--$Revision: 6.12 $
--****************************************************************
--
--  NCBI MIME type (chemical/ncbi-asn1-ascii and chemical/ncbi-asn1-binary)
--  by Jonathan Epstein, February 1996
--
--****************************************************************

NCBI-Mime DEFINITIONS ::=
BEGIN

EXPORTS Ncbi-mime-asn1;
IMPORTS Biostruc, Biostruc-annot-set FROM MMDB
    Cdd FROM NCBI-Cdd
	Seq-entry FROM NCBI-Seqset
	Seq-annot FROM NCBI-Sequence
    Medline-entry FROM NCBI-Medline
    Cn3d-style-dictionary, Cn3d-user-annotations FROM NCBI-Cn3d;

Ncbi-mime-asn1 ::= CHOICE {
	entrez	Entrez-general,			-- just a structure
    alignstruc  Biostruc-align,     -- structures & sequences & alignments
	alignseq	Biostruc-align-seq,	-- sequence alignment
    strucseq    Biostruc-seq,       -- structure & sequences
    strucseqs   Biostruc-seqs,      -- structure & sequences & alignments
    general     Biostruc-seqs-aligns-cdd    -- all-purpose "grab bag"
	-- others may be added here in the future
}

-- generic bundle of sequence and alignment info
Bundle-seqs-aligns ::= SEQUENCE {
    sequences SET OF Seq-entry OPTIONAL,        -- sequences
    seqaligns SET OF Seq-annot OPTIONAL,        -- sequence alignments
    strucaligns Biostruc-annot-set OPTIONAL,    -- structure alignments
    imports SET OF Seq-annot OPTIONAL,          -- imports (updates in Cn3D)
    style-dictionary Cn3d-style-dictionary OPTIONAL,    -- Cn3D stuff
    user-annotations Cn3d-user-annotations OPTIONAL
}

Biostruc-seqs-aligns-cdd ::= SEQUENCE {
    seq-align-data CHOICE {
        bundle Bundle-seqs-aligns,          -- either seqs + alignments
        cdd Cdd                             -- or CDD (which contains these)
    },
    structures SET OF Biostruc OPTIONAL,    -- structures
    structure-type ENUMERATED {             -- type of structures to load if
        ncbi-backbone(2),                   -- not present; meanings and
        ncbi-all-atom(3),                   -- values are same as MMDB's
        pdb-model(4)                        -- Model-type
    } OPTIONAL
}

Biostruc-align ::= SEQUENCE {
	master	Biostruc,
	slaves	SET OF Biostruc,
	alignments	Biostruc-annot-set,	-- structure alignments
	sequences SET OF Seq-entry,	-- sequences
	seqalign SET OF Seq-annot,
	style-dictionary Cn3d-style-dictionary OPTIONAL,
	user-annotations Cn3d-user-annotations OPTIONAL
}

Biostruc-align-seq ::= SEQUENCE {	-- display seq structure align only
	sequences SET OF Seq-entry,	-- sequences
	seqalign SET OF Seq-annot,
	style-dictionary Cn3d-style-dictionary OPTIONAL,
	user-annotations Cn3d-user-annotations OPTIONAL
}

Biostruc-seq ::= SEQUENCE {	-- display  structure seq added by yanli
	structure Biostruc,
	sequences SET OF Seq-entry,
	style-dictionary Cn3d-style-dictionary OPTIONAL,
	user-annotations Cn3d-user-annotations OPTIONAL
}

Biostruc-seqs ::= SEQUENCE { -- display blast alignment along with neighbor's structure added by yanli
	structure Biostruc,
	sequences SET OF Seq-entry,	-- sequences
	seqalign SET OF Seq-annot,
	style-dictionary Cn3d-style-dictionary OPTIONAL,
	user-annotations Cn3d-user-annotations OPTIONAL
}

Entrez-style ::= ENUMERATED {
	docsum (1),
	genbank (2) ,
	genpept (3) ,
	fasta (4) ,
	asn1 (5) ,
	graphic (6) ,
	alignment (7) ,
	globalview (8) ,
	report (9) ,
	medlars (10) ,
	embl (11) ,
	pdb (12) ,
	kinemage (13) }

Entrez-general ::= SEQUENCE {
	title VisibleString OPTIONAL,
	data CHOICE {
		ml	Medline-entry ,
		prot	Seq-entry ,
		nuc	Seq-entry ,
		genome	Seq-entry ,
		structure Biostruc ,
		strucAnnot Biostruc-annot-set } ,
	style Entrez-style ,
	location VisibleString OPTIONAL }
END