = NULL, dsp_next; SeqLitPtr slip; if (bsp == NULL || bsp->repr != Seq_repr_delta) { return; } for (dsp = (DeltaSeqPtr) bsp->seq_ext; dsp != NULL; dsp = dsp_next) { dsp_next = dsp->next; if (dsp->choice == 2 && (slip = (SeqLitPtr) (dsp->data.ptrvalue)) != NULL && slip->length == 0 && slip->seq_data_type == 1 && slip->seq_data != NULL) { if (prev == NULL) { bsp->seq_ext = dsp->next; } else { prev->next = dsp->next; } dsp->next = NULL; dsp = DeltaSeqFree (dsp); } else { prev = dsp; } } } static Boolean CleanUpSeqIdText (SeqIdPtr sip) { ObjectIdPtr oip; Boolean rval = FALSE; if (sip == NULL) return FALSE; if (sip->choice == SEQID_LOCAL) { oip = (ObjectIdPtr) sip->data.ptrvalue; if (oip != NULL) { if (StringDoesHaveText (oip->str)) { if (isspace (oip->str[0]) || isspace (oip->str[StringLen (oip->str) - 1])) { TrimSpacesAroundString (oip->str); rval = TRUE; } } } } return rval; } static void CleanUpSeqId ( SeqIdPtr sip, Pointer userdata ) { CleanUpSeqIdText (sip); } static void CleanSeqIdInBioseq (BioseqPtr bsp, Pointer userdata) { SeqIdPtr sip; Boolean need_reindex = FALSE; for (sip = bsp->id; sip != NULL; sip = sip->next) { if (CleanUpSeqIdText (sip)) { need_reindex = TRUE; } } if (need_reindex) { SeqMgrReplaceInBioseqIndex (bsp); } } static void CleanSeqIdInSeqFeat (SeqFeatPtr sfp, Pointer userdata) { VisitSeqIdsInSeqFeat (sfp, NULL, CleanUpSeqId); } static void CleanSeqIdInSeqAlign (SeqAlignPtr sap, Pointer userdata) { VisitSeqIdsInSeqAlign (sap, NULL, CleanUpSeqId); } static void CleanSeqIdInSeqGraph (SeqGraphPtr sgp, Pointer userdata) { VisitSeqIdsInSeqGraph (sgp, NULL, CleanUpSeqId); } static void CleanSeqIdInSeqAnnot (SeqAnnotPtr annot, Pointer userdata) { VisitSeqIdsInSeqAnnot (annot, NULL, CleanUpSeqId); } typedef struct npcounts { Int4 nucs; Int4 prots; Boolean make_genbank; } NPCounts, PNTR NPCountsPtr; static void CountNucsAndProts (BioseqPtr bsp, Pointer userdata) { NPCountsPtr ncp; if (bsp == NULL) return; ncp = (NPCountsPtr) userdata; if (ncp == NULL) return; if (ISA_na (bsp->mol)) { (ncp->nucs)++; } else if (ISA_aa (bsp->mol)) { (ncp->prots)++; } } static void CheckInnerSets (BioseqSetPtr bssp, Pointer userdata) { NPCountsPtr ncp; if (bssp == NULL) return; ncp = (NPCountsPtr) userdata; if (ncp == NULL) return; if (bssp->_class == BioseqseqSet_class_segset || bssp->_class == BioseqseqSet_class_parts) return; ncp->make_genbank = TRUE; } static void FixBadSetClass (BioseqSetPtr bssp, Pointer userdata) { NPCounts nc; if (bssp == NULL) return; if (bssp->_class != BioseqseqSet_class_not_set && bssp->_class != BioseqseqSet_class_other) return; MemSet ((Pointer) &nc, 0, sizeof (NPCounts)); VisitSequencesInSet (bssp, (Pointer) &nc, VISIT_MAINS, CountNucsAndProts); VisitSetsInSet (bssp, (Pointer) &nc, CheckInnerSets); if (nc.nucs == 1 && nc.prots > 0 && (! nc.make_genbank)) { bssp->_class = BioseqseqSet_class_nuc_prot; } else { bssp->_class = BioseqseqSet_class_genbank; } } static void RemoveDuplicateSeqIds (BioseqPtr bsp) { SeqIdPtr sip, sip_cmp, sip_prev, sip_next; if (bsp == NULL) { return; } for (sip = bsp->id; sip != NULL; sip = sip->next) { sip_prev = sip; for (sip_cmp = sip->next; sip_cmp != NULL; sip_cmp = sip_next) { sip_next = sip_cmp->next; if (SeqIdComp (sip, sip_cmp) == SIC_YES) { sip_prev->next = sip_cmp->next; sip_cmp->next = NULL; sip_cmp = SeqIdFree (sip_cmp); } else { sip_prev = sip_cmp; } } } } static void BasicSeqEntryCleanupInternal ( SeqEntryPtr sep, ValNodePtr PNTR publist, Boolean isEmblOrDdbj, Boolean isJscan, Boolean stripSerial ) { BioSourcePtr biop; BioseqPtr bsp; BioseqSetPtr bssp; SeqDescrPtr desc; Char div [10]; GBBlockPtr gbp; MolInfoPtr mip; OrgNamePtr onp; OrgRefPtr orp; SeqAnnotPtr sap = NULL; ValNodePtr sdp = NULL; SeqFeatPtr sfp; SeqGraphPtr sgp; SeqEntryPtr tmp; if (sep == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp == NULL) return; /* remove duplicate SeqIds on the same Bioseq */ RemoveDuplicateSeqIds (bsp); /* repair damaged delta sequences */ RemoveZeroLengthSeqLits (bsp); sap = bsp->annot; sdp = bsp->descr; desc = GetNextDescriptorUnindexed (bsp, Seq_descr_molinfo, NULL); if (desc != NULL && desc->choice == Seq_descr_molinfo) { mip = (MolInfoPtr) desc->data.ptrvalue; if (mip != NULL) { /* repair if bsp.mol is not-set */ if (bsp->mol == 0) { switch (mip->biomol) { case MOLECULE_TYPE_GENOMIC : bsp->mol = Seq_mol_na; break; case MOLECULE_TYPE_PRE_MRNA : case MOLECULE_TYPE_MRNA : case MOLECULE_TYPE_RRNA : case MOLECULE_TYPE_TRNA : case MOLECULE_TYPE_SNRNA : case MOLECULE_TYPE_SCRNA : case MOLECULE_TYPE_CRNA : case MOLECULE_TYPE_SNORNA : case MOLECULE_TYPE_TRANSCRIBED_RNA : case MOLECULE_TYPE_NCRNA : case MOLECULE_TYPE_TMRNA : bsp->mol = Seq_mol_rna; break; case MOLECULE_TYPE_PEPTIDE : bsp->mol = Seq_mol_aa; break; case MOLECULE_TYPE_OTHER_GENETIC_MATERIAL : bsp->mol = Seq_mol_other; break; case MOLECULE_TYPE_GENOMIC_MRNA_MIX : bsp->mol = Seq_mol_na; break; default : break; } } else if (bsp->mol != Seq_mol_rna && (mip->biomol == MOLECULE_TYPE_CRNA || mip->biomol == MOLECULE_TYPE_MRNA)) { bsp->mol = Seq_mol_rna; } } } } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return; for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { BasicSeqEntryCleanupInternal (tmp, publist, isEmblOrDdbj, isJscan, stripSerial); } sap = bssp->annot; sdp = bssp->descr; } else return; biop = NULL; orp = NULL; gbp = NULL; div [0] = '\0'; while (sap != NULL) { if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; while (sfp != NULL) { CleanUpSeqFeat (sfp, isEmblOrDdbj, isJscan, stripSerial, TRUE, publist); sfp = sfp->next; } } else if (sap->type == 3) { sgp = (SeqGraphPtr) sap->data; while (sgp != NULL) { CleanUpSeqGraph (sgp); sgp = sgp->next; } } sap = sap->next; } while (sdp != NULL) { switch (sdp->choice) { case Seq_descr_org : orp = (OrgRefPtr) sdp->data.ptrvalue; break; case Seq_descr_genbank : gbp = (GBBlockPtr) sdp->data.ptrvalue; break; case Seq_descr_source : biop = (BioSourcePtr) sdp->data.ptrvalue; if (biop != NULL) { orp = biop->org; } break; default : break; } CleanupDescriptorStrings (sdp, stripSerial, TRUE, publist, isEmblOrDdbj); sdp = sdp->next; } /* copy genbank block division into biosource, if necessary */ if (orp != NULL && gbp != NULL) { StringNCpy_0 (div, gbp->div, sizeof (div)); if (StringHasNoText (div)) return; onp = orp->orgname; while (onp != NULL) { if (StringHasNoText (onp->div)) { onp->div = MemFree (onp->div); onp->div = StringSaveNoNull (div); } onp = onp->next; } } } static void ReplaceCitOnFeat (CitGenPtr cgp, ValNodePtr publist) { ValNodePtr nxt; ValNodePtr vnp; for (vnp = publist; vnp != NULL; vnp = vnp->next) { if (vnp->choice != 1) continue; if (StringCmp (cgp->cit, (CharPtr) vnp->data.ptrvalue) == 0) { nxt = vnp->next; if (nxt != NULL && nxt->choice == 2) { cgp->cit = MemFree (cgp->cit); cgp->cit = StringSaveNoNull ((CharPtr) nxt->data.ptrvalue); if (cgp->cit != NULL) { if (StringNICmp (cgp->cit, "unpublished", 11) == 0) { cgp->cit [0] = 'U'; } } } return; } } } static void ChangeCitsOnFeats (SeqFeatPtr sfp, Pointer userdata) { CitGenPtr cgp; ValNodePtr ppr; ValNodePtr psp; ValNodePtr vnp; psp = sfp->cit; if (psp != NULL && psp->data.ptrvalue) { for (ppr = (ValNodePtr) psp->data.ptrvalue; ppr != NULL; ppr = ppr->next) { vnp = NULL; if (ppr->choice == PUB_Gen) { vnp = ppr; } else if (ppr->choice == PUB_Equiv) { for (vnp = (ValNodePtr) ppr->data.ptrvalue; vnp != NULL && vnp->choice != PUB_Gen; vnp = vnp->next) continue; } if (vnp != NULL && vnp->choice == PUB_Gen) { cgp = (CitGenPtr) vnp->data.ptrvalue; if (cgp != NULL && (! StringHasNoText (cgp->cit))) { ReplaceCitOnFeat (cgp, (ValNodePtr) userdata); } } } } } static Int4 GetPmidForMuid (ValNodePtr pairlist, Int4 muid) { ValNodePtr vnp; vnp = pairlist; while (vnp != NULL) { if (muid == vnp->data.intvalue) { vnp = vnp->next; if (vnp == NULL) return 0; return vnp->data.intvalue; } else { vnp = vnp->next; if (vnp == NULL) return 0; vnp = vnp->next; } } return 0; } static void ChangeFeatCitsToPmid (SeqFeatPtr sfp, Pointer userdata) { Int4 muid = 0; Int4 pmid = 0; ValNodePtr ppr; ValNodePtr psp; ValNodePtr vnp; psp = sfp->cit; if (psp != NULL && psp->data.ptrvalue) { for (ppr = (ValNodePtr) psp->data.ptrvalue; ppr != NULL; ppr = ppr->next) { vnp = NULL; if (ppr->choice == PUB_Muid) { vnp = ppr; } else if (ppr->choice == PUB_Equiv) { for (vnp = (ValNodePtr) ppr->data.ptrvalue; vnp != NULL && vnp->choice != PUB_Muid; vnp = vnp->next) continue; } if (vnp != NULL && vnp->choice == PUB_Muid) { muid = vnp->data.intvalue; if (muid != 0) { pmid = GetPmidForMuid ((ValNodePtr) userdata, muid); if (pmid != 0) { vnp->choice = PUB_PMid; vnp->data.intvalue = pmid; } } } } } } static void GetMuidPmidPairs (PubdescPtr pdp, Pointer userdata) { Int4 muid = 0; Int4 pmid = 0; ValNodePtr vnp; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { switch (vnp->choice) { case PUB_Muid : muid = vnp->data.intvalue; break; case PUB_PMid : pmid = vnp->data.intvalue; break; default : break; } } if (muid == 0 || pmid == 0) return; ValNodeAddInt ((ValNodePtr PNTR) userdata, 0, muid); ValNodeAddInt ((ValNodePtr PNTR) userdata, 0, pmid); } static void FlattenPubSet (ValNodePtr PNTR prev) { ValNodePtr next; ValNodePtr ppr; ValNodePtr vnp; if (prev == NULL || *prev == NULL) return; ppr = *prev; while (ppr != NULL) { next = ppr->next; if (ppr->choice == PUB_Equiv) { vnp = (ValNodePtr) ppr->data.ptrvalue; if (vnp != NULL && vnp->next == NULL) { ppr->choice = vnp->choice; switch (vnp->choice) { case PUB_Muid : case PUB_PMid : ppr->data.intvalue = vnp->data.intvalue; break; default : ppr->data.ptrvalue = vnp->data.ptrvalue; break; } ValNodeFree (vnp); } } ppr = next; } } static void FlattenDupInPubSet (ValNodePtr PNTR prev) { ValNodePtr next; ValNodePtr nxt; ValNodePtr ppr; ValNodePtr vnp; if (prev == NULL || *prev == NULL) return; ppr = *prev; while (ppr != NULL) { next = ppr->next; if (ppr->choice == PUB_Equiv) { vnp = (ValNodePtr) ppr->data.ptrvalue; if (vnp != NULL) { nxt = vnp->next; if (nxt != NULL && nxt->next == NULL && vnp->choice == nxt->choice) { switch (vnp->choice) { case PUB_Muid : case PUB_PMid : if (vnp->data.intvalue == nxt->data.intvalue) { vnp->next = ValNodeFree (nxt); } break; default : break; } } } } ppr = next; } } static void FlattenPubdesc (PubdescPtr pdp, Pointer userdata) { FlattenPubSet (&(pdp->pub)); } static void FlattenSfpCit (SeqFeatPtr sfp, Pointer userdata) { ValNodePtr psp; psp = sfp->cit; if (psp == NULL) return; FlattenDupInPubSet ((ValNodePtr PNTR) &(psp->data.ptrvalue)); FlattenPubSet ((ValNodePtr PNTR) &(psp->data.ptrvalue)); } typedef struct fastnode { ValNodePtr head; ValNodePtr tail; } FastNode, PNTR FastNodePtr; static void GetCitGenLabels (PubdescPtr pdp, Pointer userdata) { Char buf [121]; CitGenPtr cgp; FastNodePtr labellist; ValNodePtr tmp; ValNodePtr vnp; if (pdp == NULL) return; labellist = (FastNodePtr) userdata; if (labellist == NULL) return; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { if (vnp->choice != PUB_Gen) continue; cgp = (CitGenPtr) vnp->data.ptrvalue; if (cgp == NULL) continue; if (cgp->cit == NULL && cgp->journal == NULL && cgp->date == NULL && cgp->serial_number) continue; PubLabelUnique (vnp, buf, sizeof (buf) - 1, OM_LABEL_CONTENT, TRUE); tmp = ValNodeCopyStr (&(labellist->tail), 0, buf); if (labellist->head == NULL) { labellist->head = tmp; } labellist->tail = tmp; } } static void ReplaceShortCitGenOnFeat (CitGenPtr cgp, ValNodePtr labellist) { Char buf [128]; Char ch; size_t len1; size_t len2; CharPtr ptr; CharPtr str; CharPtr tmp; ValNodePtr vnp; for (vnp = labellist; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; len1 = StringLen (cgp->cit); if (len1 < 2 || len1 > 120) continue; StringCpy (buf, cgp->cit); ptr = StringStr (buf, "Unpublished"); if (ptr != NULL) { ptr += 11; *ptr = '\0'; tmp = StringStr (cgp->cit, "Unpublished"); if (tmp != NULL) { tmp += 11; ch = *tmp; while (ch == ' ') { tmp++; ch = *tmp; } StringCat (buf, tmp); } } len1 = StringLen (buf); if (buf [len1 - 1] != '>') continue; len1--; len2 = StringLen (str); if (len1 >= len2) continue; if (StringNCmp (str, buf, len1) == 0) { cgp->cit = MemFree (cgp->cit); cgp->cit = StringSaveNoNull (str); if (cgp->cit != NULL) { if (StringNICmp (cgp->cit, "unpublished", 11) == 0) { cgp->cit [0] = 'U'; } } return; } } } static void UpdateShortFeatCits (SeqFeatPtr sfp, Pointer userdata) { CitGenPtr cgp; ValNodePtr ppr; ValNodePtr psp; ValNodePtr vnp; psp = sfp->cit; if (psp != NULL && psp->data.ptrvalue) { for (ppr = (ValNodePtr) psp->data.ptrvalue; ppr != NULL; ppr = ppr->next) { vnp = NULL; if (ppr->choice == PUB_Gen) { vnp = ppr; } else if (ppr->choice == PUB_Equiv) { for (vnp = (ValNodePtr) ppr->data.ptrvalue; vnp != NULL && vnp->choice != PUB_Gen; vnp = vnp->next) continue; } if (vnp != NULL && vnp->choice == PUB_Gen) { cgp = (CitGenPtr) vnp->data.ptrvalue; if (cgp != NULL && (! StringHasNoText (cgp->cit))) { ReplaceShortCitGenOnFeat (cgp, (ValNodePtr) userdata); } } } } } NLM_EXTERN void BasicSeqAnnotCleanup (SeqAnnotPtr sap) { SeqFeatPtr sfp; SeqGraphPtr sgp; if (sap == NULL) return; VisitSeqIdsInSeqAnnot (sap, NULL, CleanUpSeqId); if (sap->type == 1) { sfp = (SeqFeatPtr) sap->data; while (sfp != NULL) { CleanUpSeqFeat (sfp, FALSE, FALSE, TRUE, TRUE, NULL); sfp = sfp->next; } } else if (sap->type == 3) { sgp = (SeqGraphPtr) sap->data; while (sgp != NULL) { CleanUpSeqGraph (sgp); sgp = sgp->next; } } } /* static CharPtr proteinOrganellePrefix [] = { NULL, NULL, "chloroplast", "chromoplast", "kinetoplast", "mitochondrion", "plastid", "macronuclear", "extrachromosomal", "plasmid", NULL, NULL, "cyanelle", "proviral", "virus", "nucleomorph", "apicoplast", "leucoplast", "protoplast", "endogenous virus", "hydrogenosome", "chromosome", "chromatophore" }; */ static CharPtr proteinOrganellePrefix [] = { NULL, NULL, "chloroplast", NULL, NULL, "mitochondrion", NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, NULL, }; static CharPtr TitleEndsInOrganism ( CharPtr title, CharPtr organism, CharPtr organelle, CharPtr PNTR onlp ) { int genome; size_t len1, len2, len3; CharPtr onl, ptr, tmp; if (onlp != NULL) { *onlp = NULL; } if (StringHasNoText (title) || StringHasNoText (organism)) return NULL; len1 = StringLen (title); len2 = StringLen (organism); if (len2 + 4 >= len1) return NULL; tmp = title + len1 - len2 - 3; if (tmp [0] != ' ' || tmp [1] != '[' || tmp [len2 + 2] != ']') return NULL; if (StringNICmp (tmp + 2, organism, len2) != 0) return NULL; if (onlp != NULL) { len3 = len1 - len2 - 3; for (genome = GENOME_chloroplast; genome <= GENOME_chromatophore; genome++) { ptr = proteinOrganellePrefix [genome]; if (ptr == NULL) continue; len2 = StringLen (ptr); if (len2 + 4 >= len3) continue; onl = title + len3 - len2 - 3; if (onl [0] != ' ' || onl [1] != '(' || onl [len2 + 2] != ')') continue; if (StringNICmp (onl + 2, ptr, len2) != 0) continue; *onlp = onl; break; } } return tmp; } static void AddPartialToProteinTitle ( BioseqPtr bsp, Pointer userdata ) { BioSourcePtr biop; int genome = 0; size_t len; MolInfoPtr mip; CharPtr oldname = NULL; OrgModPtr omp; OrgNamePtr onp; CharPtr organelle = NULL; OrgRefPtr orp; Boolean partial = FALSE; CharPtr penult = NULL; SeqDescrPtr sdp; SeqIdPtr sip; CharPtr str; CharPtr suffix = NULL; CharPtr taxname = NULL; CharPtr title; CharPtr tmp; SeqDescrPtr ttl = NULL; if (bsp == NULL) return; if (! ISA_aa (bsp->mol)) return; for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_SWISSPROT) return; } ttl = BioseqGetSeqDescr (bsp, Seq_descr_title, NULL); if (ttl == NULL || ttl->choice != Seq_descr_title) return; str = (CharPtr) ttl->data.ptrvalue; if (StringHasNoText (str)) return; sdp = GetNextDescriptorUnindexed (bsp, Seq_descr_molinfo, NULL); if (sdp != NULL && sdp->choice == Seq_descr_molinfo) { mip = (MolInfoPtr) sdp->data.ptrvalue; if (mip != NULL && mip->completeness > 1 && mip->completeness < 6) { partial = TRUE; } } sdp = GetNextDescriptorUnindexed (bsp, Seq_descr_source, NULL); if (sdp != NULL && sdp->choice == Seq_descr_source) { biop = (BioSourcePtr) sdp->data.ptrvalue; if (biop != NULL) { genome = biop->genome; if (genome >= GENOME_chloroplast && genome <= GENOME_chromatophore) { organelle = proteinOrganellePrefix [genome]; } orp = biop->org; if (orp != NULL) { taxname = orp->taxname; if (StringNICmp (organelle, taxname, StringLen (organelle)) == 0) { organelle = NULL; } onp = orp->orgname; if (onp != NULL) { for (omp = onp->mod; omp != NULL; omp = omp->next) { if (omp->subtype == ORGMOD_old_name) { oldname = omp->subname; } } } } } } /* search for partial, must be just before parenthesized organelle or bracketed organism */ tmp = StringSearch (str, ", partial ["); if (tmp == NULL) { tmp = StringSearch (str, ", partial ("); } /* find oldname or taxname in brackets at end of protein title */ if (oldname != NULL && taxname != NULL) { suffix = TitleEndsInOrganism (str, oldname, organelle, &penult); } if (suffix == NULL && taxname != NULL) { suffix = TitleEndsInOrganism (str, taxname, organelle, &penult); if (suffix != NULL) { if (organelle == NULL && penult != NULL) { } else if (organelle != NULL && penult == NULL) { } else if (StringCmp (organelle, penult) != 0) { } else { /* bail if no need to change partial text (organelle) [organism name] */ if (partial) { if (tmp != NULL) return; } else { if (tmp == NULL) return; } } } } /* do not change unless [genus species] was at the end */ if (suffix == NULL) return; /* truncate bracketed info from end of title, will replace with current taxname */ *suffix = '\0'; suffix = taxname; /* truncate parenthesized info from just before bracketed taxname, will replace with current organelle */ if (penult != NULL) { *penult = '\0'; } /* if ", partial [/(" was indeed just before the [genus species] or (organelle), it will now be ", partial" */ if (! partial && tmp != NULL && StringCmp (tmp, ", partial") == 0) { *tmp = '\0'; } TrimSpacesAroundString (str); len = StringLen (str) + StringLen (organelle) + StringLen (suffix) + 20; title = MemNew (sizeof (Char) * len); if (title == NULL) return; StringCpy (title, str); if (partial && tmp == NULL) { StringCat (title, ", partial"); } if (organelle != NULL) { StringCat (title, " ("); StringCat (title, organelle); StringCat (title, ")"); } if (suffix != NULL) { StringCat (title, " ["); StringCat (title, suffix); StringCat (title, "]"); } MemFree (str); ttl->data.ptrvalue = title; } NLM_EXTERN void CleanUpProteinTitles (SeqEntryPtr sep) { if (sep == NULL) return; VisitBioseqsInSep (sep, NULL, AddPartialToProteinTitle); } NLM_EXTERN void BasicSeqEntryCleanup (SeqEntryPtr sep) { AuthorPtr ap; ContactInfoPtr cip; CitSubPtr csp; Uint2 entityID; Boolean isEmblOrDdbj = FALSE; Boolean isJscan = FALSE; FastNode labelnode; ValNodePtr pairlist = NULL; ValNodePtr publist = NULL; SeqEntryPtr oldscope; ObjMgrDataPtr omdp; SubmitBlockPtr sbp; SeqSubmitPtr ssp; Boolean stripSerial = TRUE; if (sep == NULL) return; /* InGpsGenomic needs idx fields assigned */ entityID = SeqMgrGetEntityIDForSeqEntry (sep); AssignIDsInEntityEx (entityID, 0, NULL, NULL); /* HandleXrefOnCDS call to GetBestProteinFeatureUnindexed now scoped within record */ oldscope = SeqEntrySetScope (sep); /* clean up spaces in local IDs */ VisitBioseqsInSep (sep, NULL, CleanSeqIdInBioseq); VisitFeaturesInSep (sep, NULL, CleanSeqIdInSeqFeat); VisitAlignmentsInSep (sep, NULL, CleanSeqIdInSeqAlign); VisitGraphsInSep (sep, NULL, CleanSeqIdInSeqGraph); VisitAnnotsInSep (sep, NULL, CleanSeqIdInSeqAnnot); /* Fix Bioseq-sets with class 0 */ VisitSetsInSep (sep, NULL, FixBadSetClass); /* removed unnecessarily nested Pub-equivs */ VisitPubdescsInSep (sep, NULL, FlattenPubdesc); VisitFeaturesInSep (sep, NULL, FlattenSfpCit); SeqEntryExplore (sep, (Pointer) &stripSerial, CheckForSwissProtID); SeqEntryExplore (sep, (Pointer) &isEmblOrDdbj, CheckForEmblDdbjID); SeqEntryExplore (sep, (Pointer) &isJscan, CheckForJournalScanID); #ifdef SUPPRESS_STRIP_SERIAL_DIFFERENCES stripSerial = FALSE; #endif BasicSeqEntryCleanupInternal (sep, &publist, isEmblOrDdbj, isJscan, stripSerial); if (publist != NULL) { VisitFeaturesInSep (sep, (Pointer) publist, ChangeCitsOnFeats); } ValNodeFreeData (publist); /* now get muid/pmid pairs, update sfp->cits to pmids */ VisitPubdescsInSep (sep, (Pointer) &pairlist, GetMuidPmidPairs); if (pairlist != NULL) { VisitFeaturesInSep (sep, (Pointer) pairlist, ChangeFeatCitsToPmid); } ValNodeFree (pairlist); labelnode.head = NULL; labelnode.tail = NULL; VisitPubdescsInSep (sep, (Pointer) &labelnode, GetCitGenLabels); if (labelnode.head != NULL) { VisitFeaturesInSep (sep, (Pointer) labelnode.head, UpdateShortFeatCits); } ValNodeFreeData (labelnode.head); SeqEntrySetScope (oldscope); /* also normalize authors on submit block citation */ entityID = SeqMgrGetEntityIDForSeqEntry (sep); omdp = ObjMgrGetData (entityID); if (omdp != NULL && omdp->datatype == OBJ_SEQSUB) { ssp = (SeqSubmitPtr) omdp->dataptr; if (ssp != NULL && ssp->datatype == 1) { sbp = ssp->sub; if (sbp != NULL) { csp = sbp->cit; if (csp != NULL) { NormalizeAuthors (csp->authors, TRUE); } cip = sbp->contact; if (cip != NULL) { ap = cip->contact; if (ap != NULL) { ap->affil = CleanAffil (ap->affil); } } } } } /* dynamically add missing partial to already instantiated protein titles, in between main title and bracketed organism name */ VisitBioseqsInSep (sep, NULL, AddPartialToProteinTitle); } typedef struct bsecsmfedata { Int4 max; Int4 num_at_max; } BsecSmfeData, PNTR BsecSmfePtr; static Boolean LIBCALLBACK BsecSMFEProc ( SeqFeatPtr sfp, SeqMgrFeatContextPtr context ) { BsecSmfePtr bsp; Int4 len; if (sfp == NULL || context == NULL) return TRUE; bsp = context->userdata; if (bsp == NULL) return TRUE; len = SeqLocLen (sfp->location); if (len < bsp->max) { bsp->max = len; bsp->num_at_max = 1; } else if (len == bsp->max) { (bsp->num_at_max)++; } return TRUE; } NLM_EXTERN void RemoveUnnecessaryGeneXrefs ( SeqFeatPtr sfp, Pointer userdata ) { BsecSmfeData bsd; SeqFeatPtr cds; Int2 count; SeqFeatXrefPtr curr, next; SeqMgrFeatContext fcontext; GeneRefPtr grp, grpx; SeqFeatXrefPtr PNTR last; BioseqPtr prd; SeqFeatPtr sfpx; CharPtr syn1, syn2; if (sfp == NULL || sfp->data.choice == SEQFEAT_GENE) return; grp = SeqMgrGetGeneXref (sfp); if (grp == NULL || SeqMgrGeneIsSuppressed (grp)) return; grpx = NULL; sfpx = SeqMgrGetOverlappingGene (sfp->location, &fcontext); if (sfpx != NULL) { if (sfpx->data.choice != SEQFEAT_GENE) return; grpx = (GeneRefPtr) sfpx->data.value.ptrvalue; } else { prd = BioseqFindFromSeqLoc (sfp->location); if (prd != NULL && ISA_aa (prd->mol)) { cds = SeqMgrGetCDSgivenProduct (prd, NULL); if (cds != NULL) { grpx = SeqMgrGetGeneXref (cds); if (grpx == NULL) { sfpx = SeqMgrGetOverlappingGene (cds->location, &fcontext); if (sfpx != NULL && sfpx->data.choice == SEQFEAT_GENE) { grpx = (GeneRefPtr) sfpx->data.value.ptrvalue; } } } } } if (grpx == NULL || SeqMgrGeneIsSuppressed (grp)) return; if (StringDoesHaveText (grp->locus_tag) && StringDoesHaveText (grpx->locus_tag)) { if (StringICmp (grp->locus_tag, grpx->locus_tag) != 0) return; } else if (StringDoesHaveText (grp->locus) && StringDoesHaveText (grpx->locus)) { if (StringICmp (grp->locus, grpx->locus) != 0) return; } else if (grp->syn != NULL && grpx->syn != NULL) { syn1 = (CharPtr) grp->syn->data.ptrvalue; syn2 = (CharPtr) grpx->syn->data.ptrvalue; if (StringDoesHaveText (syn1) && StringDoesHaveText (syn2)) { if (StringICmp (syn1, syn2) != 0) return; } } MemSet ((Pointer) &bsd, 0, sizeof (BsecSmfeData)); bsd.max = INT4_MAX; bsd.num_at_max = 0; count = SeqMgrGetAllOverlappingFeatures (sfp->location, FEATDEF_GENE, NULL, 0, LOCATION_SUBSET, (Pointer) &bsd, BsecSMFEProc); if (bsd.num_at_max < 2) { last = (SeqFeatXrefPtr PNTR) &(sfp->xref); curr = sfp->xref; while (curr != NULL) { next = curr->next; if (curr->data.choice == SEQFEAT_GENE) { *last = next; curr->next = NULL; SeqFeatXrefFree (curr); } else { last = &(curr->next); } curr = next; } } } static void SortSeqFeatFields ( SeqFeatPtr sfp, Pointer userdata ) { CdRegionPtr crp; ValNodePtr psp; if (sfp == NULL) return; sfp->qual = SortFeatureGBQuals (sfp->qual); sfp->qual = SortIllegalGBQuals (sfp->qual); sfp->dbxref = ValNodeSort (sfp->dbxref, SortDbxref); psp = sfp->cit; if (psp != NULL && psp->data.ptrvalue) { psp->data.ptrvalue = ValNodeSort ((ValNodePtr) psp->data.ptrvalue, SortCits); } if (sfp->data.choice == SEQFEAT_CDREGION) { crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { crp->code_break = SortCodeBreaks (sfp, crp->code_break); } } } static void SortBioSourceFields ( BioSourcePtr biop, Pointer userdata ) { OrgNamePtr onp; OrgRefPtr orp; if (biop == NULL) return; orp = biop->org; if (orp != NULL) { orp->db = ValNodeSort (orp->db, SortDbxref); for (onp = orp->orgname; onp != NULL; onp = onp->next) { onp->mod = SortOrgModList (onp->mod); } } biop->subtype = SortSubSourceList (biop->subtype); } NLM_EXTERN void SortSeqEntryQualifiers ( SeqEntryPtr sep ) { if (sep == NULL) return; VisitFeaturesInSep (sep, NULL, SortSeqFeatFields); VisitBioSourcesInSep (sep, NULL, SortBioSourceFields); } /* end BasicSeqEntryCleanup section */ NLM_EXTERN void ResynchCDSPartials (SeqFeatPtr sfp, Pointer userdata) { SeqFeatPtr bestprot; BioseqPtr bsp; MolInfoPtr mip; Boolean partial5; Boolean partial3; SeqEntryPtr sep; SeqIdPtr sip; SeqLocPtr slp; ValNodePtr vnp; /* variables for logging */ LogInfoPtr lip; CharPtr orig_loc = NULL, new_loc; Char id_buf[100]; if (sfp->data.choice != SEQFEAT_CDREGION) return; CheckSeqLocForPartial (sfp->location, &partial5, &partial3); sfp->partial = (Boolean) (sfp->partial || partial5 || partial3); /* slp = SeqLocFindNext (sfp->location, NULL); if (slp == NULL) return; */ sip = SeqLocId (sfp->product); if (sip == NULL) return; bsp = BioseqFind (sip); if (bsp == NULL || !ISA_aa (bsp->mol) || bsp->repr != Seq_repr_raw) return; bestprot = SeqMgrGetBestProteinFeature (bsp, NULL); if (bestprot == NULL) { bestprot = GetBestProteinFeatureUnindexed (sfp->product); } if (bestprot == NULL) return; sep = SeqMgrGetSeqEntryForData (bsp); if (sep == NULL) return; if ((lip = (LogInfoPtr)userdata) != NULL) { orig_loc = SeqLocPrintUseBestID (bestprot->location); } slp = NULL; sip = SeqLocId (bestprot->location); if (sip != NULL) { slp = WholeIntervalFromSeqId (sip); } if (slp == NULL) { slp = CreateWholeInterval (sep); } if (slp != NULL) { bestprot->location = SeqLocFree (bestprot->location); bestprot->location = slp; } SetSeqLocPartial (bestprot->location, partial5, partial3); bestprot->partial = sfp->partial; if (lip != NULL) { new_loc = SeqLocPrintUseBestID (bestprot->location); if (StringCmp (orig_loc, new_loc) != 0) { lip->data_in_log = TRUE; if (lip->fp != NULL) { fprintf (lip->fp, "Synchronized coding region partials for protein feature location at %s\n", orig_loc, new_loc); } } new_loc = MemFree (new_loc); } orig_loc = MemFree (orig_loc); vnp = SeqEntryGetSeqDescr (sep, Seq_descr_molinfo, NULL); id_buf[0] = 0; if (vnp == NULL) { vnp = CreateNewDescriptor (sep, Seq_descr_molinfo); if (vnp != NULL) { mip = MolInfoNew (); vnp->data.ptrvalue = (Pointer) mip; if (mip != NULL) { mip->biomol = 8; /* peptide */ mip->tech = 13; /* concept-trans-author */ if (lip != NULL) { if (lip->fp != NULL) { SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_buf, PRINTID_FASTA_SHORT, sizeof (id_buf) - 1); fprintf (lip->fp, "Added MolInfo descriptor for %s\n", id_buf); } lip->data_in_log = TRUE; } } } } if (vnp != NULL) { mip = (MolInfoPtr) vnp->data.ptrvalue; if (mip != NULL) { if (partial5 && partial3) { if (mip->completeness != 5) { mip->completeness = 5; if (lip != NULL) { if (lip->fp != NULL) { if (id_buf[0] == 0) { SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_buf, PRINTID_FASTA_SHORT, sizeof (id_buf) - 1); } fprintf (lip->fp, "Adjusted completeness for MolInfo descriptor on %s\n", id_buf); lip->data_in_log = TRUE; } } } } else if (partial5) { if (mip->completeness != 3) { mip->completeness = 3; if (lip != NULL) { if (lip->fp != NULL) { if (id_buf[0] == 0) { SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_buf, PRINTID_FASTA_SHORT, sizeof (id_buf) - 1); } fprintf (lip->fp, "Adjusted completeness for MolInfo descriptor on %s\n", id_buf); } lip->data_in_log = TRUE; } } } else if (partial3) { if (mip->completeness != 4) { mip->completeness = 4; if (lip != NULL) { if (lip->fp != NULL) { if (id_buf[0] == 0) { SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_buf, PRINTID_FASTA_SHORT, sizeof (id_buf) - 1); } fprintf (lip->fp, "Adjusted completeness for MolInfo descriptor on %s\n", id_buf); } lip->data_in_log = TRUE; } } } else if (sfp->partial) { if (mip->completeness != 2) { mip->completeness = 2; if (lip != NULL) { if (lip->fp != NULL) { if (id_buf[0] == 0) { SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_buf, PRINTID_FASTA_SHORT, sizeof (id_buf) - 1); } fprintf (lip->fp, "Adjusted completeness for MolInfo descriptor on %s\n", id_buf); } lip->data_in_log = TRUE; } } } else { if (mip->completeness != 0) { mip->completeness = 0; if (lip != NULL) { if (lip->fp != NULL) { if (id_buf[0] == 0) { SeqIdWrite (SeqIdFindBest (bsp->id, SEQID_GENBANK), id_buf, PRINTID_FASTA_SHORT, sizeof (id_buf) - 1); } fprintf (lip->fp, "Adjusted completeness for MolInfo descriptor on %s\n", id_buf); } lip->data_in_log = TRUE; } } } } } } NLM_EXTERN Boolean ResynchCodingRegionPartialsEx (SeqEntryPtr sep, FILE *log_fp) { LogInfoData lid; MemSet (&lid, 0, sizeof (LogInfoData)); lid.fp = log_fp; VisitFeaturesInSep (sep, &lid, ResynchCDSPartials); return lid.data_in_log; } NLM_EXTERN void ResynchCodingRegionPartials (SeqEntryPtr sep) { ResynchCodingRegionPartialsEx (sep, NULL); } NLM_EXTERN void ResynchMRNAPartials (SeqFeatPtr sfp, Pointer userdata) { BioseqPtr bsp; MolInfoPtr mip; Boolean partial5; Boolean partial3; RnaRefPtr rrp; SeqEntryPtr sep; SeqIdPtr sip; SeqLocPtr slp; ValNodePtr vnp; if (sfp->data.choice != SEQFEAT_RNA) return; rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp == NULL || rrp->type != 2) return; CheckSeqLocForPartial (sfp->location, &partial5, &partial3); sfp->partial = (Boolean) (sfp->partial || partial5 || partial3); slp = SeqLocFindNext (sfp->location, NULL); if (slp == NULL) return; sip = SeqLocId (sfp->product); if (sip == NULL) return; bsp = BioseqFind (sip); if (bsp != NULL && ISA_na (bsp->mol) && bsp->repr == Seq_repr_raw) { sep = SeqMgrGetSeqEntryForData (bsp); if (sep == NULL) return; vnp = SeqEntryGetSeqDescr (sep, Seq_descr_molinfo, NULL); if (vnp == NULL) { vnp = CreateNewDescriptor (sep, Seq_descr_molinfo); if (vnp != NULL) { mip = MolInfoNew (); vnp->data.ptrvalue = (Pointer) mip; if (mip != NULL) { mip->biomol = 3; /* mRNA */ mip->tech = 1; /* standard */ } } } if (vnp != NULL) { mip = (MolInfoPtr) vnp->data.ptrvalue; if (mip != NULL) { if (partial5 && partial3) { mip->completeness = 5; } else if (partial5) { mip->completeness = 3; } else if (partial3) { mip->completeness = 4; } else if (sfp->partial) { mip->completeness = 2; } else { mip->completeness = 0; } } } } } NLM_EXTERN void ResynchMessengerRNAPartials (SeqEntryPtr sep) { VisitFeaturesInSep (sep, NULL, ResynchMRNAPartials); } NLM_EXTERN void ResynchPeptidePartials (SeqFeatPtr sfp, Pointer userdata) { SeqFeatPtr bestprot; BioseqPtr bsp; MolInfoPtr mip; Boolean partial5; Boolean partial3; ProtRefPtr prp; SeqEntryPtr sep; SeqIdPtr sip; SeqLocPtr slp; ValNodePtr vnp; if (sfp->data.choice != SEQFEAT_PROT) return; prp = (ProtRefPtr) sfp->data.value.ptrvalue; if (prp == NULL) return; if (prp->processed < 1 || prp->processed > 4) return; CheckSeqLocForPartial (sfp->location, &partial5, &partial3); sfp->partial = (Boolean) (sfp->partial || partial5 || partial3); /* slp = SeqLocFindNext (sfp->location, NULL); if (slp == NULL) return; */ sip = SeqLocId (sfp->product); if (sip == NULL) return; bsp = BioseqFind (sip); if (bsp != NULL && ISA_aa (bsp->mol) && bsp->repr == Seq_repr_raw) { sep = SeqMgrGetSeqEntryForData (bsp); if (sep == NULL) return; bestprot = SeqMgrGetBestProteinFeature (bsp, NULL); if (bestprot == NULL) { bestprot = GetBestProteinFeatureUnindexed (sfp->product); } if (bestprot != NULL) { slp = NULL; sip = SeqLocId (bestprot->location); if (sip != NULL) { slp = WholeIntervalFromSeqId (sip); } if (slp == NULL) { slp = CreateWholeInterval (sep); } if (slp != NULL) { bestprot->location = SeqLocFree (bestprot->location); bestprot->location = slp; } SetSeqLocPartial (bestprot->location, partial5, partial3); bestprot->partial = sfp->partial; } vnp = SeqEntryGetSeqDescr (sep, Seq_descr_molinfo, NULL); if (vnp == NULL) { vnp = CreateNewDescriptor (sep, Seq_descr_molinfo); if (vnp != NULL) { mip = MolInfoNew (); vnp->data.ptrvalue = (Pointer) mip; if (mip != NULL) { mip->biomol = 8; mip->tech = 13; } } } if (vnp != NULL) { mip = (MolInfoPtr) vnp->data.ptrvalue; if (mip != NULL) { if (partial5 && partial3) { mip->completeness = 5; } else if (partial5) { mip->completeness = 3; } else if (partial3) { mip->completeness = 4; } else if (sfp->partial) { mip->completeness = 2; } else { mip->completeness = 0; } } } } } NLM_EXTERN void ResynchProteinPartials (SeqEntryPtr sep) { VisitFeaturesInSep (sep, NULL, ResynchPeptidePartials); } /* SeqIdStripLocus removes the SeqId.name field if accession is set */ NLM_EXTERN SeqIdPtr SeqIdStripLocus (SeqIdPtr sip) { TextSeqIdPtr tip; if (sip != NULL) { switch (sip->choice) { case SEQID_GENBANK : case SEQID_EMBL : case SEQID_DDBJ : case SEQID_OTHER : case SEQID_TPG: case SEQID_TPE: case SEQID_TPD: case SEQID_GPIPE: tip = (TextSeqIdPtr) sip->data.ptrvalue; if (tip != NULL) { if (! HasNoText (tip->accession)) { tip->name = MemFree (tip->name); } } break; default : break; } } return sip; } NLM_EXTERN SeqLocPtr StripLocusFromSeqLoc (SeqLocPtr location) { SeqLocPtr loc; SeqLocPtr next; PackSeqPntPtr psp; SeqBondPtr sbp; SeqIntPtr sinp; SeqIdPtr sip; SeqLocPtr slp; SeqPntPtr spp; if (location == NULL) return NULL; slp = SeqLocFindNext (location, NULL); while (slp != NULL) { next = SeqLocFindNext (location, slp); switch (slp->choice) { case SEQLOC_EMPTY : case SEQLOC_WHOLE : sip = (SeqIdPtr) slp->data.ptrvalue; SeqIdStripLocus (sip); break; case SEQLOC_INT : sinp = (SeqIntPtr) slp->data.ptrvalue; if (sinp != NULL) { SeqIdStripLocus (sinp->id); } break; case SEQLOC_PACKED_INT : case SEQLOC_MIX : case SEQLOC_EQUIV : loc = (SeqLocPtr) slp->data.ptrvalue; while (loc != NULL) { sip = SeqLocId (loc); SeqIdStripLocus (sip); loc = loc->next; } break; case SEQLOC_BOND : sbp = (SeqBondPtr) slp->data.ptrvalue; if (sbp != NULL) { spp = sbp->a; if (spp != NULL) { SeqIdStripLocus (spp->id); } spp = sbp->b; if (spp != NULL) { SeqIdStripLocus (spp->id); } } break; case SEQLOC_PNT : spp = (SeqPntPtr) slp->data.ptrvalue; if (spp != NULL) { SeqIdStripLocus (spp->id); } break; case SEQLOC_PACKED_PNT : psp = (PackSeqPntPtr) slp->data.ptrvalue; if (psp != NULL) { SeqIdStripLocus (psp->id); } break; default : break; } slp = next; } return location; } static void GetRidOfLocusCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; BioseqSetPtr bssp; SeqAnnotPtr sap; SeqFeatPtr sfp; if (sep == NULL || sep->data.ptrvalue == NULL) return; sap = NULL; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; sap = bsp->annot; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; sap = bssp->annot; } else return; while (sap != NULL) { if (sap->type == 1 && sap->data != NULL) { sfp = (SeqFeatPtr) sap->data; while (sfp != NULL) { StripLocusFromSeqLoc (sfp->location); StripLocusFromSeqLoc (sfp->product); sfp = sfp->next; } } sap = sap->next; } } NLM_EXTERN void GetRidOfLocusInSeqIds (Uint2 entityID, SeqEntryPtr sep) { if (entityID < 1 && sep == NULL) return; if (entityID > 0 && sep == NULL) { sep = GetTopSeqEntryForEntityID (entityID); } if (sep == NULL) return; SeqEntryExplore (sep, NULL, GetRidOfLocusCallback); } /* Mac can now use static parse tables by using Make Strings Read-Only and Store Static Data in TOC #ifdef OS_MAC #define ASNLOAD_NEEDED 1 #endif */ #if defined(OS_DOS) || defined(WIN16) #define ASNLOAD_NEEDED 1 #endif static Boolean FileExists (CharPtr dirname, CharPtr subname, CharPtr filename) { Char path [PATH_MAX]; StringNCpy_0 (path, dirname, sizeof (path)); FileBuildPath (path, subname, NULL); FileBuildPath (path, NULL, filename); return (Boolean) (FileLength (path) > 0); } /* static Boolean CheckAsnloadPath (CharPtr dirname, CharPtr subdir) { #ifdef ASNLOAD_NEEDED Char fname [16]; int i; for (i = 60; i <= 99; ++i) { sprintf (fname, "asnmedli.l%02d", (int) i); if (FileExists (dirname, subdir, fname)) { return TRUE; } } return FALSE; #else return TRUE; #endif } */ static Boolean CheckDataPath (CharPtr dirname, CharPtr subdir) { if (FileExists (dirname, subdir, "seqcode.val")) return TRUE; return (Boolean) (FileExists (dirname, subdir, "objprt.prt")); } static Boolean CheckErrMsgPath (CharPtr dirname, CharPtr subdir) { return (Boolean) (FileExists (dirname, subdir, "valid.msg")); } static void SetTransientPath (CharPtr dirname, CharPtr subname, CharPtr file, CharPtr section, CharPtr type) { Char path [PATH_MAX]; StringNCpy_0 (path, dirname, sizeof (path)); FileBuildPath (path, subname, NULL); TransientSetAppParam (file, section, type, path); } NLM_EXTERN Boolean UseLocalAsnloadDataAndErrMsg (void) { Boolean dataFound; Char path [PATH_MAX]; Char appPath[PATH_MAX]; CharPtr ptr; ProgramPath (appPath, sizeof (appPath)); StrCpy(path, appPath); /* data a sibling of our application? */ ptr = StringRChr (path, DIRDELIMCHR); if (ptr != NULL) { ptr++; *ptr = '\0'; } dataFound = CheckDataPath (path, "data"); if (! (dataFound)) { /* data an uncle of our application? */ if (ptr != NULL) { ptr--; *ptr = '\0'; ptr = StringRChr (path, DIRDELIMCHR); if (ptr != NULL) { ptr++; *ptr = '\0'; } dataFound = CheckDataPath (path, "data"); } } #ifdef OS_UNIX_DARWIN if (! (dataFound) && IsApplicationPackage (appPath)) { /* is data inside our application within Contents/Resources? */ StrCpy (path, appPath); FileBuildPath (path, "Contents", NULL); FileBuildPath (path, "Resources", NULL); dataFound = CheckDataPath (path, "data"); if (! dataFound) { StrCpy (path, appPath); ptr = StringStr (path, "/ncbi/build/"); if (ptr != NULL) { /* see if running under older Xcode 3 build environment */ ptr [5] = '\0'; dataFound = CheckDataPath (path, "data"); } } if (! dataFound) { StrCpy (path, appPath); ptr = StringStr (path, "/ncbi/make/"); if (ptr != NULL) { /* see if running under newer Xcode 3 build environment */ ptr [5] = '\0'; dataFound = CheckDataPath (path, "data"); } } if (! dataFound) { StrCpy (path, appPath); ptr = StringStr (path, "/Library/Developer/"); if (ptr != NULL) { /* see if running under Xcode 4 build environment */ ptr [19] = '\0'; dataFound = CheckDataPath (path, "data"); } } } #endif if (dataFound) { SetTransientPath (path, "asnload", "NCBI", "NCBI", "ASNLOAD"); SetTransientPath (path, "data", "NCBI", "NCBI", "DATA"); if (CheckErrMsgPath (path, "errmsg")) { SetTransientPath (path, "errmsg", "NCBI", "ErrorProcessing", "MsgPath"); TransientSetAppParam ("NCBI", "ErrorProcessing", "EO_BEEP", "No"); } return TRUE; } return FALSE; } typedef struct miscdata { SeqEntryPtr sep; Int2 count; Int2 desired; Uint1 _class; } MiscData, PNTR MiscDataPtr; static void FindNthSeqEntryCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { MiscDataPtr mdp; if (sep != NULL && mydata != NULL) { mdp = (MiscDataPtr) mydata; (mdp->count)++; if (mdp->count == mdp->desired) { mdp->sep = sep; } } } NLM_EXTERN SeqEntryPtr LIBCALL FindNthSeqEntry (SeqEntryPtr sep, Int2 seq) { MiscData md; md.sep = NULL; md.count = 0; md.desired = seq; if (sep != NULL) { SeqEntryExplore (sep, (Pointer) (&md), FindNthSeqEntryCallback); } return md.sep; } NLM_EXTERN SeqEntryPtr LIBCALL FindNthBioseq (SeqEntryPtr sep, Int2 seq) { MiscData md; md.sep = NULL; md.count = 0; md.desired = seq; if (sep != NULL) { BioseqExplore (sep, (Pointer) (&md), FindNthSeqEntryCallback); } return md.sep; } NLM_EXTERN SeqEntryPtr LIBCALL FindNthSequinEntry (SeqEntryPtr sep, Int2 seq) { MiscData md; md.sep = NULL; md.count = 0; md.desired = seq; if (sep != NULL) { SequinEntryExplore (sep, (Pointer) (&md), FindNthSeqEntryCallback); } return md.sep; } static void FindNucSeqEntryCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; MiscDataPtr mdp; if (sep != NULL && sep->choice == 1 && mydata != NULL) { mdp = (MiscDataPtr) mydata; bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp != NULL && ISA_na (bsp->mol)) { if (mdp->sep == NULL) { mdp->sep = sep; } } } } NLM_EXTERN SeqEntryPtr LIBCALL FindNucSeqEntry (SeqEntryPtr sep) { MiscData md; md.sep = NULL; md.count = 0; md.desired = 0; if (sep != NULL) { BioseqExplore (sep, (Pointer) (&md), FindNucSeqEntryCallback); } return md.sep; } NLM_EXTERN BioseqPtr LIBCALL FindNucBioseq (SeqEntryPtr sep) { BioseqPtr nbsp; SeqEntryPtr nsep; nsep = FindNucSeqEntry (sep); if (nsep == NULL) return NULL; if (! IS_Bioseq (nsep)) return NULL; nbsp = (BioseqPtr) nsep->data.ptrvalue; return nbsp; } static void FindBioseqSetByClassCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqSetPtr bssp; MiscDataPtr mdp; if (sep != NULL && sep->choice == 2 && mydata != NULL) { mdp = (MiscDataPtr) mydata; bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp != NULL && bssp->_class == mdp->_class) { if (mdp->sep == NULL) { mdp->sep = sep; } } } } NLM_EXTERN SeqEntryPtr LIBCALL FindBioseqSetByClass (SeqEntryPtr sep, Uint1 _class) { MiscData md; md.sep = NULL; md.count = 0; md.desired = 0; md._class = _class; if (sep != NULL) { SeqEntryExplore (sep, (Pointer) (&md), FindBioseqSetByClassCallback); } return md.sep; } typedef struct kinddata { Boolean hasNuc; Boolean hasProt; } KindData, PNTR KindPtr; static void HasNucOrProtCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; KindPtr kptr; if (sep != NULL && sep->choice == 1 && sep->data.ptrvalue != NULL && mydata != NULL) { kptr = (KindPtr) mydata; bsp = (BioseqPtr) sep->data.ptrvalue; if (ISA_na (bsp->mol)) { kptr->hasNuc = TRUE; } else if (ISA_aa (bsp->mol)) { kptr->hasProt = TRUE; } } } NLM_EXTERN Boolean LIBCALL SeqEntryHasNucs (SeqEntryPtr sep) { KindData kd; kd.hasNuc = FALSE; kd.hasProt = FALSE; if (sep != NULL) { BioseqExplore (sep, (Pointer) (&kd), HasNucOrProtCallback); } return kd.hasNuc; } NLM_EXTERN Boolean LIBCALL SeqEntryHasProts (SeqEntryPtr sep) { KindData kd; kd.hasNuc = FALSE; kd.hasProt = FALSE; if (sep != NULL) { BioseqExplore (sep, (Pointer) (&kd), HasNucOrProtCallback); } return kd.hasProt; } static Boolean CheckForAlignments (GatherContextPtr gcp) { BoolPtr boolptr; if (gcp == NULL) return TRUE; boolptr = (BoolPtr) gcp->userdata; if (boolptr == NULL ) return TRUE; switch (gcp->thistype) { case OBJ_SEQALIGN : case OBJ_SEQHIST_ALIGN : *boolptr = TRUE; return TRUE; default : break; } return TRUE; } NLM_EXTERN Boolean LIBCALL SeqEntryHasAligns (Uint2 entityID, SeqEntryPtr sep) { GatherScope gs; Boolean rsult; rsult = FALSE; if (entityID == 0 || sep == NULL) return FALSE; MemSet ((Pointer) (&gs), 0, sizeof (GatherScope)); gs.seglevels = 1; MemSet((Pointer) (gs.ignore), (int) (TRUE), (size_t) (OBJ_MAX * sizeof (Boolean))); gs.ignore[OBJ_BIOSEQ] = FALSE; gs.ignore[OBJ_BIOSEQ_SEG] = FALSE; gs.ignore[OBJ_SEQALIGN] = FALSE; gs.ignore[OBJ_SEQANNOT] = FALSE; gs.ignore[OBJ_SEQHIST] = FALSE; gs.ignore[OBJ_SEQHIST_ALIGN] = FALSE; gs.scope = sep; GatherEntity (entityID, (Pointer) (&rsult), CheckForAlignments, &gs); return rsult; } static void FindPowerBLASTAsnCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { AnnotDescrPtr desc; ObjectIdPtr oip; SeqAnnotPtr sap; BoolPtr rsult; if (sep == NULL || sep->data.ptrvalue == NULL || mydata == NULL) return; rsult = (BoolPtr) mydata; sap = (IS_Bioseq (sep)) ? ((BioseqPtr) sep->data.ptrvalue)->annot : ((BioseqSetPtr) sep->data.ptrvalue)->annot; while (sap != NULL) { if (sap->type == 2) { desc = NULL; while ((desc = ValNodeFindNext (sap->desc, desc, Annot_descr_user)) != NULL) { if (desc->data.ptrvalue != NULL) { oip = ((UserObjectPtr) desc->data.ptrvalue)->type; if (oip != NULL && StringCmp (oip->str, "Hist Seqalign") == 0) { *rsult = TRUE; } } } } sap = sap->next; } } NLM_EXTERN Boolean LIBCALL PowerBLASTASN1Detected (SeqEntryPtr sep) { Boolean rsult; rsult = FALSE; SeqEntryExplore (sep, (Pointer) &rsult, FindPowerBLASTAsnCallback); return rsult; } NLM_EXTERN SeqLocPtr CreateWholeInterval (SeqEntryPtr sep) { BioseqPtr bsp; SeqIntPtr sip; SeqLocPtr slp; slp = NULL; if (sep != NULL && sep->choice == 1 && sep->data.ptrvalue != NULL) { bsp = (BioseqPtr) sep->data.ptrvalue; slp = ValNodeNew (NULL); if (slp != NULL) { sip = SeqIntNew (); if (sip != NULL) { slp->choice = SEQLOC_INT; slp->data.ptrvalue = (Pointer) sip; sip->from = 0; sip->to = bsp->length - 1; if (ISA_na (bsp->mol)) { sip->strand = Seq_strand_plus; } sip->id = SeqIdStripLocus (SeqIdDup (SeqIdFindBest (bsp->id, 0))); } } } return slp; } NLM_EXTERN SeqLocPtr WholeIntervalFromSeqId (SeqIdPtr sip) { BioseqPtr bsp; SeqIntPtr sintp; SeqLocPtr slp; if (sip == NULL) return NULL; bsp = BioseqFindCore (sip); if (bsp == NULL) return NULL; slp = ValNodeNew (NULL); if (slp == NULL) return NULL; sintp = SeqIntNew (); if (sintp == NULL) return NULL; slp->choice = SEQLOC_INT; slp->data.ptrvalue = (Pointer) sintp; sintp->from = 0; sintp->to = bsp->length - 1; if (ISA_na (bsp->mol)) { sintp->strand = Seq_strand_plus; } sintp->id = SeqIdStripLocus (SeqIdDup (sip)); return slp; } NLM_EXTERN void FreeAllFuzz (SeqLocPtr location) { SeqIntPtr sip; SeqLocPtr slp; if (location == NULL) return; slp = SeqLocFindNext (location, NULL); while (slp != NULL) { if (slp->choice == SEQLOC_INT) { sip = (SeqIntPtr) slp->data.ptrvalue; if (sip != NULL) { sip->if_to = IntFuzzFree (sip->if_to); sip->if_from = IntFuzzFree (sip->if_from); } } slp = SeqLocFindNext (location, slp); } } NLM_EXTERN Boolean LocationHasNullsBetween (SeqLocPtr location) { SeqLocPtr slp; if (location == NULL) return FALSE; slp = SeqLocFindNext (location, NULL); while (slp != NULL) { if (slp->choice == SEQLOC_NULL) return TRUE; slp = SeqLocFindNext (location, slp); } return FALSE; } NLM_EXTERN void NormalizeNullsBetween (SeqLocPtr location) { SeqLocPtr next, tmp, vnp; if (location == NULL) return; if (! LocationHasNullsBetween (location)) return; if (location->choice != SEQLOC_MIX) return; vnp = (ValNodePtr) location->data.ptrvalue; if (vnp == NULL) return; while (vnp != NULL && vnp->next != NULL) { next = vnp->next; if (vnp->choice != SEQLOC_NULL && next->choice != SEQLOC_NULL) { tmp = ValNodeNew (NULL); if (tmp != NULL) { tmp->choice = SEQLOC_NULL; tmp->next = vnp->next; vnp->next = tmp; } } vnp = next; } } NLM_EXTERN Uint1 FindFeatFromFeatDefType (Uint2 subtype) { switch (subtype) { case FEATDEF_GENE : return SEQFEAT_GENE; case FEATDEF_ORG : return SEQFEAT_ORG; case FEATDEF_CDS : return SEQFEAT_CDREGION; case FEATDEF_PROT : return SEQFEAT_PROT; case FEATDEF_PUB : return SEQFEAT_PUB; case FEATDEF_SEQ : return SEQFEAT_SEQ; case FEATDEF_REGION : return SEQFEAT_REGION; case FEATDEF_COMMENT : return SEQFEAT_COMMENT; case FEATDEF_BOND : return SEQFEAT_BOND; case FEATDEF_SITE : return SEQFEAT_SITE; case FEATDEF_RSITE : return SEQFEAT_RSITE; case FEATDEF_USER : return SEQFEAT_USER; case FEATDEF_TXINIT : return SEQFEAT_TXINIT; case FEATDEF_NUM : return SEQFEAT_NUM; case FEATDEF_PSEC_STR : return SEQFEAT_PSEC_STR; case FEATDEF_NON_STD_RESIDUE : return SEQFEAT_NON_STD_RESIDUE; case FEATDEF_HET : return SEQFEAT_HET; case FEATDEF_BIOSRC : return SEQFEAT_BIOSRC; default : if (subtype >= FEATDEF_preRNA && subtype <= FEATDEF_otherRNA) { return SEQFEAT_RNA; } if (subtype == FEATDEF_snoRNA) { return SEQFEAT_RNA; } if (subtype >= FEATDEF_ncRNA && subtype <= FEATDEF_tmRNA) { return SEQFEAT_RNA; } if (subtype >= FEATDEF_preprotein && subtype <= FEATDEF_transit_peptide_aa) { return SEQFEAT_PROT; } if (subtype >= FEATDEF_IMP && subtype <= FEATDEF_site_ref) { return SEQFEAT_IMP; } if (subtype >= FEATDEF_gap && subtype <= FEATDEF_oriT) { return SEQFEAT_IMP; } if (subtype == FEATDEF_mobile_element) { return SEQFEAT_IMP; } } return 0; } NLM_EXTERN SeqIdPtr MakeSeqID (CharPtr str) { CharPtr buf; Int4 len; SeqIdPtr sip; sip = NULL; if (str != NULL && *str != '\0') { if (StringChr (str, '|') != NULL) { sip = SeqIdParse (str); } else { len = StringLen (str) + 5; buf = (CharPtr) MemNew (sizeof (Char) * len); sprintf (buf, "lcl|%s", str); sip = SeqIdParse (buf); buf = MemFree (buf); } } return sip; } NLM_EXTERN SeqIdPtr MakeUniqueSeqID (CharPtr prefix) { Char buf[40]; CharPtr tmp; Int2 ctr; ValNodePtr newid; ObjectIdPtr oid; ValNode vn; TextSeqId tsi; ValNodePtr altid; size_t len; altid = &vn; vn.choice = SEQID_GENBANK; vn.next = NULL; vn.data.ptrvalue = &tsi; tsi.name = NULL; tsi.accession = NULL; tsi.release = NULL; tsi.version = INT2_MIN; len = StringLen (prefix); if (len > 0 && len < 32) { tmp = StringMove(buf, prefix); } else { tmp = StringMove(buf, "tmpseq_"); } newid = ValNodeNew(NULL); oid = ObjectIdNew(); oid->str = buf; /* allocate this later */ newid->choice = SEQID_LOCAL; newid->data.ptrvalue = oid; tsi.name = buf; /* check for alternative form */ for (ctr = 1; ctr < 32000; ctr++) { sprintf(tmp, "%d", (int)ctr); if ((BioseqFindCore(newid) == NULL) && (BioseqFindCore(altid) == NULL)) { oid->str = StringSave(buf); return newid; } } return NULL; } NLM_EXTERN SeqIdPtr SeqIdFindWorst (SeqIdPtr sip) { Uint1 order [NUM_SEQID]; SeqIdBestRank (order, NUM_SEQID); order [SEQID_LOCAL] = 10; order [SEQID_GENBANK] = 5; order [SEQID_EMBL] = 5; order [SEQID_PIR] = 5; order [SEQID_SWISSPROT] = 5; order [SEQID_DDBJ] = 5; order [SEQID_PRF] = 5; order [SEQID_PDB] = 5; order [SEQID_TPG] = 5; order [SEQID_TPE] = 5; order [SEQID_TPD] = 5; order [SEQID_GPIPE] = 9; order [SEQID_NAMED_ANNOT_TRACK] = 9; order [SEQID_PATENT] = 10; order [SEQID_OTHER] = 8; order [SEQID_GENERAL] = 15; order [SEQID_GIBBSQ] = 15; order [SEQID_GIBBMT] = 15; order [SEQID_GIIM] = 20; order [SEQID_GI] = 20; return SeqIdSelect (sip, order, NUM_SEQID); } NLM_EXTERN SeqFeatPtr CreateNewFeature (SeqEntryPtr sep, SeqEntryPtr placeHere, Uint1 choice, SeqFeatPtr useThis) { BioseqPtr bsp; BioseqSetPtr bssp; SeqFeatPtr prev; SeqAnnotPtr sap; SeqFeatPtr sfp; if (sep == NULL || sep->choice != 1) return NULL; sfp = NULL; bsp = NULL; bssp = NULL; if (placeHere == NULL) { placeHere = sep; } if (placeHere != NULL && placeHere->data.ptrvalue != NULL) { if (placeHere->choice == 1) { bsp = (BioseqPtr) placeHere->data.ptrvalue; sap = bsp->annot; while (sap != NULL && (sap->name != NULL || sap->desc != NULL || sap->type != 1)) { sap = sap->next; } if (sap == NULL) { sap = SeqAnnotNew (); if (sap != NULL) { sap->type = 1; sap->next = bsp->annot; bsp->annot = sap; } sap = bsp->annot; } } else if (placeHere->choice == 2) { bssp = (BioseqSetPtr) placeHere->data.ptrvalue; sap = bssp->annot; while (sap != NULL && (sap->name != NULL || sap->desc != NULL || sap->type != 1)) { sap = sap->next; } if (sap == NULL) { sap = SeqAnnotNew (); if (sap != NULL) { sap->type = 1; sap->next = bssp->annot; bssp->annot = sap; } sap = bssp->annot; } } else { return NULL; } if (sap != NULL) { bsp = (BioseqPtr) sep->data.ptrvalue; if (useThis != NULL) { sfp = useThis; } else { sfp = SeqFeatNew (); } if (sap->data != NULL) { prev = sap->data; while (prev->next != NULL) { prev = prev->next; } prev->next = sfp; } else { sap->data = (Pointer) sfp; } if (sfp != NULL) { sfp->data.choice = choice; if (useThis == NULL) { sfp->location = CreateWholeInterval (sep); } } } } return sfp; } NLM_EXTERN SeqFeatPtr CreateNewFeatureOnBioseq (BioseqPtr bsp, Uint1 choice, SeqLocPtr slp) { SeqEntryPtr sep; SeqFeatPtr sfp; if (bsp == NULL) return NULL; sep = SeqMgrGetSeqEntryForData (bsp); if (sep == NULL) return NULL; sfp = CreateNewFeature (sep, NULL, choice, NULL); if (sfp == NULL) return NULL; if (slp != NULL) { sfp->location = SeqLocFree (sfp->location); sfp->location = AsnIoMemCopy (slp, (AsnReadFunc) SeqLocAsnRead, (AsnWriteFunc) SeqLocAsnWrite); } return sfp; } NLM_EXTERN ValNodePtr CreateNewDescriptor (SeqEntryPtr sep, Uint1 choice) { BioseqPtr bsp; BioseqSetPtr bssp; Uint1 _class; ValNodePtr descr; SeqEntryPtr seqentry; ValNodePtr vnp; vnp = NULL; if (sep != NULL) { descr = NULL; vnp = NULL; bsp = NULL; bssp = NULL; seqentry = sep; while (seqentry != NULL) { if (seqentry->choice == 1) { bsp = (BioseqPtr) seqentry->data.ptrvalue; if (bsp != NULL) { descr = bsp->descr; vnp = SeqDescrNew (descr); if (descr == NULL) { bsp->descr = vnp; } } seqentry = NULL; } else if (seqentry->choice == 2) { bssp = (BioseqSetPtr) seqentry->data.ptrvalue; if (bssp != NULL) { _class = bssp->_class; if (_class == 7) { descr = bssp->descr; vnp = SeqDescrNew (descr); if (descr == NULL) { bssp->descr = vnp; } seqentry = NULL; } else if ((_class >= 5 && _class <= 8) || _class == 11 /* || _class == BioseqseqSet_class_gen_prod_set */) { seqentry = bssp->seq_set; } else { descr = bssp->descr; vnp = SeqDescrNew (descr); if (descr == NULL) { bssp->descr = vnp; } seqentry = NULL; } } else { seqentry = NULL; } } else { seqentry = NULL; } } if (vnp != NULL) { vnp->choice = choice; } } return vnp; } NLM_EXTERN ValNodePtr CreateNewDescriptorOnBioseq (BioseqPtr bsp, Uint1 choice) { SeqEntryPtr sep; if (bsp == NULL) return NULL; sep = SeqMgrGetSeqEntryForData (bsp); if (sep == NULL) return NULL; return CreateNewDescriptor (sep, choice); } /* common functions to scan binary ASN.1 file of entire release as Bioseq-set */ static Int4 VisitSeqIdList (SeqIdPtr sip, Pointer userdata, VisitSeqIdFunc callback) { Int4 index = 0; while (sip != NULL) { if (callback != NULL) { callback (sip, userdata); } index++; sip = sip->next; } return index; } NLM_EXTERN Int4 VisitSeqIdsInSeqLoc (SeqLocPtr slp, Pointer userdata, VisitSeqIdFunc callback) { Int4 index = 0; SeqLocPtr loc; PackSeqPntPtr psp; SeqBondPtr sbp; SeqIntPtr sinp; SeqIdPtr sip; SeqPntPtr spp; if (slp == NULL) return index; while (slp != NULL) { switch (slp->choice) { case SEQLOC_NULL : break; case SEQLOC_EMPTY : case SEQLOC_WHOLE : sip = (SeqIdPtr) slp->data.ptrvalue; index += VisitSeqIdList (sip, userdata, callback); break; case SEQLOC_INT : sinp = (SeqIntPtr) slp->data.ptrvalue; if (sinp != NULL) { sip = sinp->id; index += VisitSeqIdList (sip, userdata, callback); } break; case SEQLOC_PNT : spp = (SeqPntPtr) slp->data.ptrvalue; if (spp != NULL) { sip = spp->id; index += VisitSeqIdList (sip, userdata, callback); } break; case SEQLOC_PACKED_PNT : psp = (PackSeqPntPtr) slp->data.ptrvalue; if (psp != NULL) { sip = psp->id; index += VisitSeqIdList (sip, userdata, callback); } break; case SEQLOC_PACKED_INT : case SEQLOC_MIX : case SEQLOC_EQUIV : loc = (SeqLocPtr) slp->data.ptrvalue; while (loc != NULL) { index += VisitSeqIdsInSeqLoc (loc, userdata, callback); loc = loc->next; } break; case SEQLOC_BOND : sbp = (SeqBondPtr) slp->data.ptrvalue; if (sbp != NULL) { spp = (SeqPntPtr) sbp->a; if (spp != NULL) { sip = spp->id; index += VisitSeqIdList (sip, userdata, callback); } spp = (SeqPntPtr) sbp->b; if (spp != NULL) { sip = spp->id; index += VisitSeqIdList (sip, userdata, callback); } } break; case SEQLOC_FEAT : break; default : break; } slp = slp->next; } return index; } NLM_EXTERN Int4 VisitSeqIdsInBioseq (BioseqPtr bsp, Pointer userdata, VisitSeqIdFunc callback) { Int4 index = 0; if (bsp == NULL) return index; if (bsp->id != NULL) { index += VisitSeqIdList (bsp->id, userdata, callback); } return index; } NLM_EXTERN Int4 VisitSeqIdsInSeqFeat (SeqFeatPtr sfp, Pointer userdata, VisitSeqIdFunc callback) { CodeBreakPtr cbp; CdRegionPtr crp; Int4 index = 0; RnaRefPtr rrp; tRNAPtr trp; if (sfp == NULL) return index; index += VisitSeqIdsInSeqLoc (sfp->location, userdata, callback); index += VisitSeqIdsInSeqLoc (sfp->product, userdata, callback); switch (sfp->data.choice) { case SEQFEAT_CDREGION : crp = (CdRegionPtr) sfp->data.value.ptrvalue; if (crp != NULL) { for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) { index += VisitSeqIdsInSeqLoc (cbp->loc, userdata, callback); } } break; case SEQFEAT_RNA : rrp = (RnaRefPtr) sfp->data.value.ptrvalue; if (rrp != NULL && rrp->ext.choice == 2) { trp = (tRNAPtr) rrp->ext.value.ptrvalue; if (trp != NULL && trp->anticodon != NULL) { index += VisitSeqIdsInSeqLoc (trp->anticodon, userdata, callback); } } break; default : break; } return index; } NLM_EXTERN Int4 VisitSeqIdsInSeqAlign (SeqAlignPtr sap, Pointer userdata, VisitSeqIdFunc callback) { DenseDiagPtr ddp; DenseSegPtr dsp; Int4 index = 0; SeqIdPtr sip; SeqLocPtr slp = NULL; StdSegPtr ssp; if (sap == NULL) return index; if (sap->bounds != NULL) { sip = SeqLocId (sap->bounds); index += VisitSeqIdList (sip, userdata, callback); } if (sap->segs == NULL) return index; switch (sap->segtype) { case SAS_DENDIAG : ddp = (DenseDiagPtr) sap->segs; if (ddp != NULL) { for (sip = ddp->id; sip != NULL; sip = sip->next) { index += VisitSeqIdList (sip, userdata, callback); } } break; case SAS_DENSEG : dsp = (DenseSegPtr) sap->segs; if (dsp != NULL) { for (sip = dsp->ids; sip != NULL; sip = sip->next) { index += VisitSeqIdList (sip, userdata, callback); } } break; case SAS_STD : ssp = (StdSegPtr) sap->segs; for (slp = ssp->loc; slp != NULL; slp = slp->next) { sip = SeqLocId (slp); index += VisitSeqIdList (sip, userdata, callback); } break; case SAS_DISC : /* recursive */ for (sap = (SeqAlignPtr) sap->segs; sap != NULL; sap = sap->next) { index += VisitSeqIdsInSeqAlign (sap, userdata, callback); } break; default : break; } return index; } NLM_EXTERN Int4 VisitSeqIdsInSeqGraph (SeqGraphPtr sgp, Pointer userdata, VisitSeqIdFunc callback) { Int4 index = 0; SeqIdPtr sip; if (sgp == NULL) return index; if (sgp->loc != NULL) { sip = SeqLocId (sgp->loc); index += VisitSeqIdList (sip, userdata, callback); } return index; } NLM_EXTERN Int4 VisitSeqIdsInSeqAnnot (SeqAnnotPtr annot, Pointer userdata, VisitSeqIdFunc callback) { Int4 index = 0; SeqAlignPtr sap; SeqFeatPtr sfp; SeqGraphPtr sgp; if (annot == NULL || annot->data == NULL) return index; switch (annot->type) { case 1 : for (sfp = (SeqFeatPtr) annot->data; sfp != NULL; sfp = sfp->next) { index += VisitSeqIdsInSeqFeat (sfp, userdata, callback); } break; case 2 : for (sap = (SeqAlignPtr) annot->data; sap != NULL; sap = sap->next) { index += VisitSeqIdsInSeqAlign (sap, userdata, callback); } break; case 3 : for (sgp = (SeqGraphPtr) annot->data; sgp != NULL; sgp = sgp->next) { index += VisitSeqIdsInSeqGraph (sgp, userdata, callback); } break; default : break; } return index; } NLM_EXTERN Int4 VisitUserFieldsInUfp (UserFieldPtr ufp, Pointer userdata, VisitUserFieldsFunc callback) { UserFieldPtr curr; Int4 index = 0; Boolean nested = FALSE; if (ufp == NULL) return index; if (ufp->choice == 11) { for (curr = (UserFieldPtr) ufp->data.ptrvalue; curr != NULL; curr = curr->next) { index += VisitUserFieldsInUfp (curr, userdata,callback); nested = TRUE; } } if (! nested) { if (callback != NULL) { callback (ufp, userdata); } index++; } return index; } NLM_EXTERN Int4 VisitUserFieldsInUop (UserObjectPtr uop, Pointer userdata, VisitUserFieldsFunc callback) { Int4 index = 0; UserFieldPtr ufp; if (uop == NULL) return index; for (ufp = uop->data; ufp != NULL; ufp = ufp->next) { if (callback != NULL) { callback (ufp, userdata); } index++; } return index; } /* Visits only unnested nodes */ NLM_EXTERN Int4 VisitUserObjectsInUop (UserObjectPtr uop, Pointer userdata, VisitUserObjectFunc callback) { Int4 index = 0; Boolean nested = FALSE; UserObjectPtr obj; UserFieldPtr ufp; if (uop == NULL) return index; for (ufp = uop->data; ufp != NULL; ufp = ufp->next) { if (ufp->choice == 6) { obj = (UserObjectPtr) ufp->data.ptrvalue; index += VisitUserObjectsInUop (obj, userdata, callback); nested = TRUE; } else if (ufp->choice == 12) { for (obj = (UserObjectPtr) ufp->data.ptrvalue; obj != NULL; obj = obj->next) { index += VisitUserObjectsInUop (obj, userdata, callback); } nested = TRUE; } } if (! nested) { if (callback != NULL) { callback (uop, userdata); } index++; } return index; } NLM_EXTERN Int4 VisitAllUserObjectsInUop (UserObjectPtr uop, Pointer userdata, VisitUserObjectFunc callback) { Int4 index = 0; UserObjectPtr obj; UserFieldPtr ufp; if (uop == NULL) return index; for (ufp = uop->data; ufp != NULL; ufp = ufp->next) { if (ufp->choice == 6) { obj = (UserObjectPtr) ufp->data.ptrvalue; index += VisitAllUserObjectsInUop (obj, userdata, callback); } else if (ufp->choice == 12) { for (obj = (UserObjectPtr) ufp->data.ptrvalue; obj != NULL; obj = obj->next) { index += VisitAllUserObjectsInUop (obj, userdata, callback); } } } if (callback != NULL) { callback (uop, userdata); } index++; return index; } typedef struct uopdata { UserObjectPtr rsult; CharPtr tag; } UopData, PNTR UopDataPtr; static void FindUopProc ( UserObjectPtr uop, Pointer userdata ) { ObjectIdPtr oip; UopDataPtr udp; if (uop == NULL || userdata == NULL) return; oip = uop->type; if (oip == NULL) return; udp = (UopDataPtr) userdata; if (StringICmp (oip->str, udp->tag) != 0) return; udp->rsult = uop; } NLM_EXTERN UserObjectPtr FindUopByTag (UserObjectPtr top, CharPtr tag) { UopData ud; if (top == NULL || StringHasNoText (tag)) return NULL; ud.rsult = NULL; ud.tag = tag; VisitUserObjectsInUop (top, (Pointer) &ud, FindUopProc); return ud.rsult; } NLM_EXTERN UserObjectPtr CombineUserObjects (UserObjectPtr origuop, UserObjectPtr newuop) { UserFieldPtr prev = NULL; ObjectIdPtr oip; UserFieldPtr ufp; UserObjectPtr uop; if (newuop == NULL) return origuop; if (origuop == NULL) return newuop; /* adding to an object that already chaperones at least two user objects */ oip = origuop->type; if (oip != NULL && StringICmp (oip->str, "CombinedFeatureUserObjects") == 0) { for (ufp = origuop->data; ufp != NULL; ufp = ufp->next) { prev = ufp; } ufp = UserFieldNew (); oip = ObjectIdNew (); oip->id = 0; ufp->label = oip; ufp->choice = 6; /* user object */ ufp->data.ptrvalue = (Pointer) newuop; /* link new set at end of list */ if (prev != NULL) { prev->next = ufp; } else { origuop->data = ufp; } return origuop; } /* creating a new chaperone, link in first two user objects */ uop = UserObjectNew (); oip = ObjectIdNew (); oip->str = StringSave ("CombinedFeatureUserObjects"); uop->type = oip; ufp = UserFieldNew (); oip = ObjectIdNew (); oip->id = 0; ufp->label = oip; ufp->choice = 6; /* user object */ ufp->data.ptrvalue = (Pointer) origuop; uop->data = ufp; prev = ufp; ufp = UserFieldNew (); oip = ObjectIdNew (); oip->id = 0; ufp->label = oip; ufp->choice = 6; /* user object */ ufp->data.ptrvalue = (Pointer) newuop; prev->next = ufp; return uop; } static Int4 VisitDescriptorsProc (SeqDescrPtr descr, Pointer userdata, VisitDescriptorsFunc callback) { Int4 index = 0; SeqDescrPtr sdp; for (sdp = descr; sdp != NULL; sdp = sdp->next) { if (callback != NULL) { callback (sdp, userdata); } index++; } return index; } NLM_EXTERN Int4 VisitDescriptorsOnBsp (BioseqPtr bsp, Pointer userdata, VisitDescriptorsFunc callback) { Int4 index = 0; if (bsp == NULL) return index; index += VisitDescriptorsProc (bsp->descr, userdata, callback); return index; } NLM_EXTERN Int4 VisitDescriptorsOnSet (BioseqSetPtr bssp, Pointer userdata, VisitDescriptorsFunc callback) { Int4 index = 0; if (bssp == NULL) return index; index += VisitDescriptorsProc (bssp->descr, userdata, callback); return index; } NLM_EXTERN Int4 VisitDescriptorsInSet (BioseqSetPtr bssp, Pointer userdata, VisitDescriptorsFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; index += VisitDescriptorsProc (bssp->descr, userdata, callback); for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitDescriptorsInSep (tmp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitDescriptorsOnSep (SeqEntryPtr sep, Pointer userdata, VisitDescriptorsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitDescriptorsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitDescriptorsOnSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitDescriptorsInSep (SeqEntryPtr sep, Pointer userdata, VisitDescriptorsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitDescriptorsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitDescriptorsInSet (bssp, userdata, callback); } return index; } static Int4 VisitFeaturesProc (SeqAnnotPtr annot, Pointer userdata, VisitFeaturesFunc callback) { Int4 index = 0; SeqAnnotPtr sap; SeqFeatPtr sfp; for (sap = annot; sap != NULL; sap = sap->next) { if (sap->type != 1) continue; for (sfp = (SeqFeatPtr) sap->data; sfp != NULL; sfp = sfp->next) { if (callback != NULL) { callback (sfp, userdata); } index++; } } return index; } NLM_EXTERN Int4 VisitFeaturesOnSap (SeqAnnotPtr sap, Pointer userdata, VisitFeaturesFunc callback) { Int4 index = 0; SeqFeatPtr sfp; if (sap == NULL) return index; if (sap->type != 1) return index; for (sfp = (SeqFeatPtr) sap->data; sfp != NULL; sfp = sfp->next) { if (callback != NULL) { callback (sfp, userdata); } index++; } return index; } NLM_EXTERN Int4 VisitFeaturesOnBsp (BioseqPtr bsp, Pointer userdata, VisitFeaturesFunc callback) { Int4 index = 0; if (bsp == NULL) return index; index += VisitFeaturesProc (bsp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitFeaturesOnSet (BioseqSetPtr bssp, Pointer userdata, VisitFeaturesFunc callback) { Int4 index = 0; if (bssp == NULL) return index; index += VisitFeaturesProc (bssp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitFeaturesInSet (BioseqSetPtr bssp, Pointer userdata, VisitFeaturesFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; index += VisitFeaturesProc (bssp->annot, userdata, callback); for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitFeaturesInSep (tmp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitFeaturesOnSep (SeqEntryPtr sep, Pointer userdata, VisitFeaturesFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitFeaturesOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitFeaturesOnSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitFeaturesInSep (SeqEntryPtr sep, Pointer userdata, VisitFeaturesFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitFeaturesOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitFeaturesInSet (bssp, userdata, callback); } return index; } static Int4 VisitAlignmentsOnDisc (Pointer segs, Pointer userdata, VisitAlignmentsFunc callback) { Int4 index = 0; SeqAlignPtr salp; for (salp = (SeqAlignPtr) segs; salp != NULL; salp = salp->next) { if (callback != NULL) { callback (salp, userdata); } index++; if (salp->segtype == SAS_DISC) { index += VisitAlignmentsOnDisc (salp->segs, userdata, callback); } } return index; } static Int4 VisitAlignmentsProc (SeqAnnotPtr annot, Pointer userdata, VisitAlignmentsFunc callback) { Int4 index = 0; SeqAlignPtr salp; SeqAnnotPtr sap; for (sap = annot; sap != NULL; sap = sap->next) { if (sap->type != 2) continue; for (salp = (SeqAlignPtr) sap->data; salp != NULL; salp = salp->next) { if (callback != NULL) { callback (salp, userdata); } index++; if (salp->segtype == SAS_DISC) { index += VisitAlignmentsOnDisc (salp->segs, userdata, callback); } } } return index; } NLM_EXTERN Int4 VisitAlignmentsOnSap (SeqAnnotPtr sap, Pointer userdata, VisitAlignmentsFunc callback) { Int4 index = 0; SeqAlignPtr salp; if (sap == NULL) return index; if (sap->type != 2) return index; for (salp = (SeqAlignPtr) sap->data; salp != NULL; salp = salp->next) { if (callback != NULL) { callback (salp, userdata); } index++; if (salp->segtype == SAS_DISC) { index += VisitAlignmentsOnDisc (salp->segs, userdata, callback); } } return index; } NLM_EXTERN Int4 VisitAlignmentsOnBsp (BioseqPtr bsp, Pointer userdata, VisitAlignmentsFunc callback) { Int4 index = 0; if (bsp == NULL) return index; index += VisitAlignmentsProc (bsp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitAlignmentsOnSet (BioseqSetPtr bssp, Pointer userdata, VisitAlignmentsFunc callback) { Int4 index = 0; if (bssp == NULL) return index; index += VisitAlignmentsProc (bssp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitAlignmentsInSet (BioseqSetPtr bssp, Pointer userdata, VisitAlignmentsFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; index += VisitAlignmentsProc (bssp->annot, userdata, callback); for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitAlignmentsInSep (tmp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitAlignmentsOnSep (SeqEntryPtr sep, Pointer userdata, VisitAlignmentsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitAlignmentsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitAlignmentsOnSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitAlignmentsInSep (SeqEntryPtr sep, Pointer userdata, VisitAlignmentsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitAlignmentsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitAlignmentsInSet (bssp, userdata, callback); } return index; } static Int4 VisitGraphsProc (SeqAnnotPtr annot, Pointer userdata, VisitGraphsFunc callback) { Int4 index = 0; SeqAnnotPtr sap; SeqGraphPtr sgp; for (sap = annot; sap != NULL; sap = sap->next) { if (sap->type != 3) continue; for (sgp = (SeqGraphPtr) sap->data; sgp != NULL; sgp = sgp->next) { if (callback != NULL) { callback (sgp, userdata); } index++; } } return index; } NLM_EXTERN Int4 VisitGraphsOnSap (SeqAnnotPtr sap, Pointer userdata, VisitGraphsFunc callback) { Int4 index = 0; SeqGraphPtr sgp; if (sap == NULL) return index; if (sap->type != 3) return index; for (sgp = (SeqGraphPtr) sap->data; sgp != NULL; sgp = sgp->next) { if (callback != NULL) { callback (sgp, userdata); } index++; } return index; } NLM_EXTERN Int4 VisitGraphsOnBsp (BioseqPtr bsp, Pointer userdata, VisitGraphsFunc callback) { Int4 index = 0; if (bsp == NULL) return index; index += VisitGraphsProc (bsp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitGraphsOnSet (BioseqSetPtr bssp, Pointer userdata, VisitGraphsFunc callback) { Int4 index = 0; if (bssp == NULL) return index; index += VisitGraphsProc (bssp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitGraphsInSet (BioseqSetPtr bssp, Pointer userdata, VisitGraphsFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; index += VisitGraphsProc (bssp->annot, userdata, callback); for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitGraphsInSep (tmp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitGraphsOnSep (SeqEntryPtr sep, Pointer userdata, VisitGraphsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitGraphsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitGraphsOnSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitGraphsInSep (SeqEntryPtr sep, Pointer userdata, VisitGraphsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitGraphsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitGraphsInSet (bssp, userdata, callback); } return index; } static Int4 VisitAnnotsProc (SeqAnnotPtr annot, Pointer userdata, VisitAnnotsFunc callback) { Int4 index = 0; SeqAnnotPtr sap; for (sap = annot; sap != NULL; sap = sap->next) { if (callback != NULL) { callback (sap, userdata); } index++; } return index; } NLM_EXTERN Int4 VisitAnnotsOnBsp (BioseqPtr bsp, Pointer userdata, VisitAnnotsFunc callback) { Int4 index = 0; if (bsp == NULL) return index; index += VisitAnnotsProc (bsp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitAnnotsOnSet (BioseqSetPtr bssp, Pointer userdata, VisitAnnotsFunc callback) { Int4 index = 0; if (bssp == NULL) return index; index += VisitAnnotsProc (bssp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitAnnotsInSet (BioseqSetPtr bssp, Pointer userdata, VisitAnnotsFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; index += VisitAnnotsProc (bssp->annot, userdata, callback); for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitAnnotsInSep (tmp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitAnnotsOnSep (SeqEntryPtr sep, Pointer userdata, VisitAnnotsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitAnnotsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitAnnotsOnSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitAnnotsInSep (SeqEntryPtr sep, Pointer userdata, VisitAnnotsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitAnnotsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitAnnotsInSet (bssp, userdata, callback); } return index; } static Int4 VisitAuthorsProc (AuthListPtr alp, Pointer userdata, VisitAuthorFunc callback) { AuthorPtr ap; Int4 index = 0; ValNodePtr names; NameStdPtr nsp; PersonIdPtr pid; if (alp == NULL || alp->choice != 1) return index; for (names = alp->names; names != NULL; names = names->next) { ap = names->data.ptrvalue; if (ap == NULL) continue; pid = ap->name; if (pid == NULL || pid->choice != 2) continue; nsp = pid->data; if (nsp == NULL) continue; if (callback != NULL) { callback (nsp, userdata); } index++; } return index; } NLM_EXTERN Int4 VisitAuthorsInPub (PubdescPtr pdp, Pointer userdata, VisitAuthorFunc callback) { CitArtPtr cap; CitBookPtr cbp; CitGenPtr cgp; CitPatPtr cpp; CitSubPtr csp; Int4 index = 0; ValNodePtr vnp; if (pdp == NULL) return index; for (vnp = pdp->pub; vnp != NULL; vnp = vnp->next) { if (vnp->choice == PUB_PMid || vnp->choice == PUB_Muid) continue; if (vnp->data.ptrvalue == NULL) continue; switch (vnp->choice) { case PUB_Gen : cgp = (CitGenPtr) vnp->data.ptrvalue; index += VisitAuthorsProc (cgp->authors, userdata, callback); break; case PUB_Sub : csp = (CitSubPtr) vnp->data.ptrvalue; index += VisitAuthorsProc (csp->authors, userdata, callback); break; case PUB_Article : cap = (CitArtPtr) vnp->data.ptrvalue; index += VisitAuthorsProc (cap->authors, userdata, callback); if (cap->from == 2 || cap->from == 3) { cbp = (CitBookPtr) cap->fromptr; if (cbp != NULL) { index += VisitAuthorsProc (cbp->authors, userdata, callback); } } break; case PUB_Book : cbp = (CitBookPtr) vnp->data.ptrvalue; index += VisitAuthorsProc (cbp->authors, userdata, callback); break; case PUB_Man : cbp = (CitBookPtr) vnp->data.ptrvalue; if (cbp->othertype == 2 && cbp->let_type == 3) { index += VisitAuthorsProc (cbp->authors, userdata, callback); } break; case PUB_Patent : cpp = (CitPatPtr) vnp->data.ptrvalue; index += VisitAuthorsProc (cpp->authors, userdata, callback); index += VisitAuthorsProc (cpp->applicants, userdata, callback); index += VisitAuthorsProc (cpp->assignees, userdata, callback); break; default : break; } } return index; } static Int4 VisitPubdescsProc (SeqDescrPtr descr, SeqAnnotPtr annot, Pointer userdata, VisitPubdescsFunc callback) { Int4 index = 0; PubdescPtr pdp; SeqAnnotPtr sap; SeqDescrPtr sdp; SeqFeatPtr sfp; for (sdp = descr; sdp != NULL; sdp = sdp->next) { if (sdp->choice == Seq_descr_pub) { pdp = (PubdescPtr) sdp->data.ptrvalue; if (pdp != NULL) { if (callback != NULL) { callback (pdp, userdata); } index++; } } } for (sap = annot; sap != NULL; sap = sap->next) { if (sap->type != 1) continue; for (sfp = (SeqFeatPtr) sap->data; sfp != NULL; sfp = sfp->next) { if (sfp->data.choice == SEQFEAT_PUB) { pdp = (PubdescPtr) sfp->data.value.ptrvalue; if (pdp != NULL) { if (callback != NULL) { callback (pdp, userdata); } index++; } } } } return index; } NLM_EXTERN Int4 VisitPubdescsOnBsp (BioseqPtr bsp, Pointer userdata, VisitPubdescsFunc callback) { Int4 index = 0; if (bsp == NULL) return index; index += VisitPubdescsProc (bsp->descr, bsp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitPubdescsOnSet (BioseqSetPtr bssp, Pointer userdata, VisitPubdescsFunc callback) { Int4 index = 0; if (bssp == NULL) return index; index += VisitPubdescsProc (bssp->descr, bssp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitPubdescsInSet (BioseqSetPtr bssp, Pointer userdata, VisitPubdescsFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; index += VisitPubdescsProc (bssp->descr, bssp->annot, userdata, callback); for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitPubdescsInSep (tmp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitPubdescsOnSep (SeqEntryPtr sep, Pointer userdata, VisitPubdescsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitPubdescsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitPubdescsOnSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitPubdescsInSep (SeqEntryPtr sep, Pointer userdata, VisitPubdescsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitPubdescsOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitPubdescsInSet (bssp, userdata, callback); } return index; } static Int4 VisitBioSourcesProc (SeqDescrPtr descr, SeqAnnotPtr annot, Pointer userdata, VisitBioSourcesFunc callback) { BioSourcePtr biop; Int4 index = 0; SeqAnnotPtr sap; SeqDescrPtr sdp; SeqFeatPtr sfp; for (sdp = descr; sdp != NULL; sdp = sdp->next) { if (sdp->choice == Seq_descr_source) { biop = (BioSourcePtr) sdp->data.ptrvalue; if (biop != NULL) { if (callback != NULL) { callback (biop, userdata); } index++; } } } for (sap = annot; sap != NULL; sap = sap->next) { if (sap->type != 1) continue; for (sfp = (SeqFeatPtr) sap->data; sfp != NULL; sfp = sfp->next) { if (sfp->data.choice == SEQFEAT_BIOSRC) { biop = (BioSourcePtr) sfp->data.value.ptrvalue; if (biop != NULL) { if (callback != NULL) { callback (biop, userdata); } index++; } } } } return index; } NLM_EXTERN Int4 VisitBioSourcesOnBsp (BioseqPtr bsp, Pointer userdata, VisitBioSourcesFunc callback) { Int4 index = 0; if (bsp == NULL) return index; index += VisitBioSourcesProc (bsp->descr, bsp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitBioSourcesOnSet (BioseqSetPtr bssp, Pointer userdata, VisitBioSourcesFunc callback) { Int4 index = 0; if (bssp == NULL) return index; index += VisitBioSourcesProc (bssp->descr, bssp->annot, userdata, callback); return index; } NLM_EXTERN Int4 VisitBioSourcesInSet (BioseqSetPtr bssp, Pointer userdata, VisitBioSourcesFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; index += VisitBioSourcesProc (bssp->descr, bssp->annot, userdata, callback); for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitBioSourcesInSep (tmp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitBioSourcesOnSep (SeqEntryPtr sep, Pointer userdata, VisitBioSourcesFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitBioSourcesOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitBioSourcesOnSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitBioSourcesInSep (SeqEntryPtr sep, Pointer userdata, VisitBioSourcesFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; index += VisitBioSourcesOnBsp (bsp, userdata, callback); } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitBioSourcesInSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitBioseqsInSet (BioseqSetPtr bssp, Pointer userdata, VisitBioseqsFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitBioseqsInSep (tmp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitBioseqsInSep (SeqEntryPtr sep, Pointer userdata, VisitBioseqsFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (callback != NULL) { callback (bsp, userdata); } index++; } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitBioseqsInSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitSequencesInSet (BioseqSetPtr bssp, Pointer userdata, Int2 filter, VisitSequencesFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; if (bssp->_class == BioseqseqSet_class_parts) { if (filter != VISIT_PARTS) return index; filter = VISIT_MAINS; } for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitSequencesInSep (tmp, userdata, filter, callback); } return index; } NLM_EXTERN Int4 VisitSequencesInSep (SeqEntryPtr sep, Pointer userdata, Int2 filter, VisitSequencesFunc callback) { BioseqPtr bsp; BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (filter == VISIT_MAINS || (filter == VISIT_NUCS && ISA_na (bsp->mol)) || (filter == VISIT_PROTS && ISA_aa (bsp->mol))) { if (callback != NULL) { callback (bsp, userdata); } index++; } } else if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitSequencesInSet (bssp, userdata, filter, callback); } return index; } NLM_EXTERN Int4 VisitSetsInSet (BioseqSetPtr bssp, Pointer userdata, VisitSetsFunc callback) { Int4 index = 0; SeqEntryPtr tmp; if (bssp == NULL) return index; if (callback != NULL) { callback (bssp, userdata); } index++; for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitSetsInSep (tmp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitSetsInSep (SeqEntryPtr sep, Pointer userdata, VisitSetsFunc callback) { BioseqSetPtr bssp; Int4 index = 0; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; index += VisitSetsInSet (bssp, userdata, callback); } return index; } NLM_EXTERN Int4 VisitElementsInSep (SeqEntryPtr sep, Pointer userdata, VisitElementsFunc callback) { BioseqSetPtr bssp; Int4 index = 0; SeqEntryPtr tmp; if (sep == NULL || sep->data.ptrvalue == NULL) return index; if (IS_Bioseq_set (sep)) { bssp = (BioseqSetPtr) sep->data.ptrvalue; if (bssp == NULL) return index; if (bssp->_class == 7 || (bssp->_class >= 13 && bssp->_class <= 16) || bssp->_class == BioseqseqSet_class_wgs_set || bssp->_class == BioseqseqSet_class_gen_prod_set || bssp->_class == BioseqseqSet_class_small_genome_set) { for (tmp = bssp->seq_set; tmp != NULL; tmp = tmp->next) { index += VisitElementsInSep (tmp, userdata, callback); } return index; } } if (callback != NULL) { callback (sep, userdata); } index++; return index; } NLM_EXTERN Boolean IsPopPhyEtcSet (Uint1 _class) { if (_class == BioseqseqSet_class_mut_set || _class == BioseqseqSet_class_pop_set || _class == BioseqseqSet_class_phy_set || _class == BioseqseqSet_class_eco_set || _class == BioseqseqSet_class_wgs_set || _class == BioseqseqSet_class_small_genome_set) return TRUE; return FALSE; } static Int4 ScanBioseqSetReleaseInt ( CharPtr inputFile, Boolean binary, Boolean compressed, Pointer userdata, ScanBioseqSetFunc callback, Boolean freesep, TNlmMutexPtr mutex ) { AsnIoPtr aip; AsnModulePtr amp; AsnTypePtr atp, atp_bss, atp_se; FILE *fp; Int4 index = 0; SeqEntryPtr sep; #ifdef OS_UNIX Char cmmd [256]; CharPtr gzcatprog; int ret; Boolean usedPopen = FALSE; #endif if (StringHasNoText (inputFile) || callback == NULL) return index; #ifndef OS_UNIX if (compressed) { Message (MSG_ERROR, "Can only decompress on-the-fly on UNIX machines"); return index; } #endif amp = AsnAllModPtr (); if (amp == NULL) { Message (MSG_ERROR, "Unable to load AsnAllModPtr"); return index; } atp_bss = AsnFind ("Bioseq-set"); if (atp_bss == NULL) { Message (MSG_ERROR, "Unable to find ASN.1 type Bioseq-set"); return index; } atp_se = AsnFind ("Bioseq-set.seq-set.E"); if (atp_se == NULL) { Message (MSG_ERROR, "Unable to find ASN.1 type Bioseq-set.seq-set.E"); return index; } #ifdef OS_UNIX if (compressed) { gzcatprog = getenv ("NCBI_UNCOMPRESS_BINARY"); if (gzcatprog != NULL) { sprintf (cmmd, "%s %s", gzcatprog, inputFile); } else { ret = system ("gzcat -h >/dev/null 2>&1"); if (ret == 0) { sprintf (cmmd, "gzcat %s", inputFile); } else if (ret == -1) { Message (MSG_FATAL, "Unable to fork or exec gzcat in ScanBioseqSetRelease"); return index; } else { ret = system ("zcat -h >/dev/null 2>&1"); if (ret == 0) { sprintf (cmmd, "zcat %s", inputFile); } else if (ret == -1) { Message (MSG_FATAL, "Unable to fork or exec zcat in ScanBioseqSetRelease"); return index; } else { Message (MSG_FATAL, "Unable to find zcat or gzcat in ScanBioseqSetRelease - please edit your PATH environment variable"); return index; } } } fp = popen (cmmd, /* binary? "rb" : */ "r"); usedPopen = TRUE; } else { fp = FileOpen (inputFile, binary? "rb" : "r"); } #else fp = FileOpen (inputFile, binary? "rb" : "r"); #endif if (fp == NULL) { Message (MSG_POSTERR, "FileOpen failed for input file '%s'", inputFile); return index; } aip = AsnIoNew (binary? ASNIO_BIN_IN : ASNIO_TEXT_IN, fp, NULL, NULL, NULL); if (aip == NULL) { Message (MSG_ERROR, "AsnIoNew failed for input file '%s'", inputFile); return index; } atp = atp_bss; while ((atp = AsnReadId (aip, amp, atp)) != NULL) { if (atp == atp_se) { if (mutex != NULL) { NlmMutexLockEx (mutex); } SeqMgrHoldIndexing (TRUE); sep = SeqEntryAsnRead (aip, atp); SeqMgrHoldIndexing (FALSE); if (mutex != NULL) { NlmMutexUnlock (*mutex); } callback (sep, userdata); if (freesep) { SeqEntryFree (sep); } index++; } else { AsnReadVal (aip, atp, NULL); } } AsnIoFree (aip, FALSE); #ifdef OS_UNIX if (usedPopen) { pclose (fp); } else { FileClose (fp); } #else FileClose (fp); #endif return index; } NLM_EXTERN Int4 ScanBioseqSetRelease ( CharPtr inputFile, Boolean binary, Boolean compressed, Pointer userdata, ScanBioseqSetFunc callback ) { return ScanBioseqSetReleaseInt (inputFile, binary, compressed, userdata, callback, TRUE, NULL); } static TNlmMutex scan_bioseq_set_release_mutex = NULL; NLM_EXTERN Int4 ScanBioseqSetReleaseMT ( CharPtr inputFile, Boolean binary, Boolean compressed, Pointer userdata, ScanBioseqSetFunc callback ) { return ScanBioseqSetReleaseInt (inputFile, binary, compressed, userdata, callback, FALSE, &scan_bioseq_set_release_mutex); } NLM_EXTERN SeqEntryPtr LIBCALL FreeScanSeqEntryMT ( SeqEntryPtr sep ) { if (sep == NULL) return NULL; NlmMutexLockEx (&scan_bioseq_set_release_mutex); SeqMgrHoldIndexing (TRUE); SeqEntryFree (sep); SeqMgrHoldIndexing (FALSE); NlmMutexUnlock (scan_bioseq_set_release_mutex); return NULL; } NLM_EXTERN Int4 ScanEntrezgeneSetRelease ( CharPtr inputFile, Boolean binary, Boolean compressed, Pointer userdata, ScanEntrezgeneSetFunc callback ) { AsnIoPtr aip; AsnModulePtr amp; AsnTypePtr atp, atp_egs, atp_egse; EntrezgenePtr egp; FILE *fp; Int4 index = 0; #ifdef OS_UNIX Char cmmd [256]; CharPtr gzcatprog; int ret; Boolean usedPopen = FALSE; #endif if (StringHasNoText (inputFile) || callback == NULL) return index; #ifndef OS_UNIX if (compressed) { Message (MSG_ERROR, "Can only decompress on-the-fly on UNIX machines"); return index; } #endif amp = AsnAllModPtr (); if (amp == NULL) { Message (MSG_ERROR, "Unable to load AsnAllModPtr"); return index; } atp_egs = AsnFind ("Entrezgene-Set"); if (atp_egs == NULL) { Message (MSG_ERROR, "Unable to find ASN.1 type Entrezgene-Set"); return index; } atp_egse = AsnFind ("Entrezgene-Set.E"); if (atp_egse == NULL) { Message (MSG_ERROR, "Unable to find ASN.1 type Entrezgene-Set.E"); return index; } #ifdef OS_UNIX if (compressed) { gzcatprog = getenv ("NCBI_UNCOMPRESS_BINARY"); if (gzcatprog != NULL) { sprintf (cmmd, "%s %s", gzcatprog, inputFile); } else { ret = system ("gzcat -h >/dev/null 2>&1"); if (ret == 0) { sprintf (cmmd, "gzcat %s", inputFile); } else if (ret == -1) { Message (MSG_FATAL, "Unable to fork or exec gzcat in ScanEntrezgeneSetRelease"); return index; } else { ret = system ("zcat -h >/dev/null 2>&1"); if (ret == 0) { sprintf (cmmd, "zcat %s", inputFile); } else if (ret == -1) { Message (MSG_FATAL, "Unable to fork or exec zcat in ScanEntrezgeneSetRelease"); return index; } else { Message (MSG_FATAL, "Unable to find zcat or gzcat in ScanEntrezgeneSetRelease - please edit your PATH environment variable"); return index; } } } fp = popen (cmmd, /* binary? "rb" : */ "r"); usedPopen = TRUE; } else { fp = FileOpen (inputFile, binary? "rb" : "r"); } #else fp = FileOpen (inputFile, binary? "rb" : "r"); #endif if (fp == NULL) { Message (MSG_POSTERR, "FileOpen failed for input file '%s'", inputFile); return index; } aip = AsnIoNew (binary? ASNIO_BIN_IN : ASNIO_TEXT_IN, fp, NULL, NULL, NULL); if (aip == NULL) { Message (MSG_ERROR, "AsnIoNew failed for input file '%s'", inputFile); return index; } atp = atp_egs; while ((atp = AsnReadId (aip, amp, atp)) != NULL) { if (atp == atp_egse) { egp = EntrezgeneAsnRead (aip, atp); callback (egp, userdata); EntrezgeneFree (egp); index++; } else { AsnReadVal (aip, atp, NULL); } } AsnIoFree (aip, FALSE); #ifdef OS_UNIX if (usedPopen) { pclose (fp); } else { FileClose (fp); } #else FileClose (fp); #endif return index; } NLM_EXTERN int LIBCALL ObjectIdCompare (ObjectIdPtr a, ObjectIdPtr b) { int rval = 0; Char buf[30]; if (a == b) { rval = 0; } else if (a == NULL) { rval = -1; } else if (b == NULL) { rval = 1; } else if (a->str == NULL && b->str == NULL) { if (a->id < b->id) { rval = -1; } else if (a->id > b->id) { rval = 1; } } else if (a->str == NULL) { sprintf (buf, "%d", a->id); rval = StringCmp (buf, b->str); } else if (b->str == NULL) { sprintf (buf, "%d", b->id); rval = StringCmp (a->str, buf); } else { rval = StringCmp (a->str, b->str); } return rval; } /***************************************************************************** * * DbtagMatch(a, b) * *****************************************************************************/ NLM_EXTERN int LIBCALL DbtagCompare (DbtagPtr a, DbtagPtr b) { int rval = 0; if (a == b) { rval = 0; } else if (a == NULL) { rval = -1; } else if (b == NULL) { rval = 1; } else if ((rval = StringICmp (a->db, b->db)) == 0) { rval = ObjectIdCompare (a->tag, b->tag); } return rval; } static int LIBCALLBACK SortVnpByDbtag (VoidPtr ptr1, VoidPtr ptr2) { ValNodePtr vnp1; ValNodePtr vnp2; if (ptr1 != NULL && ptr2 != NULL) { vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 != NULL && vnp2 != NULL) { return DbtagCompare (vnp1->data.ptrvalue, vnp2->data.ptrvalue); } } return 0; } NLM_EXTERN int LIBCALL OrgModSetCompare (OrgModPtr mod1, OrgModPtr mod2) { int rval = 0; while (mod1 != NULL && mod2 != NULL && rval == 0) { if (mod1->subtype < mod2->subtype) { rval = -1; } else if (mod1->subtype > mod2->subtype) { rval = 1; } else if ((rval = StringCmp (mod1->subname, mod2->subname)) == 0 && (rval = StringCmp (mod1->attrib, mod2->attrib)) == 0) { mod1 = mod1->next; mod2 = mod2->next; } } if (rval == 0) { if (mod1 == NULL && mod2 == NULL) { rval = 0; } else if (mod1 == NULL) { rval = -1; } else if (mod2 == NULL) { rval = 1; } } return rval; } NLM_EXTERN int LIBCALL OrgNameCompare (OrgNamePtr onp1, OrgNamePtr onp2) { int rval = 0; while (onp1 != NULL && onp2 != NULL && rval == 0) { if ((rval = OrgModSetCompare(onp1->mod, onp2->mod)) != 0 || (rval = StringCmp (onp1->lineage, onp2->lineage)) != 0 || (rval = StringCmp (onp1->div, onp2->div)) != 0 || (rval = StringCmp (onp1->attrib, onp2->attrib)) != 0) { /* no further processing */ } else if (onp1->choice < onp2->choice) { rval = -1; } else if (onp1->choice > onp2->choice) { rval = 1; } else if (onp1->gcode < onp2->gcode) { rval = -1; } else if (onp1->gcode > onp2->gcode) { rval = 1; } else if (onp1->mgcode < onp2->mgcode) { rval = -1; } else if (onp1->mgcode > onp2->mgcode) { rval = 1; } else if (onp1->pgcode < onp2->pgcode) { rval = -1; } else if (onp1->pgcode > onp2->pgcode) { rval = 1; } onp1 = onp1->next; onp2 = onp2->next; } if (rval == 0) { if (onp1 == NULL && onp2 == NULL) { rval = 0; } else if (onp1 == NULL) { rval = -1; } else if (onp2 == NULL) { rval = 1; } } return rval; } /***************************************************************************** * * OrgRefCompare (orp1, orp2) * *****************************************************************************/ NLM_EXTERN int LIBCALL OrgRefCompare (OrgRefPtr orp1, OrgRefPtr orp2) { int rval = 0; if (orp1 == NULL && orp2 == NULL) { return 0; } else if (orp1 == NULL) { return -1; } else if (orp2 == NULL) { return 1; } else if ((rval = StringCmp (orp1->taxname, orp2->taxname)) != 0) { return rval; } else if ((rval = StringCmp (orp1->common, orp2->common)) != 0) { return rval; } else if ((rval = ValNodeCompare (orp1->syn, orp2->syn, SortVnpByString)) != 0) { return rval; } else if ((rval = ValNodeCompare (orp1->db, orp2->db, SortVnpByDbtag)) != 0) { return rval; } else { rval = OrgNameCompare (orp1->orgname, orp2->orgname); } return rval; } static Boolean DoStringsMatch (CharPtr str1, CharPtr str2, Boolean case_sensitive) { Boolean rval = FALSE; if (case_sensitive) { if (StringCmp (str1, str2) == 0) { rval = TRUE; } } else if (StringICmp (str1, str2) == 0) { rval = TRUE; } return rval; } static Boolean DoGBQualListsMatch (GBQualPtr gbq1, GBQualPtr gbq2, Boolean case_sensitive) { Boolean rval = TRUE; while (rval && gbq1 != NULL && gbq2 != NULL) { if (!DoStringsMatch (gbq1->qual, gbq2->qual, case_sensitive)) { rval = FALSE; } else if (!DoStringsMatch (gbq1->val, gbq2->val, case_sensitive)) { rval = FALSE; } else { gbq1 = gbq1->next; gbq2 = gbq2->next; } } if (gbq1 != NULL || gbq2 != NULL) { rval = FALSE; } return rval; } static Boolean CheckBioseqForPartial (BioseqPtr bsp, BoolPtr partial5, BoolPtr partial3) { SeqMgrDescContext context; SeqDescrPtr sdp; MolInfoPtr mip; Boolean rval = FALSE; if (bsp == NULL) { return FALSE; } if (partial5 != NULL) { *partial5 = FALSE; } if (partial3 != NULL) { *partial3 = FALSE; } sdp = SeqMgrGetNextDescriptor (bsp, NULL, Seq_descr_molinfo, &context); if (sdp != NULL && (mip = (MolInfoPtr) sdp->data.ptrvalue) != NULL) { /* partial 5 */ if (mip->completeness == 3 || mip->completeness == 5) { if (partial5 != NULL) { *partial5 = TRUE; } rval = TRUE; } /* partial 3 */ if (mip->completeness == 4 || mip->completeness == 5) { if (partial3 != NULL) { *partial3 = TRUE; } rval = TRUE; } if (mip->completeness == 2) { rval = TRUE; } } return rval; } static Boolean ProductsMatch (SeqLocPtr slp1, SeqLocPtr slp2, Boolean case_sensitive, Boolean ignore_partial) { BioseqPtr bsp1, bsp2; Int2 ctr, pos1, pos2; Char buf1[51]; Char buf2[51]; Int4 len = 50; SeqFeatPtr sfp1, sfp2; SeqMgrFeatContext fcontext1, fcontext2; Boolean partial5_1, partial5_2, partial3_1, partial3_2; if (slp1 == NULL && slp2 == NULL) { return TRUE; } else if (slp1 == NULL || slp2 == NULL) { return FALSE; } else if (SeqLocCompare (slp1, slp2) == SLC_A_EQ_B) { return TRUE; } else { bsp1 = BioseqFindFromSeqLoc (slp1); bsp2 = BioseqFindFromSeqLoc (slp2); if (bsp1 == NULL || bsp2 == NULL) { /* can't compare, assume they don't match */ return FALSE; } else if (bsp1->length != bsp2->length) { return FALSE; } else { CheckBioseqForPartial (bsp1, &partial5_1, &partial3_1); CheckBioseqForPartial (bsp2, &partial5_2, &partial3_2); if (!ignore_partial && ((partial5_1 && !partial5_2) || (!partial5_1 && partial5_2) || (partial3_1 && !partial3_2) || (!partial3_1 && partial3_2))) { return FALSE; } /* check that translation sequences match */ pos1 = 0; pos2 = 0; if (ignore_partial) { if (partial5_1 || partial5_2) { pos1++; pos2++; } } while (pos1 < bsp1->length && pos2 < bsp2->length) { ctr = SeqPortStreamInt (bsp1, pos1, MIN(pos1 + len - 1, bsp1->length - 1), Seq_strand_plus, STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, (Pointer) buf1, NULL); ctr = SeqPortStreamInt (bsp2, pos2, MIN(pos2 + len - 1, bsp2->length - 1), Seq_strand_plus, STREAM_EXPAND_GAPS | STREAM_CORRECT_INVAL, (Pointer) buf2, NULL); if (StringNCmp (buf1, buf2, ctr) != 0) { return FALSE; } pos1 += len; pos2 += len; } /* now check that protein features match */ sfp1 = SeqMgrGetNextFeature (bsp1, NULL, 0, 0, &fcontext1); sfp2 = SeqMgrGetNextFeature (bsp2, NULL, 0, 0, &fcontext2); while (sfp1 != NULL && sfp2 != NULL) { if (!DoFeaturesMatch (sfp1, sfp2, TRUE, case_sensitive, ignore_partial)) { return FALSE; } sfp1 = SeqMgrGetNextFeature (bsp1, sfp1, SEQFEAT_PROT, 0, &fcontext1); sfp2 = SeqMgrGetNextFeature (bsp2, sfp2, SEQFEAT_PROT, 0, &fcontext2); } if (sfp1 != NULL || sfp2 != NULL) { return FALSE; } else { return TRUE; } } } } static Boolean DoLocationPartialsMatch (SeqLocPtr slp1, SeqLocPtr slp2) { Boolean partial5_1, partial3_1, partial1; Boolean partial5_2, partial3_2, partial2; partial1 = CheckSeqLocForPartial (slp1, &partial5_1, &partial3_1); partial2 = CheckSeqLocForPartial (slp2, &partial5_2, &partial3_2); if ((partial1 && !partial2) || (!partial1 && partial2)) { return FALSE; } if ((partial5_1 && !partial5_2) || (!partial5_1 && partial5_2)) { return FALSE; } if ((partial3_1 && !partial3_2) || (!partial3_1 && partial3_2)) { return FALSE; } return TRUE; } static Boolean DoLocationsMatch (SeqLocPtr slp1, SeqLocPtr slp2, Boolean allow_different_sequences, Boolean ignore_partial) { SeqLocPtr slp_tmp1, slp_tmp2; if (slp1 == NULL && slp2 == NULL) { return TRUE; } else if (slp1 == NULL || slp2 == NULL) { return FALSE; } if (!ignore_partial && !DoLocationPartialsMatch (slp1, slp2)) { return FALSE; } if (allow_different_sequences) { for (slp_tmp1 = SeqLocFindNext (slp1, NULL), slp_tmp2 = SeqLocFindNext (slp2, NULL); slp_tmp1 != NULL && slp_tmp2 != NULL; slp_tmp1 = SeqLocFindNext (slp1, slp_tmp1), slp_tmp2 = SeqLocFindNext (slp2, slp_tmp2)) { if (SeqLocStart (slp_tmp1) != SeqLocStart (slp_tmp2) || SeqLocStop (slp_tmp1) != SeqLocStop (slp_tmp2) || (!ignore_partial && !DoLocationPartialsMatch (slp_tmp1, slp_tmp2))) { return FALSE; } } } else if (SeqLocCompare (slp1, slp2) != SLC_A_EQ_B) { return FALSE; } return TRUE; } static Boolean DoCdRegionsMatch (CdRegionPtr crp1, CdRegionPtr crp2) { if (crp1 == NULL && crp2 == NULL) { return TRUE; } else if (crp1 == NULL || crp2 == NULL) { return FALSE; } else if ((crp1->orf && !crp2->orf) || (!crp1->orf && crp2->orf)){ return FALSE; } else if ((crp1->conflict && !crp2->conflict) || (!crp1->conflict && crp2->conflict)){ return FALSE; } else if (crp1->gaps != crp2->gaps) { return FALSE; } else if (crp1->mismatch != crp2->mismatch) { return FALSE; } else if (crp1->stops != crp2->stops) { return FALSE; } else if ((crp1->genetic_code == NULL && crp2->genetic_code != NULL) || (crp1->genetic_code != NULL && crp2->genetic_code == NULL) || (crp1->genetic_code != NULL && crp2->genetic_code != NULL && !AsnIoMemComp (crp1->genetic_code, crp2->genetic_code, (AsnWriteFunc) GeneticCodeAsnWrite))) { return FALSE; } else if ((crp1->code_break == NULL && crp2->code_break != NULL) || (crp1->code_break != NULL && crp2->code_break == NULL) || (crp1->code_break != NULL && crp2->code_break != NULL && !AsnIoMemComp (crp1->code_break, crp2->code_break, (AsnWriteFunc) CodeBreakAsnWrite))) { return FALSE; } else if (crp1->frame != crp2->frame) { if ((crp1->frame == 0 || crp1->frame == 1) && (crp2->frame == 0 || crp2->frame == 1)) { /* both effectively frame 1, ignore this difference */ } else { return FALSE; } } return TRUE; } static Boolean DoesSeqFeatDataMatch (ChoicePtr d1, ChoicePtr d2) { if (d1 == NULL && d2 == NULL) { return TRUE; } else if (d1 == NULL || d2 == NULL) { return FALSE; } else if (d1->choice != d2->choice) { return FALSE; } else if (d1->choice == SEQFEAT_CDREGION) { return DoCdRegionsMatch(d1->value.ptrvalue, d2->value.ptrvalue); } else { return AsnIoMemComp(d1, d2, (AsnWriteFunc) SeqFeatDataAsnWrite); } } NLM_EXTERN Boolean DoFeaturesMatch (SeqFeatPtr sfp1, SeqFeatPtr sfp2, Boolean allow_different_sequences, Boolean case_sensitive, Boolean ignore_partial) { if (sfp1 == NULL && sfp2 == NULL) { return TRUE; } else if (sfp1 == NULL || sfp2 == NULL) { return FALSE; } if (sfp1->data.choice != sfp2->data.choice) { return FALSE; } else if (sfp1->idx.subtype != sfp2->idx.subtype) { return FALSE; } else if (!ignore_partial && ((sfp1->partial && !sfp2->partial) || (!sfp1->partial && sfp2->partial))) { return FALSE; } else if ((sfp1->pseudo && !sfp2->pseudo) || (!sfp1->pseudo && sfp2->pseudo)) { return FALSE; } else if ((sfp1->excpt && !sfp2->excpt) || (!sfp1->excpt && sfp2->excpt)) { return FALSE; } else if (!DoLocationsMatch (sfp1->location, sfp2->location, allow_different_sequences, ignore_partial)) { return FALSE; } else if (!DoStringsMatch (sfp1->comment, sfp2->comment, case_sensitive)) { return FALSE; } else if (!DoStringsMatch (sfp1->title, sfp2->title, case_sensitive)) { return FALSE; } else if (sfp1->ext != NULL || sfp2->ext != NULL) { return FALSE; } else if (sfp1->exts != NULL || sfp2->exts != NULL) { return FALSE; } else if (!DoStringsMatch (sfp1->except_text, sfp2->except_text, case_sensitive)) { return FALSE; } else if (sfp1->exp_ev != sfp2->exp_ev) { return FALSE; } else if (!DoGBQualListsMatch (sfp1->qual, sfp2->qual, case_sensitive)) { return FALSE; } else if ((sfp1->cit != NULL || sfp2->cit != NULL) && PubMatch (sfp1->cit, sfp2->cit) != 0) { return FALSE; } else if (!DbxrefsMatch (sfp1->dbxref, sfp2->dbxref, case_sensitive)) { return FALSE; } else if (!DoesSeqFeatDataMatch(&(sfp1->data), &(sfp2->data))) { return FALSE; } else if (!XrefsMatch (sfp1->xref, sfp2->xref)) { return FALSE; } else if (!ProductsMatch (sfp1->product, sfp2->product, case_sensitive, ignore_partial)) { return FALSE; } else { return TRUE; } } NLM_EXTERN void CleanupStringsForOneDescriptor (SeqDescPtr sdp, SeqEntryPtr sep) { Boolean stripSerial = FALSE; Boolean isEmblOrDdbj = FALSE; if (sdp == NULL) { return; } SeqEntryExplore (sep, (Pointer) &stripSerial, CheckForSwissProtID); SeqEntryExplore (sep, (Pointer) &isEmblOrDdbj, CheckForEmblDdbjID); if (sdp->choice == Seq_descr_pub) { FlattenPubdesc (sdp->data.ptrvalue, NULL); } CleanupDescriptorStrings (sdp, stripSerial, TRUE, NULL, isEmblOrDdbj); } NLM_EXTERN void CleanupOneSeqFeat (SeqFeatPtr sfp) { Boolean isEmblOrDdbj = FALSE; Boolean isJscan = FALSE; Boolean stripSerial = TRUE; ValNodePtr publist = NULL; SeqEntryPtr sep; if (sfp->idx.entityID == 0) { return; } sep = GetTopSeqEntryForEntityID (sfp->idx.entityID); SeqEntryExplore (sep, (Pointer) &stripSerial, CheckForSwissProtID); SeqEntryExplore (sep, (Pointer) &isEmblOrDdbj, CheckForEmblDdbjID); SeqEntryExplore (sep, (Pointer) &isJscan, CheckForJournalScanID); FlattenSfpCit (sfp, NULL); CleanUpSeqFeat (sfp, isEmblOrDdbj, isJscan, stripSerial, TRUE, &publist); if (publist != NULL) { ChangeCitsOnFeats (sfp, publist); } ValNodeFreeData (publist); } /* special cases for chloroplast genetic code until implemented in taxonomy database */ typedef struct pgorg { CharPtr organism; Uint1 pgcode; } PgOrg; static PgOrg pgOrgList [] = { { "Chromera velia", 4 } , { NULL, 0 } }; typedef struct pglin { CharPtr lineage; Uint1 pgcode; } PgLin; static PgLin pgLinList [] = { { "Eukaryota; Alveolata; Apicomplexa; Coccidia; ", 4 } , { NULL, 0 } }; NLM_EXTERN Uint1 GetSpecialPlastidGenCode ( CharPtr taxname, CharPtr lineage ) { Int2 i; size_t max; Uint1 pgcode = 0; if (StringDoesHaveText (taxname)) { for (i = 0; pgOrgList [i].organism != NULL; i++) { if (StringICmp (taxname, pgOrgList [i].organism) != 0) continue; pgcode = pgOrgList [i].pgcode; } } if (StringDoesHaveText (lineage)) { for (i = 0; pgLinList [i].lineage != NULL; i++) { max = StringLen (pgLinList [i].lineage); if (StringNICmp (lineage, pgLinList [i].lineage, max) != 0) continue; pgcode = pgLinList [i].pgcode; } } if (pgcode == 11) { pgcode = 0; } return pgcode; } static void TrimStopsFromCompleteCodingRegionsCallback (SeqFeatPtr sfp, Pointer data) { Boolean p5, p3; BioseqPtr protbsp; CharPtr prot_str; Int4 len; /* variables for shortening protein features */ SeqFeatPtr prot_sfp; SeqMgrFeatContext fcontext; SeqIntPtr sintp; /* variables for logging */ LogInfoPtr lip; Char id_buf[100]; if (sfp == NULL || sfp->data.choice != SEQFEAT_CDREGION || sfp->product == NULL) { return; } CheckSeqLocForPartial (sfp->location, &p5, &p3); if (p3) { return; } protbsp = BioseqFindFromSeqLoc (sfp->product); if (protbsp == NULL) { return; } prot_str = GetSequenceByBsp (protbsp); if (prot_str == NULL || (len = StringLen (prot_str)) == 0 || prot_str[len - 1] != '*') { prot_str = MemFree (prot_str); return; } BSSeek ((ByteStorePtr) protbsp->seq_data, -1, SEEK_END); BSDelete ((ByteStorePtr) protbsp->seq_data, 1); protbsp->length -= 1; prot_str = MemFree (prot_str); for (prot_sfp = SeqMgrGetNextFeature (protbsp, NULL, 0, 0, &fcontext); prot_sfp != NULL; prot_sfp = SeqMgrGetNextFeature (protbsp, prot_sfp, 0, 0, &fcontext)) { if (prot_sfp->location != NULL && prot_sfp->location->choice == SEQLOC_INT && (sintp = (SeqIntPtr)prot_sfp->location->data.ptrvalue) != NULL) { if (sintp->to > protbsp->length - 1) { sintp->to = protbsp->length - 1; } } } lip = (LogInfoPtr) data; if (lip != NULL) { if (lip->fp != NULL) { SeqIdWrite (SeqIdFindBest (protbsp->id, SEQID_GENBANK), id_buf, PRINTID_FASTA_SHORT, sizeof (id_buf) - 1); fprintf (lip->fp, "Trimmed trailing * from %s\n", id_buf); } lip->data_in_log = TRUE; } } NLM_EXTERN Boolean TrimStopsFromCompleteCodingRegions (SeqEntryPtr sep, FILE *log_fp) { LogInfoData lid; MemSet (&lid, 0, sizeof (LogInfoData)); lid.fp = log_fp; VisitFeaturesInSep (sep, &lid, TrimStopsFromCompleteCodingRegionsCallback); return lid.data_in_log; } NLM_EXTERN void FixCapitalizationInTitle (CharPtr PNTR pTitle, Boolean first_is_upper, ValNodePtr org_names) { if (pTitle == NULL) return; ResetCapitalization (first_is_upper, *pTitle); FixAbbreviationsInElement (pTitle); FixOrgNamesInString (*pTitle, org_names); } typedef struct structuredcommentconversion { Int4 num_converted; Int4 num_unable_to_convert; } StructuredCommentConversionData, PNTR StructuredCommentConversionPtr; static void CommentWithSpacesToStructuredCommentCallback (SeqDescPtr sdp, Pointer userdata) { UserObjectPtr uop; CharPtr str, start, stop; Int4 len; UserFieldPtr ufp = NULL, prev_ufp = NULL; StructuredCommentConversionPtr sd; if (sdp == NULL || sdp->choice != Seq_descr_comment || StringHasNoText (sdp->data.ptrvalue)) { return; } uop = UserObjectNew (); uop->type = ObjectIdNew (); uop->type->str = StringSave ("StructuredComment"); start = sdp->data.ptrvalue; while (*start != 0) { stop = start + StringCSpn (start, " ~"); while (*stop != 0 && *stop != '~' && !isspace (*(stop + 1)) && *(stop + 1) != 0) { stop = stop + 1 + StringCSpn (stop + 1, " ~"); } len = 1 + stop - start; str = (CharPtr) MemNew (sizeof (Char) * len); StringNCpy (str, start, len - 1); str[len - 1] = 0; if (ufp == NULL) { /* add new field */ ufp = UserFieldNew (); if (prev_ufp == NULL) { uop->data = ufp; } else { prev_ufp->next = ufp; } ufp->label = ObjectIdNew (); ufp->label->str = str; } else { /* add value to last field */ ufp->choice = 1; ufp->data.ptrvalue = str; prev_ufp = ufp; ufp = NULL; } if (*stop == 0) { start = stop; } else { start = stop + 1 + StringSpn (stop + 1, " "); } } if (prev_ufp == NULL) { uop = UserObjectFree (uop); return; } sd = (StructuredCommentConversionPtr) userdata; if (ufp == NULL) { sdp->data.ptrvalue = MemFree (sdp->data.ptrvalue); sdp->data.ptrvalue = uop; sdp->choice = Seq_descr_user; if (sd != NULL) { sd->num_converted++; } } else { uop = UserObjectFree (uop); if (sd != NULL) { sd->num_unable_to_convert++; } } } NLM_EXTERN Int4 ConvertCommentsWithSpacesToStructuredCommentsForSeqEntry (SeqEntryPtr sep) { StructuredCommentConversionData sd; MemSet (&sd, 0, sizeof (StructuredCommentConversionData)); VisitDescriptorsInSep (sep, &sd, CommentWithSpacesToStructuredCommentCallback); return sd.num_unable_to_convert; } NLM_EXTERN void RemoveFeatureLink (SeqFeatPtr sfp1, SeqFeatPtr sfp2) { SeqFeatXrefPtr xref, next, PNTR prevlink; ObjectIdPtr oip; SeqFeatPtr link_sfp; Char buf [32]; CharPtr str = NULL; if (sfp1 == NULL) return; prevlink = (SeqFeatXrefPtr PNTR) &(sfp1->xref); xref = sfp1->xref; while (xref != NULL) { next = xref->next; link_sfp = NULL; if (xref->id.choice == 3) { oip = (ObjectIdPtr) xref->id.value.ptrvalue; if (oip != NULL) { if (StringDoesHaveText (oip->str)) { str = oip->str; } else { sprintf (buf, "%ld", (long) oip->id); str = buf; } link_sfp = SeqMgrGetFeatureByFeatID (sfp1->idx.entityID, NULL, str, NULL, NULL); } } if (link_sfp == sfp2) { *prevlink = xref->next; xref->next = NULL; MemFree (xref); } else { prevlink = (SeqFeatXrefPtr PNTR) &(xref->next); } xref = next; } } NLM_EXTERN void LinkTwoFeatures (SeqFeatPtr dst, SeqFeatPtr sfp) { ChoicePtr cp; ObjectIdPtr oip; SeqFeatXrefPtr xref, prev_xref, next_xref; SeqFeatPtr old_match; if (dst == NULL || sfp == NULL) return; cp = &(dst->id); if (cp == NULL) return; if (cp->choice == 3) { /* don't create a duplicate xref, remove links to other features */ xref = sfp->xref; prev_xref = NULL; while (xref != NULL) { next_xref = xref->next; if (xref->id.choice == 3 && xref->id.value.ptrvalue != NULL) { if (ObjectIdMatch (cp->value.ptrvalue, xref->id.value.ptrvalue)) { /* already have this xref */ return; } else { old_match = SeqMgrGetFeatureByFeatID (sfp->idx.entityID, NULL, NULL, xref, NULL); RemoveFeatureLink (sfp, old_match); RemoveFeatureLink (old_match, sfp); } } else { prev_xref = xref; } xref = next_xref; } oip = (ObjectIdPtr) cp->value.ptrvalue; if (oip != NULL) { oip = AsnIoMemCopy (oip, (AsnReadFunc) ObjectIdAsnRead, (AsnWriteFunc) ObjectIdAsnWrite); if (oip != NULL) { xref = SeqFeatXrefNew (); if (xref != NULL) { xref->id.choice = 3; xref->id.value.ptrvalue = (Pointer) oip; xref->next = sfp->xref; sfp->xref = xref; } } } } } static void MakeFeatureXrefsFromProteinIdQualsCallback (SeqFeatPtr sfp, Pointer data) { GBQualPtr gbq; SeqIdPtr sip; BioseqPtr pbsp; SeqFeatPtr cds; CharPtr product; ProtRefPtr prp; SeqEntryPtr sep; if (sfp == NULL || sfp->idx.subtype != FEATDEF_mRNA || (sep = (SeqEntryPtr) data) == NULL) { return; } for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) { if (StringICmp (gbq->qual, "protein_id") == 0 || StringICmp (gbq->qual, "orig_protein_id") == 0) { sip = CreateSeqIdFromText (gbq->val, sep); pbsp = BioseqFind (sip); cds = SeqMgrGetCDSgivenProduct (pbsp, NULL); if (cds != NULL) { LinkTwoFeatures (cds, sfp); LinkTwoFeatures (sfp, cds); product = GetRNAProductString(sfp, NULL); if (StringHasNoText (product)) { prp = GetProtRefForFeature (cds); if (prp != NULL && prp->name != NULL && !StringHasNoText (prp->name->data.ptrvalue)) { SetRNAProductString (sfp, NULL, prp->name->data.ptrvalue, ExistingTextOption_replace_old); } } product = MemFree (product); } } } } NLM_EXTERN void MakeFeatureXrefsFromProteinIdQuals (SeqEntryPtr sep) { /* assign feature IDs, so that we can create xrefs that use them */ AssignFeatureIDs (sep); VisitFeaturesInSep (sep, (Pointer) sep, MakeFeatureXrefsFromProteinIdQualsCallback); } static void MakeFeatureXrefsFromTranscriptIdQualsCallback (SeqFeatPtr sfp, Pointer data) { GBQualPtr gbq; SeqIdPtr sip; BioseqPtr pbsp; SeqFeatPtr cds; CharPtr product; ProtRefPtr prp; SeqEntryPtr sep; if (sfp == NULL || sfp->idx.subtype != FEATDEF_mRNA || (sep = (SeqEntryPtr) data) == NULL) { return; } for (gbq = sfp->qual; gbq != NULL; gbq = gbq->next) { if (StringICmp (gbq->qual, "transcript_id") == 0 || StringICmp (gbq->qual, "orig_transcript_id") == 0) { sip = CreateSeqIdFromText (gbq->val, sep); pbsp = BioseqFind (sip); cds = SeqMgrGetCDSgivenProduct (pbsp, NULL); if (cds != NULL) { LinkTwoFeatures (cds, sfp); LinkTwoFeatures (sfp, cds); product = GetRNAProductString(sfp, NULL); if (StringHasNoText (product)) { prp = GetProtRefForFeature (cds); if (prp != NULL && prp->name != NULL && !StringHasNoText (prp->name->data.ptrvalue)) { SetRNAProductString (sfp, NULL, prp->name->data.ptrvalue, ExistingTextOption_replace_old); } } product = MemFree (product); } } } } NLM_EXTERN void MakeFeatureXrefsFromTranscriptIdQuals (SeqEntryPtr sep) { /* assign feature IDs, so that we can create xrefs that use them */ AssignFeatureIDs (sep); VisitFeaturesInSep (sep, (Pointer) sep, MakeFeatureXrefsFromTranscriptIdQualsCallback); } static void FinishHalfXrefsCallback (SeqFeatPtr sfp, Pointer data) { SeqFeatPtr other; SeqFeatXrefPtr xref, xref_other; Boolean has_other_xref; if (sfp == NULL) { return; } xref = sfp->xref; while (xref != NULL) { if (xref->id.choice == 3) { other = SeqMgrGetFeatureByFeatID (sfp->idx.entityID, NULL, NULL, xref, NULL); if (other != NULL) { xref_other = other->xref; has_other_xref = FALSE; while (xref_other != NULL && !has_other_xref) { if (xref_other->id.choice == 3) { has_other_xref = TRUE; } xref_other = xref_other->next; } if (!has_other_xref) { LinkTwoFeatures (sfp, other); } } } xref = xref->next; } } NLM_EXTERN void FinishHalfXrefs (SeqEntryPtr sep) { VisitFeaturesInSep (sep, (Pointer) sep, FinishHalfXrefsCallback); } NLM_EXTERN Uint1 GetAaFromtRNA (tRNAPtr trp) { Uint1 aa; Uint1 from; SeqMapTablePtr smtp; if (trp == NULL) { return 0; } aa = 0; if (trp->aatype == 2) { aa = trp->aa; } else { from = 0; switch (trp->aatype) { case 0: from = 0; break; case 1: from = Seq_code_iupacaa; break; case 2: from = Seq_code_ncbieaa; break; case 3: from = Seq_code_ncbi8aa; break; case 4: from = Seq_code_ncbistdaa; break; default: break; } smtp = SeqMapTableFind (Seq_code_ncbieaa, from); if (smtp != NULL) { aa = SeqMapTableConvert (smtp, trp->aa); } } return aa; } NLM_EXTERN CharPtr GetCodesFortRNA (SeqFeatPtr sfp, Int2 *pCode) { BioseqPtr bsp; Int2 code = 0; GeneticCodePtr gncp; ValNodePtr vnp; CharPtr codes = NULL; if (sfp == NULL) { return NULL; } /* find genetic code table */ bsp = GetBioseqGivenSeqLoc (sfp->location, sfp->idx.entityID); BioseqToGeneticCode (bsp, &code, NULL, NULL, NULL, 0, NULL); gncp = GeneticCodeFind (code, NULL); if (gncp == NULL) { gncp = GeneticCodeFind (1, NULL); code = 1; } if (gncp != NULL) { for (vnp = (ValNodePtr) gncp->data.ptrvalue; vnp != NULL; vnp = vnp->next) { if (vnp->choice != 3) continue; codes = (CharPtr) vnp->data.ptrvalue; break; } } if (pCode != NULL) { *pCode = code; } return codes; } static Boolean DoesCodonMatchAminoAcid (Uint1 aa, Uint1 index, CharPtr codes) { Uint1 taa; Boolean rval = FALSE; if (aa == 0 || aa == 255 || codes == NULL) { return TRUE; } taa = codes [index]; if (taa == aa) { rval = TRUE; } /* selenocysteine normally uses TGA (14), so ignore without requiring exception in record */ else if (aa == 'U' && taa == '*' && index == 14) { rval = TRUE; } /* pyrrolysine normally uses TAG (11) in archaebacteria, ignore without requiring exception */ else if (aa == 'O' && taa == '*' && index == 11) { rval = TRUE; } /* TAA (10) is not yet known to be used for an exceptional amino acid, but the night is young */ return rval; } static Boolean IsATGC (Char ch) { if (ch == 'A' || ch == 'T' || ch == 'G' || ch == 'C') { return TRUE; } else { return FALSE; } } static Char s_comp (Char ch) { if (ch == 'A') { return 'T'; } else if (ch == 'G') { return 'C'; } else if (ch == 'C') { return 'G'; } else if (ch == 'T') { return 'A'; } else { return 'N'; } } static CharPtr GetFlipCodonLoggingInfo (SeqFeatPtr sfp) { SeqFeatPtr gene = NULL; GeneRefPtr grp = NULL; ValNode vn; CharPtr txt = NULL; GetGeneInfoForFeature (sfp, &grp, &gene); if (grp != NULL && !StringHasNoText (grp->locus_tag)) { txt = StringSave (grp->locus_tag); } else { MemSet (&vn, 0, sizeof (ValNode)); vn.choice = OBJ_SEQFEAT; vn.data.ptrvalue = sfp; txt = GetDiscrepancyItemText (&vn); } return txt; } static Int4 CountCodonsRecognized (tRNAPtr trp) { Int4 num = 0, i; if (trp == NULL) { return 0; } for (i = 0; i < 6; i++) { if (trp->codon [i] < 64) { num++; } } return num; } static Int4 CountMatchingCodons (tRNAPtr trp, Uint1 aa, CharPtr codes) { Int4 num = 0, i; if (trp == NULL) { return 0; } for (i = 0; i < 6; i++) { if (trp->codon [i] < 64) { if (DoesCodonMatchAminoAcid (aa, trp->codon[i], codes)) { num++; } } } return num; } static Int4 CountFlippableCodons (tRNAPtr trp, Uint1 aa, CharPtr codes, Int2 code) { Int4 num = 0, i; Int2 index; Uint1 codon [4]; Uint1 rcodon [4]; if (trp == NULL) { return 0; } /* Note - it is important to set the fourth character in the codon array to NULL * because CodonForIndex only fills in the three characters of actual codon, * so if you StringCpy the codon array and the NULL character is not found after * the three codon characters, you will write in memory you did not intend to. */ codon [3] = 0; rcodon [3] = 0; for (i = 0; i < 6; i++) { if (trp->codon [i] < 64 && !DoesCodonMatchAminoAcid (aa, trp->codon[i], codes) && CodonForIndex (trp->codon [i], Seq_code_iupacna, codon) && IsATGC(codon[0]) && IsATGC(codon[1]) && IsATGC(codon[2])) { rcodon[0] = s_comp(codon[2]); rcodon[1] = s_comp(codon[1]); rcodon[2] = s_comp(codon[0]); index = IndexForCodon (rcodon, code); if (index < 64 && DoesCodonMatchAminoAcid(aa, index, codes)) { num++; } } } return num; } static Int4 FlipFlippableCodons (tRNAPtr trp, Uint1 aa, CharPtr codes, Int2 code) { Int4 num = 0, i; Int2 index; Uint1 codon [4]; Uint1 rcodon [4]; if (trp == NULL) { return 0; } /* Note - it is important to set the fourth character in the codon array to NULL * because CodonForIndex only fills in the three characters of actual codon, * so if you StringCpy the codon array and the NULL character is not found after * the three codon characters, you will write in memory you did not intend to. */ codon [3] = 0; rcodon [3] = 0; for (i = 0; i < 6; i++) { if (trp->codon [i] < 64 && !DoesCodonMatchAminoAcid (aa, trp->codon[i], codes) && CodonForIndex (trp->codon [i], Seq_code_iupacna, codon) && IsATGC(codon[0]) && IsATGC(codon[1]) && IsATGC(codon[2])) { rcodon[0] = s_comp(codon[2]); rcodon[1] = s_comp(codon[1]); rcodon[2] = s_comp(codon[0]); index = IndexForCodon (rcodon, code); if (index < 64 && DoesCodonMatchAminoAcid(aa, index, codes)) { trp->codon[i] = index; num++; } } } return num; } static Boolean IgnoretRNACodonRecognized (SeqFeatPtr sfp) { if (sfp == NULL || StringISearch (sfp->except_text, "RNA editing") != NULL || StringISearch (sfp->except_text, "modified codon recognition") != NULL) { return TRUE; } else { return FALSE; } } static void FlipCodonRecognizedCallback (SeqFeatPtr sfp, Pointer data) { RnaRefPtr rrp; tRNAPtr trp; Uint1 aa; CharPtr txt; LogInfoPtr lip; Int2 code = 0; CharPtr codes = NULL; Int4 num_codons, num_match, num_flippable; if (IgnoretRNACodonRecognized(sfp) || sfp->idx.subtype != FEATDEF_tRNA || (rrp = (RnaRefPtr) sfp->data.value.ptrvalue) == NULL || rrp->ext.choice != 2 || (trp = (tRNAPtr)(rrp->ext.value.ptrvalue)) == NULL) { return; } num_codons = CountCodonsRecognized (trp); if (num_codons == 0) { return; } lip = (LogInfoPtr) data; aa = GetAaFromtRNA (trp); /* find genetic code table */ codes = GetCodesFortRNA (sfp, &code); if (codes == NULL) return; num_match = CountMatchingCodons (trp, aa, codes); if (num_codons == num_match) { return; } else if (num_codons > 1) { if (lip != NULL) { if (lip->fp != NULL) { /* text for log */ txt = GetFlipCodonLoggingInfo (sfp); fprintf (lip->fp, "Unable to flip bad codon_recognized for %s\n", txt); txt = MemFree (txt); } lip->data_in_log = TRUE; } } else { num_flippable = CountFlippableCodons(trp, aa, codes, code); if (num_flippable == num_codons) { FlipFlippableCodons (trp, aa, codes, code); } else { if (lip != NULL) { if (lip->fp != NULL) { /* text for log */ txt = GetFlipCodonLoggingInfo (sfp); fprintf (lip->fp, "Unable to flip bad codon_recognized for %s\n", txt); txt = MemFree (txt); } lip->data_in_log = TRUE; } } } } NLM_EXTERN void FlipCodonRecognizedInSeqEntry (SeqEntryPtr sep, LogInfoPtr lip) { VisitFeaturesInSep (sep, lip, FlipCodonRecognizedCallback); } static void RemoveBadCodonRecognizedCallback (SeqFeatPtr sfp, Pointer data) { RnaRefPtr rrp; tRNAPtr trp; Int2 j, k; Uint1 aa; Uint1 codon [4]; Uint1 rcodon [4]; CharPtr txt; LogInfoPtr lip; Int2 code = 0; CharPtr codes = NULL; Int4 num_codons, num_match; if (IgnoretRNACodonRecognized(sfp) || sfp->idx.subtype != FEATDEF_tRNA || (rrp = (RnaRefPtr) sfp->data.value.ptrvalue) == NULL || rrp->ext.choice != 2 || (trp = (tRNAPtr)(rrp->ext.value.ptrvalue)) == NULL) { return; } num_codons = CountCodonsRecognized (trp); if (num_codons == 0) { return; } lip = (LogInfoPtr) data; aa = GetAaFromtRNA (trp); /* find genetic code table */ codes = GetCodesFortRNA (sfp, &code); if (codes == NULL) return; num_match = CountMatchingCodons (trp, aa, codes); if (num_match == num_codons) { return; } /* Note - it is important to set the fourth character in the codon array to NULL * because CodonForIndex only fills in the three characters of actual codon, * so if you StringCpy the codon array and the NULL character is not found after * the three codon characters, you will write in memory you did not intend to. */ codon [3] = 0; rcodon [3] = 0; for (j = 0; j < 6; j++) { if (trp->codon [j] < 64) { if (DoesCodonMatchAminoAcid (aa, trp->codon[j], codes)) { /* already ok - skip it */ } else if (CodonForIndex (trp->codon [j], Seq_code_iupacna, codon) && IsATGC(codon[0]) && IsATGC(codon[1]) && IsATGC(codon[2])) { for (k = j + 1; k < 6; k++) { trp->codon[k - 1] = trp->codon[k]; } trp->codon[5] = 255; if (lip != NULL) { if (lip->fp != NULL) { /* text for log */ txt = GetFlipCodonLoggingInfo (sfp); fprintf (lip->fp, "Removed codon_recognized '%s' for %s\n", codon, txt); txt = MemFree (txt); } lip->data_in_log = TRUE; } /* push index down, so we don't skip over a codon */ j--; } } } } NLM_EXTERN void RemoveBadCodonRecognizedInSeqEntry (SeqEntryPtr sep, LogInfoPtr lip) { VisitFeaturesInSep (sep, lip, RemoveBadCodonRecognizedCallback); } NLM_EXTERN void ReverseBioseqInAlignment (SeqAlignPtr salp, Pointer userdata) { BioseqPtr bsp; SeqIdPtr sip; Boolean found = FALSE; Int4 order; if (salp == NULL || userdata == NULL) return; bsp = (BioseqPtr) userdata; for (sip = bsp->id; sip != NULL && ! found; sip = sip->next) { order = SeqIdOrderInBioseqIdList(sip, SeqIdPtrFromSeqAlign (salp)); if (order > 0) { AlnMgr2IndexSeqAlignEx(salp, FALSE); ReverseAlignmentStrand (salp, order); SeqAlignIndexFree(salp->saip); salp->saip = NULL; found = TRUE; } } } /* need to reverse the order of the segments and flip the strands */ NLM_EXTERN void FlipAlignment (SeqAlignPtr salp) { DenseSegPtr dsp; Int4 row, seg, swap_start, swap_len, opp_seg; Score swap_score; Uint1 swap_strand; if (salp == NULL || salp->segtype != SAS_DENSEG || salp->segs == NULL) { return; } dsp = (DenseSegPtr) salp->segs; if (dsp->strands == NULL) { dsp->strands = (Uint1Ptr) MemNew (dsp->numseg * dsp->dim * sizeof (Uint1)); MemSet (dsp->strands, Seq_strand_plus, dsp->numseg * dsp->dim * sizeof (Uint1)); } for (seg = 0; seg < dsp->numseg / 2; seg++) { /* swap segments to reverse order */ opp_seg = dsp->numseg - 1 - seg; /* swap lens */ swap_len = dsp->lens[seg]; dsp->lens[seg] = dsp->lens[opp_seg]; dsp->lens[opp_seg] = swap_len; /* swap scores */ if (dsp->scores != NULL) { swap_score = dsp->scores[seg]; dsp->scores[seg] = dsp->scores[opp_seg]; dsp->scores[opp_seg] = swap_score; } for (row = 0; row < dsp->dim; row++) { /* swap strands */ swap_strand = dsp->strands[dsp->dim * seg + row]; dsp->strands[dsp->dim * seg + row] = dsp->strands[dsp->dim * opp_seg + row]; dsp->strands[dsp->dim * opp_seg + row] = swap_strand; /* swap starts */ swap_start = dsp->starts[dsp->dim * seg + row]; dsp->starts[dsp->dim * seg + row] = dsp->starts[dsp->dim * opp_seg + row]; dsp->starts[dsp->dim * opp_seg + row] = swap_start; } } /* reverse segments */ for (seg = 0; seg < dsp->numseg; seg++) { for (row = 0; row < dsp->dim; row++) { if (dsp->strands[dsp->dim * seg + row] == Seq_strand_minus) { dsp->strands[dsp->dim * seg + row] = Seq_strand_plus; } else { dsp->strands[dsp->dim * seg + row] = Seq_strand_minus; } } } SAIndex2Free2(salp->saip); salp->saip = NULL; } NLM_EXTERN void FlipEntireAlignmentIfAllSequencesFlipped (SeqAnnotPtr sap, Pointer userdata) { SeqAlignPtr salp; ValNodePtr vnp; BioseqPtr bsp; SeqIdPtr sip; Boolean found; Int4 row, num_rows; if (sap == NULL || sap->type != 2 || userdata == NULL) return; salp = (SeqAlignPtr) sap->data; if (salp == NULL || salp->idx.deleteme) return; AlnMgr2IndexSingleChildSeqAlign(salp); num_rows = AlnMgr2GetNumRows(salp); for (row = 1; row <= num_rows; row++) { sip = AlnMgr2GetNthSeqIdPtr(salp, row); found = FALSE; vnp = (ValNodePtr)userdata; while (vnp != NULL && !found) { bsp = (BioseqPtr) vnp->data.ptrvalue; if (SeqIdOrderInBioseqIdList (sip, bsp->id) > 0) { found = TRUE; } vnp = vnp->next; } if (!found) return; } FlipAlignment(salp); } NLM_EXTERN ValNodePtr ListSequencesWithAlignments (ValNodePtr bsp_list) { BioseqPtr bsp; ValNodePtr vnp, aln_bsp = NULL; for (vnp = bsp_list; vnp != NULL; vnp = vnp->next) { bsp = (BioseqPtr) vnp->data.ptrvalue; if (bsp != NULL && IsBioseqInAnyAlignment (bsp, bsp->idx.entityID)) { ValNodeAddPointer (&aln_bsp, 0, bsp); } } return aln_bsp; } NLM_EXTERN void RevCompBioseqList (ValNodePtr bsp_list, Uint2 entityID, BioseqFunc func, Boolean revCompFeats, Boolean check_for_aln) { SeqEntryPtr sep; BioseqPtr bsp; ValNodePtr vnp; sep = GetTopSeqEntryForEntityID (entityID); for (vnp = bsp_list; vnp != NULL; vnp = vnp->next) { bsp = (BioseqPtr) vnp->data.ptrvalue; if (func != NULL) { func (bsp); if (check_for_aln) { VisitAlignmentsInSep (sep, (Pointer) bsp, ReverseBioseqInAlignment); } } if (revCompFeats) { if (bsp->repr == Seq_repr_raw || bsp->repr == Seq_repr_const) { if (sep != NULL) { SeqEntryExplore (sep, (Pointer) bsp, RevCompFeats); } } } } } typedef struct bioseqinalignmentdata { Boolean found; BioseqPtr lookingfor; } BioseqInAlignmentData, PNTR BioseqInAlignmentPtr; static Boolean IsBioseqInThisAlignment (SeqAlignPtr salp, BioseqPtr bsp) { SeqIdPtr sip; Boolean found = FALSE; for (sip = bsp->id; sip != NULL && ! found; sip = sip->next) { found = SeqAlignFindSeqId (salp, sip); } return found; } static void FindAlignmentCallback (SeqAnnotPtr sap, Pointer userdata) { BioseqInAlignmentPtr biap; SeqAlignPtr salp; if (sap == NULL || sap->type != 2 || userdata == NULL) { return; } biap = (BioseqInAlignmentPtr) userdata; if (biap->found) return; salp = (SeqAlignPtr) sap->data; if (salp == NULL) return; biap->found = IsBioseqInThisAlignment (salp, biap->lookingfor); } NLM_EXTERN Boolean IsBioseqInAnyAlignment (BioseqPtr bsp, Uint2 input_entityID) { SeqEntryPtr topsep; BioseqInAlignmentData biad; topsep = GetTopSeqEntryForEntityID (input_entityID); biad.found = FALSE; biad.lookingfor = bsp; VisitAnnotsInSep (topsep, &biad, FindAlignmentCallback); return biad.found; } static void RemoveAlignmentsWithSequenceCallback (SeqAnnotPtr sap, Pointer userdata) { SeqAlignPtr salp; SeqIdPtr sip; if (sap == NULL || sap->type != 2 || userdata == NULL) return; salp = (SeqAlignPtr) sap->data; if (salp == NULL || salp->idx.deleteme) return; sip = (SeqIdPtr) userdata; while (sip != NULL && !sap->idx.deleteme) { if (FindSeqIdinSeqAlign (salp, sip)) { sap->idx.deleteme = TRUE; } sip = sip->next; } } NLM_EXTERN void RemoveAlignmentsWithSequence (BioseqPtr bsp, Uint2 input_entityID) { SeqEntryPtr topsep; if (bsp == NULL) return; topsep = GetTopSeqEntryForEntityID (input_entityID); VisitAnnotsInSep (topsep, bsp->id, RemoveAlignmentsWithSequenceCallback); } /* assumes locations on same Bioseq */ static Boolean OutOfOrder (SeqLocPtr slp_prev, SeqLocPtr slp_next) { Uint1 strand_p, strand_n; Boolean rval = FALSE; Int4 start_p, start_n, stop_p, stop_n; if (slp_prev == NULL || slp_next == NULL) { return FALSE; } strand_p = SeqLocStrand (slp_prev); strand_n = SeqLocStrand (slp_next); if (strand_p == Seq_strand_minus) { if (strand_n != Seq_strand_minus) { /* mixed strand, not necessarily out of order */ rval = FALSE; } else { start_p = SeqLocStart (slp_prev); stop_p = SeqLocStop (slp_prev); start_n = SeqLocStart (slp_next); stop_n = SeqLocStop (slp_next); if (start_p < start_n || stop_p < stop_n) { rval = TRUE; } } } else { if (strand_n == Seq_strand_minus) { /* mixed strand, not necessarily out of order */ rval = FALSE; } else { start_p = SeqLocStart (slp_prev); stop_p = SeqLocStop (slp_prev); start_n = SeqLocStart (slp_next); stop_n = SeqLocStop (slp_next); if (start_p > start_n || stop_p > stop_n) { rval = TRUE; } } } return rval; } /* assumes locations on same Bioseq and in order on same strand*/ static Boolean TooFarApartForTransSplicing (SeqLocPtr slp_prev, SeqLocPtr slp_next) { Boolean rval = FALSE; Int4 start_n, start_p, stop_n, stop_p; if (slp_prev == NULL || slp_next == NULL) { return FALSE; } if (SeqLocStrand (slp_prev) == Seq_strand_minus) { start_p = SeqLocStart (slp_prev); stop_n = SeqLocStop (slp_next); if (start_p - stop_n > 10000) { rval = TRUE; } } else { stop_p = SeqLocStop (slp_prev); start_n = SeqLocStart (slp_next); if (start_n - stop_p > 10000) { rval = TRUE; } } return rval; } NLM_EXTERN SeqLocPtr MakeGeneLocForFeatureLoc (SeqLocPtr floc, Uint2 entityID, Boolean trans_spliced) { /* in the age of small-set genomes, we're going to pretend that segmented sets do not exist. * A gene location for a feature location that includes multiple bioseqs should include * one interval per bioseq that covers all locations of the feature that occur on that bioseq. */ SeqLocPtr slp_new = NULL, slp_tmp, slp_last = NULL, add_slp; SeqLocPtr PNTR pAddSlp = NULL; BioseqPtr bsp, last_bsp = NULL; Boolean partial5 = FALSE, partial3 = FALSE; Uint2 strand, last_strand = Seq_strand_plus; pAddSlp = &slp_new; for (slp_tmp = SeqLocFindNext (floc, NULL); slp_tmp != NULL; slp_tmp = SeqLocFindNext (floc, slp_tmp)) { bsp = GetBioseqGivenSeqLoc (slp_tmp, entityID); strand = SeqLocStrand (slp_tmp); if (bsp != last_bsp || strand != last_strand || (trans_spliced && OutOfOrder (slp_last, slp_tmp)) || (trans_spliced && TooFarApartForTransSplicing(slp_last, slp_tmp))) { add_slp = SeqLocMerge (bsp, slp_tmp, NULL, TRUE, FALSE, FALSE); if (slp_last == NULL) { slp_new = add_slp; } else { slp_last->next = add_slp; pAddSlp = &(slp_last->next); } slp_last = add_slp; last_bsp = bsp; last_strand = strand; } else { add_slp = SeqLocMerge (bsp, *pAddSlp, slp_tmp, TRUE, FALSE, FALSE); *pAddSlp = SeqLocFree (*pAddSlp); *pAddSlp = add_slp; slp_last = add_slp; } } if (slp_new != NULL && slp_new->next != NULL) { slp_tmp = ValNodeNew (NULL); slp_tmp->choice = SEQLOC_MIX; slp_tmp->data.ptrvalue = slp_new; slp_new = slp_tmp; } if (slp_new != NULL) { CheckSeqLocForPartial (floc, &partial5, &partial3); SetSeqLocPartial (slp_new, partial5, partial3); } return slp_new; } /* code for resolving conflicting IDs */ typedef struct { CharPtr oldStr; SeqIdPtr newSip; } ReplaceIDStruct, PNTR ReplaceIDStructPtr; /******************************************************************** * * SeqLocReplaceLocalID * replaces the Seq-Id in a Seq-Loc (slp) with a new Seq-Id (new_sip) * only if the Seq-Id is a local one. * **********************************************************************/ static SeqLocPtr SeqLocReplaceLocalID (SeqLocPtr slp, SeqIdPtr new_sip) { SeqLocPtr curr; PackSeqPntPtr pspp; SeqIntPtr target_sit; SeqPntPtr spp; SeqIdPtr currId; switch (slp->choice) { case SEQLOC_PACKED_INT : case SEQLOC_MIX : case SEQLOC_EQUIV : curr = NULL; while ((curr = SeqLocFindNext (slp, curr)) != NULL) { curr = SeqLocReplaceLocalID (curr, new_sip); } break; case SEQLOC_PACKED_PNT : pspp = (PackSeqPntPtr) slp->data.ptrvalue; if ((pspp != NULL) && (pspp->id->choice == SEQID_LOCAL)) { SeqIdFree (pspp->id); pspp->id = SeqIdDup (new_sip); } break; case SEQLOC_EMPTY : case SEQLOC_WHOLE : currId = (SeqIdPtr) slp->data.ptrvalue; if (currId->choice == SEQID_LOCAL) { SeqIdFree (currId); slp->data.ptrvalue = (Pointer) SeqIdDup (new_sip); } break; case SEQLOC_INT : target_sit = (SeqIntPtr) slp->data.ptrvalue; if (target_sit->id->choice == SEQID_LOCAL) { SeqIdFree (target_sit->id); target_sit->id = SeqIdDup (new_sip); } break; case SEQLOC_PNT : spp = (SeqPntPtr)slp->data.ptrvalue; if (spp->id->choice == SEQID_LOCAL) { SeqIdFree(spp->id); spp->id = SeqIdDup(new_sip); } break; default : break; } return slp; } static void ReplaceIdForFeature (SeqFeatPtr sfp, SeqIdPtr sip) { CdRegionPtr crp; CodeBreakPtr cbp; RnaRefPtr rrp; tRNAPtr trp; if (sfp == NULL || sip == NULL) { return; } /* replace local ID in location */ if (sfp->location != NULL) { SeqLocReplaceLocalID (sfp->location, sip); } /* also replace local ID in code breaks */ if (sfp->data.choice == SEQFEAT_CDREGION && (crp = (CdRegionPtr)sfp->data.value.ptrvalue) != NULL && crp->code_break != NULL) { for (cbp = crp->code_break; cbp != NULL; cbp = cbp->next) { SeqLocReplaceLocalID (cbp->loc, sip); } } /* also replace local ID in anticodons */ if (sfp->data.choice == SEQFEAT_RNA && (rrp = (RnaRefPtr) sfp->data.value.ptrvalue) != NULL && rrp->type == 3 && rrp->ext.choice == 2 && (trp = (tRNAPtr) rrp->ext.value.ptrvalue) != NULL && trp->anticodon != NULL) { SeqLocReplaceLocalID (trp->anticodon, sip); } } static void ReplaceLocalIdOnLoc_callback (SeqFeatPtr sfp, Pointer userdata) { SeqIdPtr sip; if (sfp == NULL) { return; } sip = (SeqIdPtr) userdata; ReplaceIdForFeature (sfp, sip); } static void CheckFeatForNuclID_callback (SeqFeatPtr sfp, Pointer userdata) { SeqIdPtr featSip = NULL; ReplaceIDStructPtr idsPtr; ObjectIdPtr oip; Char tmpIdStr [128]; if (NULL == sfp) return; /* Get the old Seq Id and the new */ /* one that it was changed to. */ idsPtr = (ReplaceIDStructPtr) userdata; if ((NULL == idsPtr) || (NULL == idsPtr->oldStr) || (NULL == idsPtr->newSip)) return; /* Get the location Seq ID for this CDS feature */ featSip = SeqLocId (sfp->location); if (featSip == NULL) return; oip = (ObjectIdPtr) featSip->data.ptrvalue; /* If the location Seq ID matches the old Seq Id */ /* then change the location to point to the new. */ if (NULL == oip->str) { sprintf (tmpIdStr, "%d", oip->id); if (StringCmp (tmpIdStr, idsPtr->oldStr) == 0) { ReplaceIdForFeature (sfp, idsPtr->newSip); } } else if (StringCmp (oip->str, idsPtr->oldStr) == 0){ ReplaceIdForFeature (sfp, idsPtr->newSip); } } static void CheckFeatForProductID_callback (SeqFeatPtr sfp, Pointer userdata) { SeqIdPtr featSip = NULL; ReplaceIDStructPtr idsPtr; ObjectIdPtr oip; Char tmpIdStr [128]; if (NULL == sfp) return; if ((sfp->data.choice == SEQFEAT_CDREGION) && (sfp->product != NULL)) { /* Get the old Seq Id and the new */ /* one that it was changed to. */ idsPtr = (ReplaceIDStructPtr) userdata; if ((NULL == idsPtr) || (NULL == idsPtr->oldStr) || (NULL == idsPtr->newSip)) return; /* Get the product Seq ID for this CDS feature */ featSip = SeqLocId (sfp->product); oip = (ObjectIdPtr) featSip->data.ptrvalue; /* If the product Seq ID matches the old Seq Id */ /* then change the product to point to the new. */ if (NULL == oip->str) { sprintf (tmpIdStr, "%d", oip->id); if (StringCmp (tmpIdStr, idsPtr->oldStr) == 0) SeqLocReplaceLocalID (sfp->product, idsPtr->newSip); } if (StringCmp (oip->str, idsPtr->oldStr) == 0) SeqLocReplaceLocalID (sfp->product, idsPtr->newSip); } } static void ReplaceLocalID (BioseqPtr bsp, SeqIdPtr sip, CharPtr key, Int2 count) { ObjectIdPtr oip; Char str [64]; Char tmp [70]; BioseqSetPtr bssp = NULL; ReplaceIDStruct ids; BioseqPtr siblingBsp; SeqEntryPtr sep; Int2 parentType; if (bsp == NULL || sip == NULL || StringHasNoText (key)) return; oip = (ObjectIdPtr) sip->data.ptrvalue; if (oip == NULL) return; /* Create the new ID string */ StringNCpy_0 (str, key, sizeof (str)); sprintf (tmp, "%s__%d", str, (int) count); /* Save the original SeqId for later passing */ /* to CheckSetForNuclID_callback () and */ /* CheckSetForProductId_callback (). */ if (NULL != oip->str) ids.oldStr = StringSave (oip->str); else { ids.oldStr = (CharPtr) MemNew (32); sprintf (ids.oldStr, "%d", oip->id); } /* Update the Seq ID with the new string */ oip->str = StringSave (tmp); ids.newSip = sip; SeqMgrReplaceInBioseqIndex (bsp); /* Replace the local ID on all the features of the bioseq */ VisitFeaturesOnBsp (bsp, (Pointer) sip, ReplaceLocalIdOnLoc_callback); /* Check the parent (and grandparent, etc.) BioseqSet */ /* for features that use the changed ID. */ parentType = bsp->idx.parenttype; if (parentType == OBJ_BIOSEQSET) bssp = (BioseqSetPtr) bsp->idx.parentptr; while (parentType == OBJ_BIOSEQSET) { if ((bssp != NULL) && (bssp->_class == 1)) { /* Check features that are attached to */ /* the parent set itself. */ if (ISA_na(bsp->mol)) VisitFeaturesOnSet (bssp, (Pointer) &ids, CheckFeatForNuclID_callback); else if (ISA_aa(bsp->mol)) VisitFeaturesOnSet (bssp, (Pointer) &ids, CheckFeatForProductID_callback); /* Check features that are attached to */ /* other Bioseqs in the set. */ sep = bssp->seqentry; while (NULL != sep) { if (sep->choice == 1) { /* bioseq */ siblingBsp = (BioseqPtr) sep->data.ptrvalue; if (ISA_na(bsp->mol)) VisitFeaturesOnBsp (siblingBsp, (Pointer) sip, CheckFeatForNuclID_callback); else if (ISA_aa(bsp->mol)) VisitFeaturesOnBsp (siblingBsp, (Pointer) sip, CheckFeatForProductID_callback); } sep = sep->next; } sep = bssp->seq_set; while (NULL != sep) { if (sep->choice == 1) { /* bioseq */ siblingBsp = (BioseqPtr) sep->data.ptrvalue; if (ISA_na(bsp->mol)) VisitFeaturesOnBsp (siblingBsp, (Pointer) sip, CheckFeatForNuclID_callback); else if (ISA_aa(bsp->mol)) VisitFeaturesOnBsp (siblingBsp, (Pointer) sip, CheckFeatForProductID_callback); } sep = sep->next; } } parentType = bssp->idx.parenttype; bssp = (BioseqSetPtr) bssp->idx.parentptr; } /* Clean up before exiting */ MemFree (ids.oldStr); } static void BuildLclTree (LclIdListPtr PNTR head, BioseqPtr bsp, CharPtr x, SeqIdPtr sip) { Int2 comp; LclIdListPtr idlist; if (*head != NULL) { idlist = *head; comp = StringICmp (idlist->key, x); if (comp < 0) { BuildLclTree (&(idlist->right), bsp, x, sip); } else if (comp > 0) { BuildLclTree (&(idlist->left), bsp, x, sip); } else { if (idlist->firstbsp != NULL && idlist->firstsip != NULL) { ReplaceLocalID (idlist->firstbsp, idlist->firstsip, x, 1); idlist->count = 2; idlist->firstbsp = NULL; idlist->firstsip = NULL; } ReplaceLocalID (bsp, sip, x, idlist->count); (idlist->count)++; } } else { idlist = MemNew (sizeof (LclIdList)); if (idlist != NULL) { *head = idlist; idlist->firstbsp = bsp; idlist->firstsip = sip; idlist->count = 1; idlist->key = StringSave (x); idlist->left = NULL; idlist->right = NULL; } } } NLM_EXTERN void FreeLclTree (LclIdListPtr PNTR head) { LclIdListPtr idlist; if (head != NULL && *head != NULL) { idlist = *head; FreeLclTree (&(idlist->left)); FreeLclTree (&(idlist->right)); MemFree (idlist->key); MemFree (idlist); } } NLM_EXTERN void ResolveExistingIDsCallback (SeqEntryPtr sep, Pointer mydata, Int4 index, Int2 indent) { BioseqPtr bsp; LclIdListPtr PNTR head; SeqIdPtr sip; Char str [64]; head = (LclIdListPtr PNTR) mydata; if (sep == NULL || head == NULL) return; if (IS_Bioseq (sep)) { bsp = (BioseqPtr) sep->data.ptrvalue; if (bsp != NULL) { for (sip = bsp->id; sip != NULL; sip = sip->next) { if (sip->choice == SEQID_LOCAL) { SeqIdWrite (sip, str, PRINTID_REPORT, sizeof (str)); BuildLclTree (head, bsp, str, sip); } } } } } static Boolean DoesIdListHaveLocal (SeqIdPtr sip) { while (sip != NULL) { if (sip->choice == SEQID_LOCAL) { return TRUE; } sip = sip->next; } return FALSE; } static Boolean DoesSeqLocListHaveLocalId (SeqLocPtr slp) { SeqLocPtr loc; PackSeqPntPtr psp; SeqBondPtr sbp; SeqIntPtr sinp; SeqIdPtr sip; SeqPntPtr spp; Boolean has_local = FALSE; while (slp != NULL) { switch (slp->choice) { case SEQLOC_NULL : break; case SEQLOC_EMPTY : case SEQLOC_WHOLE : sip = (SeqIdPtr) slp->data.ptrvalue; has_local = DoesIdListHaveLocal (sip); break; case SEQLOC_INT : sinp = (SeqIntPtr) slp->data.ptrvalue; if (sinp != NULL) { sip = sinp->id; has_local = DoesIdListHaveLocal (sip); } break; case SEQLOC_PNT : spp = (SeqPntPtr) slp->data.ptrvalue; if (spp != NULL) { sip = spp->id; has_local = DoesIdListHaveLocal (sip); } break; case SEQLOC_PACKED_PNT : psp = (PackSeqPntPtr) slp->data.ptrvalue; if (psp != NULL) { sip = psp->id; has_local = DoesIdListHaveLocal (sip); } break; case SEQLOC_PACKED_INT : case SEQLOC_MIX : case SEQLOC_EQUIV : loc = (SeqLocPtr) slp->data.ptrvalue; while (loc != NULL && !has_local) { has_local = DoesSeqLocListHaveLocalId(loc); loc = loc->next; } break; case SEQLOC_BOND : sbp = (SeqBondPtr) slp->data.ptrvalue; if (sbp != NULL) { spp = (SeqPntPtr) sbp->a; if (spp != NULL) { sip = spp->id; has_local = DoesIdListHaveLocal (sip); } spp = (SeqPntPtr) sbp->b; if (spp != NULL) { sip = spp->id; has_local = DoesIdListHaveLocal (sip); } } break; case SEQLOC_FEAT : break; default : break; } slp = slp->next; } return FALSE; } static void SeqEntryHasAlignmentsWithLocalIDsCallback (SeqAnnotPtr sap, Pointer userdata) { DenseDiagPtr ddp; DenseSegPtr dsp; PackSegPtr psp; SeqAlignPtr salp; StdSegPtr ssp; Boolean has_local = FALSE; BoolPtr bp; if (sap == NULL || sap->type != 2 || userdata == NULL) return; salp = (SeqAlignPtr) sap->data; if (salp != NULL) { switch (salp->segtype) { case SAS_DENDIAG : for (ddp = salp->segs; ddp != NULL && !has_local; ddp = ddp->next) { has_local = DoesIdListHaveLocal (ddp->id); } break; case SAS_DENSEG : dsp = salp->segs; if (dsp != NULL) { has_local = DoesIdListHaveLocal (dsp->ids); } break; case SAS_STD : for (ssp = salp->segs; ssp != NULL && !has_local; ssp = ssp->next) { has_local = DoesIdListHaveLocal (ssp->ids); if (!has_local) { has_local = DoesSeqLocListHaveLocalId (ssp->loc); } } break; case SAS_PACKED : psp = (PackSegPtr) salp->segs; if (psp != NULL) { has_local = DoesIdListHaveLocal (psp->ids); } break; default : break; } } bp = (BoolPtr) userdata; *bp |= has_local; } NLM_EXTERN Boolean HasAlignmentsWithLocalIDs (SeqEntryPtr sep) { Boolean has_alignments = FALSE; VisitAnnotsInSep (sep, (Pointer) &has_alignments, SeqEntryHasAlignmentsWithLocalIDsCallback); return has_alignments; } /* EC number replacement - copied from Sequin, with protection multiple reads if no replacement file available */ typedef struct ecrepdata { CharPtr before; CharPtr after; } EcRepData, PNTR EcRepPtr; static ValNodePtr ec_rep_list = NULL; static EcRepPtr PNTR ec_rep_data = NULL; static Int4 ec_rep_len = 0; static Boolean ec_rep_read = FALSE; static int LIBCALLBACK SortVnpByEcBefore (VoidPtr ptr1, VoidPtr ptr2) { EcRepPtr erp1, erp2; CharPtr str1, str2; ValNodePtr vnp1, vnp2; if (ptr1 == NULL || ptr2 == NULL) return 0; vnp1 = *((ValNodePtr PNTR) ptr1); vnp2 = *((ValNodePtr PNTR) ptr2); if (vnp1 == NULL || vnp2 == NULL) return 0; erp1 = (EcRepPtr) vnp1->data.ptrvalue; erp2 = (EcRepPtr) vnp2->data.ptrvalue; if (erp1 == NULL || erp2 == NULL) return 0; str1 = erp1->before; str2 = erp2->before; if (str1 == NULL || str2 == NULL) return 0; return StringCmp (str1, str2); } static void SetupECReplacementTable (CharPtr file) { EcRepPtr erp; FileCache fc; FILE *fp = NULL; Int4 i; ValNodePtr last = NULL; Char line [512]; Char path [PATH_MAX]; CharPtr ptr; ErrSev sev; CharPtr str; ValNodePtr vnp; if (ec_rep_data != NULL) return; if (ec_rep_read) return; if (FindPath ("ncbi", "ncbi", "data", path, sizeof (path))) { FileBuildPath (path, NULL, file); sev = ErrSetMessageLevel (SEV_ERROR); fp = FileOpen (path, "r"); ErrSetMessageLevel (sev); if (fp != NULL) { FileCacheSetup (&fc, fp); str = FileCacheReadLine (&fc, line, sizeof (line), NULL); while (str != NULL) { if (StringDoesHaveText (str)) { ptr = StringChr (str, '\t'); if (ptr != NULL) { *ptr = '\0'; ptr++; /* only replace if a single destination number, not a split from one to many */ if (StringChr (ptr, '\t') == NULL) { erp = (EcRepPtr) MemNew (sizeof (EcRepData)); if (erp != NULL) { erp->before = StringSave (str); erp->after = StringSave (ptr); vnp = ValNodeAddPointer (&last, 0, (Pointer) erp); if (ec_rep_list == NULL) { ec_rep_list = vnp; } last = vnp; } } } } str = FileCacheReadLine (&fc, line, sizeof (line), NULL); } FileClose (fp); ec_rep_len = ValNodeLen (ec_rep_list); if (ec_rep_len > 0) { ec_rep_list = ValNodeSort (ec_rep_list, SortVnpByEcBefore); ec_rep_data = (EcRepPtr PNTR) MemNew (sizeof (EcRepPtr) * (ec_rep_len + 1)); if (ec_rep_data != NULL) { for (vnp = ec_rep_list, i = 0; vnp != NULL; vnp = vnp->next, i++) { erp = (EcRepPtr) vnp->data.ptrvalue; ec_rep_data [i] = erp; } } } } } ec_rep_read = TRUE; } static CharPtr GetECReplacement (CharPtr str) { EcRepPtr erp; Int4 L, R, mid; if (StringHasNoText (str)) return NULL; L = 0; R = ec_rep_len - 1; while (L < R) { mid = (L + R) / 2; erp = ec_rep_data [(int) mid]; if (erp != NULL && StringCmp (erp->before, str) < 0) { L = mid + 1; } else { R = mid; } } erp = ec_rep_data [(int) R]; if (erp != NULL && StringCmp (erp->before, str) == 0 && StringChr (erp->after, '\t') == NULL) return erp->after; return NULL; } static void UpdateProtEC (SeqFeatPtr sfp, Pointer userdata) { Int4Ptr countP; Int2 inf_loop_check; CharPtr nxt; ProtRefPtr prp; CharPtr rep; CharPtr str; ValNodePtr vnp; if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT) return; prp = (ProtRefPtr) sfp->data.value.ptrvalue; if (prp == NULL || prp->ec == NULL) return; countP = (Int4Ptr) userdata; for (vnp = prp->ec; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; rep = GetECReplacement (str); if (rep == NULL) continue; nxt = rep; inf_loop_check = 0; while (nxt != NULL && inf_loop_check < 10) { rep = nxt; inf_loop_check++; nxt = GetECReplacement (rep); } vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); vnp->data.ptrvalue = StringSave (rep); if (countP != NULL) { (*countP)++; } } } NLM_EXTERN Int4 UpdateReplacedECNumbers (SeqEntryPtr sep) { Int4 count = 0; if (sep == NULL) return 0; SetupECReplacementTable ("ecnum_replaced.txt"); if (ec_rep_data != NULL && ec_rep_len > 0) { VisitFeaturesInSep (sep, (Pointer) &count, UpdateProtEC); } return count; } static void DeleteBadProtEC (SeqFeatPtr sfp, Pointer userdata) { Int4Ptr countP; ProtRefPtr prp; CharPtr str; ValNodePtr vnp; if (sfp == NULL || sfp->data.choice != SEQFEAT_PROT) return; prp = (ProtRefPtr) sfp->data.value.ptrvalue; if (prp == NULL || prp->ec == NULL) return; countP = (Int4Ptr) userdata; for (vnp = prp->ec; vnp != NULL; vnp = vnp->next) { str = (CharPtr) vnp->data.ptrvalue; if (StringHasNoText (str)) continue; if (ValidateECnumber (str) && (! ECnumberNotInList (str))) continue; vnp->data.ptrvalue = MemFree (vnp->data.ptrvalue); if (countP != NULL) { (*countP)++; } } } NLM_EXTERN Int4 DeleteBadECNumbers (SeqEntryPtr sep) { Int4 count = 0; if (sep == NULL) return 0; VisitFeaturesInSep (sep, (Pointer) &count, DeleteBadProtEC); return count; }