seqalign.asn

ncbi源码

--
-- ===========================================================================
-- PRODUCTION $Log: seqalign.asn,v $
-- PRODUCTION Revision 1000.0  2003/10/29 21:31:04  gouriano
-- PRODUCTION PRODUCTION: IMPORTED [ORIGINAL] Dev-tree R6.0
-- PRODUCTION
-- ===========================================================================
--

--$Revision: 1000.0 $
--**********************************************************************
--
--  NCBI Sequence Alignment elements
--  by James Ostell, 1990
--
--**********************************************************************

NCBI-Seqalign DEFINITIONS ::=
BEGIN

EXPORTS Seq-align, Score, Score-set, Seq-align-set;

IMPORTS Seq-id, Seq-loc , Na-strand FROM NCBI-Seqloc
        Object-id FROM NCBI-General;

--*** Sequence Alignment ********************************
--*

Seq-align-set ::= SET OF Seq-align

Seq-align ::= SEQUENCE {
    type ENUMERATED {
        not-set (0) ,
        global (1) ,
        diags (2) ,		-- unbroken, but not ordered, diagonals
        partial (3) ,           -- mapping pieces together
	disc (4) ,              -- discontinuous alignment
        other (255) } ,
    dim INTEGER OPTIONAL ,     -- dimensionality
    score SET OF Score OPTIONAL ,   -- for whole alignment
    segs CHOICE {                   -- alignment data
        dendiag SEQUENCE OF Dense-diag ,
        denseg Dense-seg ,
        std SEQUENCE OF Std-seg ,
	packed Packed-seg ,
	disc Seq-align-set } ,
    bounds SET OF Seq-loc OPTIONAL }  -- regions of sequence over which align
                                      --  was computed

Dense-diag ::= SEQUENCE {         -- for (multiway) diagonals
    dim INTEGER DEFAULT 2 ,    -- dimensionality
    ids SEQUENCE OF Seq-id ,   -- sequences in order
    starts SEQUENCE OF INTEGER ,  -- start OFFSETS in ids order
    len INTEGER ,                 -- len of aligned segments
    strands SEQUENCE OF Na-strand OPTIONAL ,
    scores SET OF Score OPTIONAL }

    -- Dense-seg: the densist packing for sequence alignments only.
    --            a start of -1 indicates a gap for that sequence of
    --            length lens.
    --
    -- id=100  AAGGCCTTTTAGAGATGATGATGATGATGA
    -- id=200  AAGGCCTTTTAG.......GATGATGATGA
    -- id=300  ....CCTTTTAGAGATGATGAT....ATGA
    --
    -- dim = 3, numseg = 6, ids = { 100, 200, 300 }
    -- starts = { 0,0,-1, 4,4,0, 12,-1,8, 19,12,15, 22,15,-1, 26,19,18 }
    -- lens = { 4, 8, 7, 3, 4, 4 }
    --

Dense-seg ::= SEQUENCE {          -- for (multiway) global or partial alignments
    dim INTEGER DEFAULT 2 ,       -- dimensionality
    numseg INTEGER ,              -- number of segments here
    ids SEQUENCE OF Seq-id ,      -- sequences in order
    starts SEQUENCE OF INTEGER ,  -- start OFFSETS in ids order within segs
    lens SEQUENCE OF INTEGER ,    -- lengths in ids order within segs
    strands SEQUENCE OF Na-strand OPTIONAL ,
    scores SEQUENCE OF Score OPTIONAL }  -- score for each seg

Packed-seg ::= SEQUENCE {         -- for (multiway) global or partial alignments
    dim INTEGER DEFAULT 2 ,       -- dimensionality
    numseg INTEGER ,              -- number of segments here
    ids SEQUENCE OF Seq-id ,      -- sequences in order
    starts SEQUENCE OF INTEGER ,  -- start OFFSETS in ids order for whole alignment
    present OCTET STRING ,        -- Boolean if each sequence present or absent in
                                  --   each segment
    lens SEQUENCE OF INTEGER ,    -- length of each segment
    strands SEQUENCE OF Na-strand OPTIONAL ,
    scores SEQUENCE OF Score OPTIONAL }  -- score for each segment

Std-seg ::= SEQUENCE {
    dim INTEGER DEFAULT 2 ,       -- dimensionality
    ids SEQUENCE OF Seq-id OPTIONAL ,
    loc SEQUENCE OF Seq-loc ,
    scores SET OF Score OPTIONAL }

-- use of Score is discouraged for external ASN.1 specifications
Score ::= SEQUENCE {
    id Object-id OPTIONAL ,
    value CHOICE {
        real REAL ,
        int INTEGER  } }

-- use of Score-set is encouraged for external ASN.1 specifications
Score-set ::= SET OF Score

END