NCBI C Toolkit Cross Reference

C/asn/ncbimime.asn

  1 --$Revision: 6.12 $
  2 --****************************************************************
  3 --
  4 --  NCBI MIME type (chemical/ncbi-asn1-ascii and chemical/ncbi-asn1-binary)
  5 --  by Jonathan Epstein, February 1996
  6 --
  7 --****************************************************************
  8 
  9 NCBI-Mime DEFINITIONS ::=
 10 BEGIN
 11 
 12 EXPORTS Ncbi-mime-asn1;
 13 IMPORTS Biostruc, Biostruc-annot-set FROM MMDB
 14     Cdd FROM NCBI-Cdd
 15         Seq-entry FROM NCBI-Seqset
 16         Seq-annot FROM NCBI-Sequence
 17     Medline-entry FROM NCBI-Medline
 18     Cn3d-style-dictionary, Cn3d-user-annotations FROM NCBI-Cn3d;
 19 
 20 Ncbi-mime-asn1 ::= CHOICE {
 21         entrez  Entrez-general,                 -- just a structure
 22     alignstruc  Biostruc-align,     -- structures & sequences & alignments
 23         alignseq        Biostruc-align-seq,     -- sequence alignment
 24     strucseq    Biostruc-seq,       -- structure & sequences
 25     strucseqs   Biostruc-seqs,      -- structure & sequences & alignments
 26     general     Biostruc-seqs-aligns-cdd    -- all-purpose "grab bag"
 27         -- others may be added here in the future
 28 }
 29 
 30 -- generic bundle of sequence and alignment info
 31 Bundle-seqs-aligns ::= SEQUENCE {
 32     sequences SET OF Seq-entry OPTIONAL,        -- sequences
 33     seqaligns SET OF Seq-annot OPTIONAL,        -- sequence alignments
 34     strucaligns Biostruc-annot-set OPTIONAL,    -- structure alignments
 35     imports SET OF Seq-annot OPTIONAL,          -- imports (updates in Cn3D)
 36     style-dictionary Cn3d-style-dictionary OPTIONAL,    -- Cn3D stuff
 37     user-annotations Cn3d-user-annotations OPTIONAL
 38 }
 39 
 40 Biostruc-seqs-aligns-cdd ::= SEQUENCE {
 41     seq-align-data CHOICE {
 42         bundle Bundle-seqs-aligns,          -- either seqs + alignments
 43         cdd Cdd                             -- or CDD (which contains these)
 44     },
 45     structures SET OF Biostruc OPTIONAL,    -- structures
 46     structure-type ENUMERATED {             -- type of structures to load if
 47         ncbi-backbone(2),                   -- not present; meanings and
 48         ncbi-all-atom(3),                   -- values are same as MMDB's
 49         pdb-model(4)                        -- Model-type
 50     } OPTIONAL
 51 }
 52 
 53 Biostruc-align ::= SEQUENCE {
 54         master  Biostruc,
 55         slaves  SET OF Biostruc,
 56         alignments      Biostruc-annot-set,     -- structure alignments
 57         sequences SET OF Seq-entry,     -- sequences
 58         seqalign SET OF Seq-annot,
 59         style-dictionary Cn3d-style-dictionary OPTIONAL,
 60         user-annotations Cn3d-user-annotations OPTIONAL
 61 }
 62 
 63 Biostruc-align-seq ::= SEQUENCE {       -- display seq structure align only
 64         sequences SET OF Seq-entry,     -- sequences
 65         seqalign SET OF Seq-annot,
 66         style-dictionary Cn3d-style-dictionary OPTIONAL,
 67         user-annotations Cn3d-user-annotations OPTIONAL
 68 }
 69 
 70 Biostruc-seq ::= SEQUENCE {     -- display  structure seq added by yanli
 71         structure Biostruc,
 72         sequences SET OF Seq-entry,
 73         style-dictionary Cn3d-style-dictionary OPTIONAL,
 74         user-annotations Cn3d-user-annotations OPTIONAL
 75 }
 76 
 77 Biostruc-seqs ::= SEQUENCE { -- display blast alignment along with neighbor's structure added by yanli
 78         structure Biostruc,
 79         sequences SET OF Seq-entry,     -- sequences
 80         seqalign SET OF Seq-annot,
 81         style-dictionary Cn3d-style-dictionary OPTIONAL,
 82         user-annotations Cn3d-user-annotations OPTIONAL
 83 }
 84 
 85 Entrez-style ::= ENUMERATED {
 86         docsum (1),
 87         genbank (2) ,
 88         genpept (3) ,
 89         fasta (4) ,
 90         asn1 (5) ,
 91         graphic (6) ,
 92         alignment (7) ,
 93         globalview (8) ,
 94         report (9) ,
 95         medlars (10) ,
 96         embl (11) ,
 97         pdb (12) ,
 98         kinemage (13) }
 99 
100 Entrez-general ::= SEQUENCE {
101         title VisibleString OPTIONAL,
102         data CHOICE {
103                 ml      Medline-entry ,
104                 prot    Seq-entry ,
105                 nuc     Seq-entry ,
106                 genome  Seq-entry ,
107                 structure Biostruc ,
108                 strucAnnot Biostruc-annot-set } ,
109         style Entrez-style ,
110         location VisibleString OPTIONAL }
111 END
[ source navigation ] [ diff markup ] [ identifier search ] [ freetext search ] [ file search ]
This page was automatically generated by the LXR engine.
Visit the LXR main site for more information.