/* * $Id: vast2cn3dDB.c,v 1.3 2003/01/15 16:21:47 chenj Exp $ * * * =========================================================================== * * 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. * * =========================================================================== * * * Author: Jie Chen, Lewis Geer, Chris Hogue, Siqian He * * * $Log: vast2cn3dDB.c,v $ * Revision 1.3 2003/01/15 16:21:47 chenj * add construcMaxSdi() * * Revision 1.2 2003/01/14 20:42:32 chenj * change VastToCn3D() to VastToCn3DAndAli() * * Revision 1.1.1.1 2002/12/06 20:17:21 chenj * Imported Scouces * * * * This file fetches data from pubvast database, but for Vast Search job, it * still reads data from files. * * ========================================================================= * */ #define NLM_GENERATED_CODE_PROTO #undef DOWNLOAD_DEBUG_MODE #include #include #include #include #include #include #include #include #include #include #include #include #include "vastlocl.h" #include "mmdblocl.h" #include "mmdbdata.h" #include "vast2mage.h" #include "vastsrv.h" #include "mkbioseq.h" /* #include */ #include #include #include "CAV_lib_new/cddalignview.h" #include "/home/he/proj/VastSrv/PubVastApi.h" /* #include "./VastHe/PubVastApi.h" */ #include "vast2cn3d.h" #include "/home/he/proj/MmdbSrv/PubStructApi.h" #include "vastuti.h" #define CPUTIME_MAX 120 #define VIEW_STR_SUBBUT 0 #define VIEW_ALI_SUBBUT 1 #define VIEW_IN_Cn3DCACHE 'a' #define VIEW_IN_Cn3D_GEN 'c' #define VIEW_IN_HTML 'h' #define VIEW_IN_FASTA 'f' #define VIEW_IN_TEXT 't' #define VIEW_IN_HTML_PAGE 'H' #define VIEW_IN_FASTA_PAGE 'F' #define VIEW_IN_TEXT_PAGE 'T' #define ALL_NBR 0 #define CHECKED_NBR 1 extern void WWWPrintFileData(CharPtr FName, FILE *pFile); extern Char MAILto[PATH_MAX], Database[PATH_MAX]; extern Int4 aSdi; typedef struct { unsigned BsfId; unsigned gi; } GiBsfIdData, *GiBsfIdDataPtr; static void AddMMDBIdToBioseq(BioseqPtr bsp, Int4 mmdbid) { DbtagPtr dbtp; SeqIdPtr sip_new = NULL; SeqAnnotPtr sap_new = NULL; if (bsp == NULL) return; sap_new= SeqAnnotNew(); sap_new->type = 4; sip_new = (SeqIdPtr)ValNodeNew(NULL); sip_new->choice = SEQID_GENERAL; dbtp = (DbtagPtr)DbtagNew(); dbtp->db = (CharPtr) MemNew (10); sprintf(dbtp->db, "mmdb"); dbtp->tag = (ObjectIdPtr) ObjectIdNew(); dbtp->tag->id = mmdbid; sip_new->data.ptrvalue = dbtp; sap_new->data = sip_new; if (bsp->annot == NULL) bsp->annot = sap_new; else { sap_new->next = bsp->annot; bsp->annot = sap_new; } return; } /* AddMMDBIdToBioseq */ static Int4 GetMGPIdx(GiBsfIdDataPtr gbp, Int4 BsfId) { Int4 i=0; while (BsfId != gbp[i].BsfId) i++; return (i); } /* GetMGPIdx */ /* Display a structural alignment in Cn3D and in HTML*/ Boolean LIBCALL VastToCn3DAndAli(WWWInfoPtr www_info) { Char szName[5], AsnPath[PATH_MAX], AsnName[10]; Char cViewType, pdbname_m[5], chain_m=' '; CharPtr Name, www_arg, szTemp, JobID=NULL, pcPass; Int2 iPDB = 0, ret, complexity; Int2 nbr_complexity; Int4 iFidCount = 0, domNo_m, i, hits_num=0, iSubBut; Int4 aMmdbId, aChain, indx, Fid, Fsid, NumLabels, *BsfId; /* Fsid = aMmdbId * 10000 + aChnNo * 100 + aDomCumulNo */ /* Fid = bMmdbId * 100000 + bChnNo * 1000 + bDomCumulNo * 10 + bAlignId */ AsnIoPtr paiFile, aipr; BioseqPtr biosp; BiostrucAnnotSetPtr pbsa = NULL, pbsaShort = NULL; BiostrucAlignSeqPtr basp = NULL; BiostrucFeatureSetPtr pbsfs = NULL; BiostrucFeaturePtr pbsf = NULL; BiostrucResidueGraphSetPtr stdDictionary; BiostrucPtr pbsMaster=NULL, pbsSlave=NULL, pbsSlaveHead = NULL; BiostrucPtr pbsSlaveTail; BiostrucAlignPtr pbsaStruct; BundleSeqsAlignsPtr bsap = NULL; GiBsfIdDataPtr gbp; NcbiMimeAsn1Ptr pvnNcbi; ObjectIdPtr objid; SeqAnnotPtr psaAlignHead = NULL, psaAlignTail; SeqAlignPtr salpHead, salpTail; SeqEntryPtr sep; SeqIdPtr sid; ValNodePtr pvnFids = NULL; VastPageDataPtr vpp; if ((indx = WWWFindName(www_info, "chaindom")) >= 0) { www_arg = WWWGetValueByIndex(www_info, indx); if (isdigit(www_arg[0])) Fsid = atoi(www_arg); else PrtMes(MAILto, "VASTSRV", "Invalid Biostruc-feature-set-id: chaindom = ", www_arg, FALSE); } else if ((indx = WWWFindName(www_info, "sdid")) >=0) { int maxsdi; www_arg = WWWGetValueByIndex(www_info, indx); if (isdigit(www_arg[0]) || www_arg[0] == '-') aSdi= (long) atol(www_arg); else PrtMes(MAILto, "VASTSRV", "Non-numeric Structure Domain Identifier: sdid = ", www_arg,FALSE); maxsdi = constructMaxSdi(); if (aSdi > maxsdi || !aSdi) PrtMes(NULL, "VASTSRV", "Vast neighbor data for this domain is not yet available. Please try later again.", NULL, FALSE); if (aSdi < 0) PrtMes(NULL, "VASTSRV", "This is an obsolete domain, no VAST information.", NULL, FALSE); Fsid = SdiToLongDomId(aSdi); if (!Fsid) { Char str[10]; sprintf(str, "%d", aSdi); PrtMes(MAILto, "VASTSRV", "Error: No domain exists for this identifier: sdid = ", str,FALSE); } } else PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "No chaindom or sdid -- please input chaindom or Structure Domain identifier .", NULL, FALSE); aMmdbId = Fsid / 10000; aChain = (Fsid % 10000) / 100; /* vsid and pass are to look at alignments from VAST Search */ if ((indx = WWWFindName(www_info, "vsid")) >= 0) { www_arg = WWWGetValueByIndex(www_info, indx); JobID = StringSave(www_arg); if ((indx = WWWFindName(www_info, "pass")) < 0) { PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "Please input the password of the Vast Search job.", NULL, TRUE); return 0; } else { www_arg = WWWGetValueByIndex(www_info, indx); pcPass = StringSave(www_arg); if ((ret = Check_VastSearch_Password(pcPass, JobID)) != 1) { if (ret == 2) return 0; PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "Incorrect password.", NULL, TRUE); return 0; } } } else { aSdi = LongDomIdToSdi(Fsid); if (!aSdi) { char str[20]; sprintf(str, "%d", Fsid); PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "VAST structure neighbor calculations for this entry are in progress or an incorrect chaindom = ", str, FALSE); } } /* action == 0 indicates MIME; action == 1 is text; action == 2 is save */ if ((indx = WWWFindName(www_info, "action")) < 0) iPDB = 0; else { www_arg = WWWGetValueByIndex(www_info, indx); if (isdigit(www_arg[0])) iPDB = (Int4) atoi(www_arg); else iPDB = 0; } if ((indx=WWWFindName(www_info, "viewstr")) >=0) iSubBut=VIEW_STR_SUBBUT; else if ((indx=WWWFindName(www_info, "viewali")) >=0) iSubBut=VIEW_ALI_SUBBUT; else { PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "Please click either \"View 3D Structure\" or \"View Alignment\".", NULL, TRUE); return 0; } if (iSubBut == VIEW_STR_SUBBUT) { if ((indx = WWWFindName(www_info, "calltype")) >=0) { www_arg = WWWGetValueByIndex(www_info, indx); cViewType = www_arg[0]; } else { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "No calltype code -- Please choose either Cn3D or Cn3D/Cache.\n", NULL, TRUE); return 0; } } else if ((indx = WWWFindName(www_info, "alitype")) >=0) { CharPtr www_arg2; www_arg = WWWGetValueByIndex(www_info, indx); if ((indx = WWWFindName(www_info, "nbr_complexity")) >=0) { www_arg2 = WWWGetValueByIndex(www_info, indx); if (isdigit(www_arg2[0])) nbr_complexity = (Int2)atoi(www_arg2); else nbr_complexity = ALL_NBR; } else nbr_complexity = ALL_NBR; cViewType = www_arg[0]; if (nbr_complexity == ALL_NBR) { if (cViewType == VIEW_IN_HTML) cViewType = VIEW_IN_HTML_PAGE; else if (cViewType == VIEW_IN_FASTA) cViewType = VIEW_IN_FASTA_PAGE; else if (cViewType == VIEW_IN_TEXT) cViewType = VIEW_IN_TEXT_PAGE; } } else { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "No alitype code -- Please choose Hypertext, Plain text or mFASTA.", NULL, TRUE); return 0; } if ((indx = WWWFindName(www_info, "atm_complexity")) < 0) complexity = ONECOORDRES; /* select alpha Carbons only by default */ else { www_arg = WWWGetValueByIndex(www_info, indx); if (isdigit(www_arg[0])) complexity = (Int2) atoi(www_arg); else complexity = ONECOORDRES; } if ((complexity != ONECOORDRES) && (complexity != ONECOORDATOM)) complexity = ONECOORDRES; /* bizarre value, but default to alpha-Carbons only */ /* if ((indx = WWWFindName(www_info, "asdi")) < 0) { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "No asdi was submitted.", NULL, TRUE); return 0; } www_arg = WWWGetValueByIndex(www_info, indx); aSdi = (Int4) atol (www_arg); */ if (cViewType == 'H' || cViewType == 'F' || cViewType == 'T') { nbr_complexity = ALL_NBR; if ((indx = WWWFindName(www_info, "allbsfid")) < 0) { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "No \"allbsfid\" was submitted!", NULL, TRUE); return 0; } www_arg = WWWGetValueByIndex(www_info, indx); MakeNbrList(www_arg, NULL, &BsfId, &hits_num, 0); gbp = (GiBsfIdDataPtr) MemNew (hits_num *sizeof(GiBsfIdData)); gbp[0].BsfId = BsfId[0]; for (i=1; i< hits_num; i++) { Fid = gbp[i].BsfId = BsfId[i]; if (JobID) ValNodeAddInt(&pvnFids, 0, Fid); } iFidCount = i-1; } else { CharPtr ptr = NULL; nbr_complexity = CHECKED_NBR; if ((indx = WWWFindName(www_info, "hit")) <0) { if ((indx = WWWFindName(www_info, "defhit")) <0) { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "No defhit was submitted!", NULL, TRUE); return 0; } else { www_arg = WWWGetValueByIndex(www_info, indx); hits_num = 2; gbp = (GiBsfIdDataPtr) MemNew (2*sizeof(GiBsfIdData)); BsfId = (Int4Ptr) MemNew (2*sizeof(Int4)); gbp[0].BsfId = BsfId[0] = Fsid * 10; if (isdigit(www_arg[0])) BsfId[1] = Fid = gbp[1].BsfId = atol(www_arg); else { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "Non-numeric defhit: defhit = ", ptr+1, TRUE); return 0; } if (cViewType == VIEW_IN_Cn3D_GEN || JobID) { ValNodeAddInt(&pvnFids, 0, Fid); iFidCount=1; } } } else { /* loop over all the "hit" values in the list */ NumLabels = WWWGetNumEntries(www_info); for (indx = 0; indx < NumLabels; indx++) { Name = WWWGetNameByIndex(www_info, indx); if (!StrICmp(Name, "hit")) hits_num++; } gbp = (GiBsfIdDataPtr) MemNew (++hits_num * sizeof(GiBsfIdData)); BsfId = (Int4Ptr) MemNew(hits_num * sizeof(Int4)); BsfId[0] = gbp[0].BsfId = Fsid * 10; for (indx = 0; indx < NumLabels; indx++) { Name = WWWGetNameByIndex(www_info, indx); if (!StrICmp(Name, "hit")) { www_arg = WWWGetValueByIndex(www_info, indx); if (isdigit(www_arg[0])) Fid =atoi(www_arg); else { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "Non-numeric hit: hit = .", ptr+1, TRUE); return 0; } if (++iFidCount > 10 && cViewType == VIEW_IN_Cn3D_GEN) break; /* up to 10 boxes, ignore the rest. */ ValNodeAddInt(&pvnFids, 0, Fid); BsfId[iFidCount] = gbp[iFidCount].BsfId = Fid; } } } } if (VASTInit(JobID) != TRUE) { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "Can't find VAST data on server.", NULL, TRUE); return 0; } /* Get BiostrucAnnotSet and SeqAnnot */ if (JobID) { /* VastSearch */ OpenMMDBAPI((POWER_VIEW /* ^ FETCH_ENTREZ */), NULL); pbsa = LocalGetFeatureSet(aMmdbId, Fsid, JobID); } else { VastPageDataPtr vpptmp; vpptmp = (VastPageDataPtr) MemNew ((hits_num-1) * sizeof(VastPageData)); vpp = (VastPageDataPtr) MemNew ((hits_num-1) * sizeof(VastPageData)); for (i=0; i< hits_num+1; i++) vpptmp[i].bBsfId = BsfId[i+1]; i =constructVastPagesByNbrs(vpptmp, (unsigned *)(BsfId+1),hits_num-1, aSdi); if (i != hits_num-1) { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "Error in getting VAST data.", NULL, TRUE); return 0; } OrderCopyVpp(vpptmp, vpp, hits_num-1, &(BsfId[1])); MemFree(vpptmp); pbsa = constructBASPFromVastPagePtr(vpp, hits_num-1); MemFree(vpp); } if (pbsa == NULL) { printf("Content-type: text/html\n\n"); printf("

VASTSERV Error (VastToCn3D):

\n"); printf("No alignment record exists for master mmdb_id = %d.\n", aMmdbId); printf("Please alert \"%s\" of this problem.

\n",MAILto); return 0; } if (JobID) { /* VastSearch */ for (i=1; i< hits_num; i++) { Int4 bsfid; bsfid = gbp[i].BsfId; gbp[i].gi = constructGi(bsfid/100000, (bsfid % 100000) / 1000); } pbsfs = pbsa->features; pbsf = pbsfs->features; } else for (i=0; i< hits_num; i++) { Int4 bsfid; bsfid = gbp[i].BsfId; gbp[i].gi = constructGi(bsfid/100000, (bsfid % 100000) / 1000); } if (JobID) { /* VastSearch */ if (iFidCount == 1) pbsaShort = BiostrucAnnotSetGetByFid(pbsa, Fid, Fsid); else pbsaShort = PruneBiostrucAnnotHits(pbsa, Fsid, pvnFids); } else pbsaShort = pbsa; if (pbsaShort == NULL) { PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "Can't find alignment record.", NULL, TRUE); return 0; } pbsfs = pbsaShort->features; if (pbsfs) { pbsf = pbsfs->features; szTemp = pbsf->name; StrCut(szName, pbsf->name, 1, 4); sprintf(pdbname_m, szName); chain_m = szTemp[4]; domNo_m = (Int4) atol (szTemp+5); } if (cViewType == VIEW_IN_Cn3DCACHE) bsap = BundleSeqsAlignsNew(); else if (cViewType != VIEW_IN_Cn3D_GEN) basp = BiostrucAlignSeqNew(); /* Get Biostruc for Cn3d, and SeqEntry (Bioseq) */ if (cViewType == VIEW_IN_Cn3D_GEN || JobID) { Int4 idx; pbsaStruct = BiostrucAlignNew(); if (JobID == NULL) { Boolean psok; pbsMaster = openBSP(aMmdbId, complexity, 1, TRUE, FALSE, FALSE, &psok, Database); } else { AsnName[0]='\0'; StringCpy(AsnName, "/b"); StringCat(AsnName, szName); AsnPath[0]='\0'; StringCpy(AsnPath, VSPATH); StringCat(AsnPath, JobID); StringCat(AsnPath, AsnName); pbsMaster = FetchBS(AsnPath, 0, complexity, 1, POWER_VIEW); } if (pbsMaster == NULL) { PrtMes(NULL, "VASTSERV (Vast2Cn3D)", "Unable to load master structure from a Vast Search result.", NULL, TRUE); return 0; } aipr = NULL; aipr = AsnIoOpen("bstdt", "rb"); if (aipr == NULL) { PrtMes(MAILto, "VASTSERV (Vast2Cn3D)", "Can't find standard dictionary.", NULL, TRUE); return 0; } stdDictionary = BiostrucResidueGraphSetAsnRead(aipr, NULL); AsnIoFlush(aipr); aipr = AsnIoClose(aipr); idx = GetMGPIdx(gbp, BsfId[0]); if (JobID == NULL) sep = (SeqEntryPtr) constructSeqEntryForGi(gbp[idx].gi, TRUE, Database); else { sep = (SeqEntryPtr) MakeBioseqs (pbsMaster, stdDictionary); if (sep->choice ==2) { Int2 i=1; BioseqSetPtr bssp = NULL; bssp = (BioseqSetPtr)sep->data.ptrvalue; sep = (SeqEntryPtr) bssp->seq_set; while (i< aChain) { sep = sep->next; i++; } if (sep->next) sep->next= NULL; } } if ( sep == NULL ) { PrtMes(MAILto, "VASTSERV (Vast2Cn3D)", "Unable to get SeqEntry.", NULL, TRUE); return 0; } if (cViewType == VIEW_IN_Cn3D_GEN) { ValNodeLink(&(pbsaStruct->sequences), sep); if (JobID) { biosp = (BioseqPtr)sep->data.ptrvalue; sid = biosp->id; objid = (ObjectIdPtr) sid->data.ptrvalue; } } else if (cViewType != VIEW_IN_Cn3DCACHE) ValNodeLink(&(basp->sequences), sep); else { PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "Can't work in Cn3D/Cache mode -- please try Cn3D mode.", NULL, TRUE); return 0; } /* Make a linked list of Biostrucs of the slave structures */ for (i=1; i< hits_num; i++) { idx = GetMGPIdx(gbp, BsfId[i]); if (!pbsSlaveHead) { Boolean psok; pbsSlaveHead = openBSP(gbp[idx].BsfId/100000, complexity, 1, TRUE, FALSE, FALSE, &psok, Database); if (!pbsSlaveHead) { PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "Unable to load slave structure.", NULL, TRUE); return 0; } /* Make Bioseq for Slaves */ sep = (SeqEntryPtr) constructSeqEntryForGi(gbp[idx].gi, TRUE, Database); if ( sep == NULL ) { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "Unable to get SeqEntry.", NULL, TRUE); return 0; } if (cViewType == VIEW_IN_Cn3D_GEN) ValNodeLink(&(pbsaStruct->sequences), sep); else if (cViewType != VIEW_IN_Cn3DCACHE) ValNodeLink(&(basp->sequences), sep); else { PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "Can't work in Cn3D/Cache mode -- please try Cn3D mode.", NULL, TRUE); return 0; } pbsSlaveTail = pbsSlaveHead; } else { Boolean psok; pbsSlave =openBSP(gbp[idx].BsfId/100000, complexity, 1, TRUE, FALSE, FALSE, &psok, Database); if (!pbsSlave) { PrtMes(NULL, "VASTSERV (Vast2Cn3D)", "Unable to load slave structure.", NULL, TRUE); return 0; } sep = (SeqEntryPtr) constructSeqEntryForGi(gbp[idx].gi, TRUE, Database); if ( sep == NULL ) { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "Unable to get SeqEntry.", NULL, TRUE); return 0; } if (cViewType == VIEW_IN_Cn3D_GEN) ValNodeLink(&(pbsaStruct->sequences), sep); else if (cViewType != VIEW_IN_Cn3DCACHE) ValNodeLink(&(basp->sequences), sep); else { PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "Can't work in Cn3d/Cache mode -- please try Cn3D mode.", NULL, TRUE); return 0; } pbsSlaveTail->next = pbsSlave; pbsSlaveTail = pbsSlaveTail->next; pbsSlaveTail->next = NULL; } } } else { /* cViewType != Cn3D_IN_GEN */ BioseqPtr bsp; /* Get SeqEntryPtr */ for (i=0; i< hits_num; i++) { Int4 idx; idx = GetMGPIdx(gbp, BsfId[i]); sep = constructSeqEntryForGi(gbp[idx].gi, TRUE, Database); if (sep == NULL) { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "Unable to get Bioseq.", NULL, TRUE); return 0; } bsp = sep->data.ptrvalue; AddMMDBIdToBioseq(bsp, gbp[idx].BsfId/100000); if (sep == NULL) { PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "Unable to get Bioseq.", NULL, TRUE); return 0; } if (cViewType == VIEW_IN_Cn3DCACHE) ValNodeLink(&(bsap->sequences), sep); else ValNodeLink(&(basp->sequences), sep); } } MemFree(gbp); /* Make a linked list of sequence alignments of master and slaves */ pbsf=pbsfs->features; while (pbsf) { if (!psaAlignHead) { psaAlignHead = fnPBSFtoPSA (pbsf); /* get the sequence alignments */ if (psaAlignHead == NULL || psaAlignHead->data == NULL) { PrtMes(MAILto, "VASTSERV (Vast2Cn3D)", "Unable to create SeqAnnot.", NULL, TRUE); return 0; } salpHead = (SeqAlignPtr)(psaAlignHead->data); salpTail = salpHead; if (JobID && cViewType == VIEW_IN_Cn3D_GEN) { DenseDiagPtr dendiag; for (dendiag=(DenseDiagPtr)salpHead->segs;dendiag;dendiag=dendiag->next) { sid = dendiag->id; sid->choice = 1; sid->data.ptrvalue = (ObjectIdPtr)objid; } } } else { psaAlignTail = fnPBSFtoPSA (pbsf); salpTail->next = (SeqAlignPtr)(psaAlignTail->data); if (psaAlignTail == NULL || psaAlignTail->data == NULL) { PrtMes(NULL, "VASTSRV (Vast2Cn3D)", "Unable to create SeqAnnot.", NULL, TRUE); return 0; } salpTail = salpTail->next; if (JobID && cViewType == VIEW_IN_Cn3D_GEN) { DenseDiagPtr dendiag; for (dendiag=(DenseDiagPtr)salpTail->segs;dendiag;dendiag=dendiag->next) { sid = dendiag->id; sid->choice = 1; sid->data.ptrvalue = (ObjectIdPtr)objid; } } salpTail->next = NULL; } pbsf = pbsf->next; } /* assemble pvnNcbi */ pvnNcbi = ValNodeNew(NULL); if (cViewType == VIEW_IN_Cn3D_GEN) { pbsaStruct->master = pbsMaster; pbsaStruct->slaves = pbsSlaveHead; pbsaStruct->alignments = pbsaShort; pbsaStruct->seqalign = psaAlignHead; pvnNcbi->choice = NcbiMimeAsn1_alignstruc; pvnNcbi->data.ptrvalue = pbsaStruct; /* pvnNcbi = (NcbiMimeAsn1Ptr) CheckId(pvnNcbi, JobID); */ /* to check identity, yanli */ } else if (cViewType == VIEW_IN_HTML || cViewType == VIEW_IN_FASTA || cViewType == VIEW_IN_HTML_PAGE || cViewType == VIEW_IN_FASTA_PAGE || cViewType == VIEW_IN_TEXT || cViewType == VIEW_IN_TEXT_PAGE) { basp->seqalign = psaAlignHead; pvnNcbi->choice = NcbiMimeAsn1_alignseq; pvnNcbi->data.ptrvalue = basp; if (JobID) { SeqEntryPtr sep=NULL; BioseqPtr bsp=NULL; SeqIdPtr sip=NULL, sip_next=NULL; ObjectIdPtr oip=NULL; PDBSeqIdPtr psip=NULL; sep=basp->sequences; bsp = (BioseqPtr)sep->data.ptrvalue; sip = bsp->id; if (sip->choice == SEQID_LOCAL) { sip_next = sip->next; oip = (ObjectIdPtr)sip->data.ptrvalue; psip = PDBSeqIdNew(); psip->mol= (CharPtr) MemNew (5); StrCut(psip->mol, oip->str, 1, 4); psip->chain = (Uint1)(oip->str)[5]; oip = ObjectIdFree(oip); sip->choice = SEQID_PDB; sip->next = sip_next; sip->data.ptrvalue = psip; } } } else { /*if (cViewType == VIEW_IN_Cn3dCache) */ BiostrucSeqsAlignsCddPtr bsacp; SeqAlignData_seq_align_dataPtr sadp; bsap->seqaligns = psaAlignHead; bsap->strucaligns = pbsaShort; sadp = ValNodeNew(NULL); sadp->data.ptrvalue = bsap; sadp->choice = SeqAlignData_seq_align_data_bundle; bsacp = BiostrucSeqsAlignsCddNew(); bsacp->SeqAlignData_seq_align_data = sadp; if (complexity == ONECOORDRES) bsacp->structure_type = 2; /* ncbi_backbone */ else bsacp->structure_type = 3; /* ncbi_all_atoms */ pvnNcbi->choice = NcbiMimeAsn1_general; pvnNcbi->data.ptrvalue = bsacp; } /* {AsnIoPtr aipr; aipr=AsnIoOpen("pvnNcbi.out", "w"); NcbiMimeAsn1AsnWrite(pvnNcbi, aipr, NULL); AsnIoClose(aipr); } */ if (cViewType == VIEW_IN_Cn3D_GEN || cViewType == VIEW_IN_Cn3DCACHE) { if (iPDB == 0) /* cn3d MIME */ printf ("Content-type: chemical/ncbi-asn1-binary\n\n"); else if (iPDB == 1) { /* "See File" */ printf ("Content-type: text/html\n\n"); printf ("
\n");
    }
    else        /* "Save File" */
      printf ("Content-type: application/octet-stream\n\n");

    if (iPDB != 1) paiFile = AsnIoNew(ASNIO_BIN_OUT, stdout, NULL, NULL, NULL); 
    else paiFile = AsnIoNew(ASNIO_TEXT_OUT, stdout, NULL, NULL, NULL);

    NcbiMimeAsn1AsnWrite(pvnNcbi, paiFile, NULL); 
    AsnIoFlush(paiFile); 
    AsnIoClose(paiFile);
  }
  else {

    Uint4      	size;
    BytePtr 	buf;
    Nlm_ByteStorePtr bsp = NULL;
    AsnIoBSPtr	aibp = NULL;

    bsp = Nlm_BSNew(1024);
    aibp = AsnIoBSOpen("wb", bsp);
    if (!bsp || !aibp) {
        PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "AsnIoBS creation failed.",
		NULL, TRUE); 
	return 0;
    }

    if (!(NcbiMimeAsn1AsnWrite(pvnNcbi, aibp->aip, NULL)))  {
        PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "C object -> AsnInBS failed.",
		NULL, TRUE);
	return 0;
    }

    AsnIoFlush(aibp->aip);
    AsnIoBSClose(aibp); aibp = NULL;

    size = Nlm_BSLen(bsp);
    buf = MemNew(size);
    if (!buf) {
        PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "buf allocation failed",
		NULL, TRUE); 
	return 0;
    }
       
    Nlm_BSSeek(bsp, 0, 0);
    if (Nlm_BSRead(bsp, buf, size) != size) {
        PrtMes(MAILto, "VASTSRV (Vast2Cn3D)", "AsnIoBS -> buf failed",
		NULL, TRUE); 
	return 0;
    }

    Nlm_BSFree(bsp); bsp = NULL;

    printf("Content-type: text/html\n\n");
    WWWPrintFileData("sshead.txt", stdout);
    printf("\n\n");
    PrintQueryInfo(stdout, pdbname_m, chain_m, domNo_m, aMmdbId, JobID);
    printf("
\n");
    printf("
\n");
    if (cViewType == VIEW_IN_HTML || cViewType == VIEW_IN_HTML_PAGE)
      CAV_DisplayMultiple(buf, CAV_HTML|CAV_SHOW_IDENTITY, 60, 2.0, NULL, 0, NULL); 
    else if (cViewType == VIEW_IN_FASTA || cViewType == VIEW_IN_FASTA_PAGE) {
      printf("
\n");
      CAV_DisplayMultiple(buf, 
		CAV_FASTA|CAV_LEFTTAILS|CAV_RIGHTTAILS|CAV_FASTA_LOWERCASE, 
		60, 2.0, NULL, 0, NULL);
      printf("
\n");
    }
    else if (cViewType == VIEW_IN_TEXT || cViewType == VIEW_IN_TEXT_PAGE) {
	printf("
\n");
	CAV_DisplayMultiple(buf, CAV_TEXT, 60, 2.0, NULL, 0, NULL);
	printf("
\n");
    }

    printf("
\n");
    printf("\n");

    MemFree(buf);
  }

  if (cViewType==VIEW_IN_Cn3D_GEN) {
  	CloseMMDBAPI();
  	MMDBFini();
  }
  VASTFini();

  NcbiMimeAsn1Free(pvnNcbi); 

  return 0; 
} 	/* end of VastToCn3DAndAli */