112 lines
3.6 KiB
Groff
112 lines
3.6 KiB
Groff
--$Revision: 6.12 $
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--****************************************************************
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--
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-- NCBI MIME type (chemical/ncbi-asn1-ascii and chemical/ncbi-asn1-binary)
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-- by Jonathan Epstein, February 1996
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--
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--****************************************************************
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NCBI-Mime DEFINITIONS ::=
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BEGIN
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EXPORTS Ncbi-mime-asn1;
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IMPORTS Biostruc, Biostruc-annot-set FROM MMDB
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Cdd FROM NCBI-Cdd
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Seq-entry FROM NCBI-Seqset
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Seq-annot FROM NCBI-Sequence
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Medline-entry FROM NCBI-Medline
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Cn3d-style-dictionary, Cn3d-user-annotations FROM NCBI-Cn3d;
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Ncbi-mime-asn1 ::= CHOICE {
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entrez Entrez-general, -- just a structure
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alignstruc Biostruc-align, -- structures & sequences & alignments
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alignseq Biostruc-align-seq, -- sequence alignment
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strucseq Biostruc-seq, -- structure & sequences
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strucseqs Biostruc-seqs, -- structure & sequences & alignments
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general Biostruc-seqs-aligns-cdd -- all-purpose "grab bag"
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-- others may be added here in the future
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}
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-- generic bundle of sequence and alignment info
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Bundle-seqs-aligns ::= SEQUENCE {
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sequences SET OF Seq-entry OPTIONAL, -- sequences
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seqaligns SET OF Seq-annot OPTIONAL, -- sequence alignments
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strucaligns Biostruc-annot-set OPTIONAL, -- structure alignments
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imports SET OF Seq-annot OPTIONAL, -- imports (updates in Cn3D)
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style-dictionary Cn3d-style-dictionary OPTIONAL, -- Cn3D stuff
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user-annotations Cn3d-user-annotations OPTIONAL
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}
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Biostruc-seqs-aligns-cdd ::= SEQUENCE {
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seq-align-data CHOICE {
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bundle Bundle-seqs-aligns, -- either seqs + alignments
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cdd Cdd -- or CDD (which contains these)
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},
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structures SET OF Biostruc OPTIONAL, -- structures
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structure-type ENUMERATED { -- type of structures to load if
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ncbi-backbone(2), -- not present; meanings and
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ncbi-all-atom(3), -- values are same as MMDB's
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pdb-model(4) -- Model-type
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} OPTIONAL
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}
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Biostruc-align ::= SEQUENCE {
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master Biostruc,
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slaves SET OF Biostruc,
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alignments Biostruc-annot-set, -- structure alignments
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sequences SET OF Seq-entry, -- sequences
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seqalign SET OF Seq-annot,
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style-dictionary Cn3d-style-dictionary OPTIONAL,
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user-annotations Cn3d-user-annotations OPTIONAL
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}
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Biostruc-align-seq ::= SEQUENCE { -- display seq structure align only
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sequences SET OF Seq-entry, -- sequences
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seqalign SET OF Seq-annot,
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style-dictionary Cn3d-style-dictionary OPTIONAL,
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user-annotations Cn3d-user-annotations OPTIONAL
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}
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Biostruc-seq ::= SEQUENCE { -- display structure seq added by yanli
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structure Biostruc,
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sequences SET OF Seq-entry,
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style-dictionary Cn3d-style-dictionary OPTIONAL,
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user-annotations Cn3d-user-annotations OPTIONAL
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}
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Biostruc-seqs ::= SEQUENCE { -- display blast alignment along with neighbor's structure added by yanli
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structure Biostruc,
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sequences SET OF Seq-entry, -- sequences
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seqalign SET OF Seq-annot,
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style-dictionary Cn3d-style-dictionary OPTIONAL,
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user-annotations Cn3d-user-annotations OPTIONAL
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}
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Entrez-style ::= ENUMERATED {
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docsum (1),
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genbank (2) ,
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genpept (3) ,
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fasta (4) ,
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asn1 (5) ,
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graphic (6) ,
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alignment (7) ,
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globalview (8) ,
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report (9) ,
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medlars (10) ,
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embl (11) ,
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pdb (12) ,
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kinemage (13) }
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Entrez-general ::= SEQUENCE {
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title VisibleString OPTIONAL,
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data CHOICE {
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ml Medline-entry ,
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prot Seq-entry ,
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nuc Seq-entry ,
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genome Seq-entry ,
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structure Biostruc ,
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strucAnnot Biostruc-annot-set } ,
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style Entrez-style ,
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location VisibleString OPTIONAL }
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END
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