src/objects/seqloc/seqloc.asn

--$Revision: 88993 $
--**********************************************************************
--
--  NCBI Sequence location and identifier elements
--  by James Ostell, 1990
--
--  Version 3.0 - 1994
--
--**********************************************************************

NCBI-Seqloc DEFINITIONS ::=
BEGIN

EXPORTS Seq-id, Seq-loc, Seq-interval, Packed-seqint, Seq-point, Packed-seqpnt,
        Na-strand, Giimport-id;

IMPORTS Object-id, Int-fuzz, Dbtag, Date FROM NCBI-General
        Id-pat FROM NCBI-Biblio
        Feat-id FROM NCBI-Seqfeat;

--*** Sequence identifiers ********************************
--*

Seq-id ::= CHOICE {
    local Object-id ,            -- local use
    gibbsq INTEGER ,             -- Geninfo backbone seqid
    gibbmt INTEGER ,             -- Geninfo backbone moltype
    giim Giimport-id ,           -- Geninfo import id
    genbank Textseq-id ,
    embl Textseq-id ,
    pir Textseq-id ,
    swissprot Textseq-id ,
    patent Patent-seq-id ,
    other Textseq-id ,           -- for historical reasons, 'other' = 'refseq'
    general Dbtag ,              -- for other databases
    gi INTEGER ,                 -- GenInfo Integrated Database
    ddbj Textseq-id ,            -- DDBJ
    prf Textseq-id ,             -- PRF SEQDB
    pdb PDB-seq-id ,             -- PDB sequence
    tpg Textseq-id ,             -- Third Party Annot/Seq Genbank
    tpe Textseq-id ,             -- Third Party Annot/Seq EMBL
    tpd Textseq-id ,             -- Third Party Annot/Seq DDBJ
    gpipe Textseq-id ,           -- Internal NCBI genome pipeline processing ID
    named-annot-track Textseq-id -- Internal named annotation tracking ID
}

Seq-id-set ::= SET OF Seq-id


Patent-seq-id ::= SEQUENCE {
    seqid INTEGER ,         -- number of sequence in patent
    cit Id-pat }           -- patent citation

Textseq-id ::= SEQUENCE {
    name VisibleString OPTIONAL ,
    accession VisibleString OPTIONAL ,
    release VisibleString OPTIONAL ,
    version INTEGER OPTIONAL }

Giimport-id ::= SEQUENCE {
    id INTEGER ,                     -- the id to use here
    db VisibleString OPTIONAL ,      -- dbase used in
    release VisibleString OPTIONAL } -- the release

PDB-seq-id ::= SEQUENCE {            -- 
      mol PDB-mol-id ,                    -- the molecule name
      chain INTEGER DEFAULT 32 ,          -- Deprecated:  'chain' can't support multiple character
                                          -- PDB chain identifiers (introduced in 2015).
                                          -- 'chain-id' stores chain identifiers of any length.
      rel Date OPTIONAL ,                 -- release date, month and year
      chain-id VisibleString OPTIONAL }   -- chain identifier; length-independent generalization of 'chain' 
                                          -- NB: unlike 'chain', 'chain-id' has no default

PDB-mol-id ::= VisibleString  -- name of mol, 4 chars
    
--*** Sequence locations **********************************
--*

Seq-loc ::= CHOICE {
    null NULL ,           -- not placed
    empty Seq-id ,        -- to NULL one Seq-id in a collection
    whole Seq-id ,        -- whole sequence
    int Seq-interval ,    -- from to
    packed-int Packed-seqint ,
    pnt Seq-point ,
    packed-pnt Packed-seqpnt ,
    mix Seq-loc-mix ,
    equiv Seq-loc-equiv ,  -- equivalent sets of locations
    bond Seq-bond ,
    feat Feat-id }         -- indirect, through a Seq-feat
    

Seq-interval ::= SEQUENCE {
    from INTEGER ,
    to INTEGER ,
    strand Na-strand OPTIONAL ,
    id Seq-id ,    -- WARNING: this used to be optional
    fuzz-from Int-fuzz OPTIONAL ,
    fuzz-to Int-fuzz OPTIONAL }

Packed-seqint ::= SEQUENCE OF Seq-interval

Seq-point ::= SEQUENCE {
    point INTEGER ,
    strand Na-strand OPTIONAL ,
    id Seq-id ,     -- WARNING: this used to be optional
    fuzz Int-fuzz OPTIONAL }

Packed-seqpnt ::= SEQUENCE {
    strand Na-strand OPTIONAL ,
    id Seq-id ,
    fuzz Int-fuzz OPTIONAL ,
    points SEQUENCE OF INTEGER }

Na-strand ::= ENUMERATED {          -- strand of nucleic acid
    unknown (0) ,
    plus (1) ,
    minus (2) ,               
    both (3) ,                -- in forward orientation
    both-rev (4) ,            -- in reverse orientation
    other (255) }

Seq-bond ::= SEQUENCE {         -- bond between residues
    a Seq-point ,           -- connection to a least one residue
    b Seq-point OPTIONAL }  -- other end may not be available

Seq-loc-mix ::= SEQUENCE OF Seq-loc   -- this will hold anything

Seq-loc-equiv ::= SET OF Seq-loc      -- for a set of equivalent locations

END