NCBI C Toolkit Cross Reference

C/asn/seqloc.asn

  1 --$Revision: 6.4 $
  2 --**********************************************************************
  3 --
  4 --  NCBI Sequence location and identifier elements
  5 --  by James Ostell, 1990
  6 --
  7 --  Version 3.0 - 1994
  8 --
  9 --**********************************************************************
 10 
 11 NCBI-Seqloc DEFINITIONS ::=
 12 BEGIN
 13 
 14 EXPORTS Seq-id, Seq-loc, Seq-interval, Packed-seqint, Seq-point, Packed-seqpnt,
 15         Na-strand, Giimport-id;
 16 
 17 IMPORTS Object-id, Int-fuzz, Dbtag, Date FROM NCBI-General
 18         Id-pat FROM NCBI-Biblio
 19         Feat-id FROM NCBI-Seqfeat;
 20 
 21 --*** Sequence identifiers ********************************
 22 --*
 23 
 24 Seq-id ::= CHOICE {
 25     local Object-id ,            -- local use
 26     gibbsq INTEGER ,             -- Geninfo backbone seqid
 27     gibbmt INTEGER ,             -- Geninfo backbone moltype
 28     giim Giimport-id ,           -- Geninfo import id
 29     genbank Textseq-id ,
 30     embl Textseq-id ,
 31     pir Textseq-id ,
 32     swissprot Textseq-id ,
 33     patent Patent-seq-id ,
 34     other Textseq-id ,           -- for historical reasons, 'other' = 'refseq'
 35     general Dbtag ,              -- for other databases
 36     gi INTEGER ,                 -- GenInfo Integrated Database
 37     ddbj Textseq-id ,            -- DDBJ
 38     prf Textseq-id ,             -- PRF SEQDB
 39     pdb PDB-seq-id ,             -- PDB sequence
 40     tpg Textseq-id ,             -- Third Party Annot/Seq Genbank
 41     tpe Textseq-id ,             -- Third Party Annot/Seq EMBL
 42     tpd Textseq-id ,             -- Third Party Annot/Seq DDBJ
 43     gpipe Textseq-id ,           -- Internal NCBI genome pipeline processing ID
 44     named-annot-track Textseq-id -- Internal named annotation tracking ID
 45 }
 46 
 47 
 48 Patent-seq-id ::= SEQUENCE {
 49     seqid INTEGER ,         -- number of sequence in patent
 50     cit Id-pat }           -- patent citation
 51 
 52 Textseq-id ::= SEQUENCE {
 53     name VisibleString OPTIONAL ,
 54     accession VisibleString OPTIONAL ,
 55     release VisibleString OPTIONAL ,
 56     version INTEGER OPTIONAL }
 57 
 58 Giimport-id ::= SEQUENCE {
 59     id INTEGER ,                     -- the id to use here
 60     db VisibleString OPTIONAL ,      -- dbase used in
 61     release VisibleString OPTIONAL } -- the release
 62 
 63 PDB-seq-id ::= SEQUENCE {
 64     mol PDB-mol-id ,           -- the molecule name
 65     chain INTEGER DEFAULT 32 , -- a single ASCII character, chain id
 66     rel Date OPTIONAL }        -- release date, month and year
 67 
 68 PDB-mol-id ::= VisibleString  -- name of mol, 4 chars
 69     
 70 --*** Sequence locations **********************************
 71 --*
 72 
 73 Seq-loc ::= CHOICE {
 74     null NULL ,           -- not placed
 75     empty Seq-id ,        -- to NULL one Seq-id in a collection
 76     whole Seq-id ,        -- whole sequence
 77     int Seq-interval ,    -- from to
 78     packed-int Packed-seqint ,
 79     pnt Seq-point ,
 80     packed-pnt Packed-seqpnt ,
 81     mix Seq-loc-mix ,
 82     equiv Seq-loc-equiv ,  -- equivalent sets of locations
 83     bond Seq-bond ,
 84     feat Feat-id }         -- indirect, through a Seq-feat
 85     
 86 
 87 Seq-interval ::= SEQUENCE {
 88     from INTEGER ,
 89     to INTEGER ,
 90     strand Na-strand OPTIONAL ,
 91     id Seq-id ,    -- WARNING: this used to be optional
 92     fuzz-from Int-fuzz OPTIONAL ,
 93     fuzz-to Int-fuzz OPTIONAL }
 94 
 95 Packed-seqint ::= SEQUENCE OF Seq-interval
 96 
 97 Seq-point ::= SEQUENCE {
 98     point INTEGER ,
 99     strand Na-strand OPTIONAL ,
100     id Seq-id ,     -- WARNING: this used to be optional
101     fuzz Int-fuzz OPTIONAL }
102 
103 Packed-seqpnt ::= SEQUENCE {
104     strand Na-strand OPTIONAL ,
105     id Seq-id ,
106     fuzz Int-fuzz OPTIONAL ,
107     points SEQUENCE OF INTEGER }
108 
109 Na-strand ::= ENUMERATED {          -- strand of nucleic acid
110     unknown (0) ,
111     plus (1) ,
112     minus (2) ,               
113     both (3) ,                -- in forward orientation
114     both-rev (4) ,            -- in reverse orientation
115     other (255) }
116 
117 Seq-bond ::= SEQUENCE {         -- bond between residues
118     a Seq-point ,           -- connection to a least one residue
119     b Seq-point OPTIONAL }  -- other end may not be available
120 
121 Seq-loc-mix ::= SEQUENCE OF Seq-loc   -- this will hold anything
122 
123 Seq-loc-equiv ::= SET OF Seq-loc      -- for a set of equivalent locations
124 
125 END
126     
127
[ 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.