256 lines
6.9 KiB
Groff
256 lines
6.9 KiB
Groff
--$Revision: 464672 $
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--********************************************************************
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--
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-- Network Id server network access
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-- Vasilchenko 2003
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--
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--
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--*********************************************************************
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--
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-- seqsplit.asn
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--
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-- representation of split sequences
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--
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--*********************************************************************
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NCBI-Seq-split DEFINITIONS ::=
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BEGIN
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EXPORTS ID2S-Chunk-Id, ID2S-Seq-annot-Info;
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IMPORTS Seq-id FROM NCBI-Seqloc
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Seq-entry FROM NCBI-Seqset
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Bioseq, Seq-annot, Seq-descr, Seq-literal FROM NCBI-Sequence
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Seq-align FROM NCBI-Seqalign;
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----------------------------------------------------------------------------
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-- Blob split info types
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----------------------------------------------------------------------------
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----------------------------------------------------------------------------
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-- Chunks split description
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ID2S-Split-Info ::= SEQUENCE {
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bioseqs-info SET OF ID2S-Bioseqs-Info OPTIONAL,
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chunks SET OF ID2S-Chunk-Info,
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skeleton Seq-entry OPTIONAL
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}
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ID2S-Bioseqs-Info ::= SEQUENCE {
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info ID2S-Bioseq-Info,
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bioseqs ID2S-Bioseq-Ids
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}
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ID2S-Bioseq-Info ::= SEQUENCE {
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gap-count INTEGER OPTIONAL,
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seq-map-has-ref BOOLEAN OPTIONAL
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}
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ID2S-Chunk-Info ::= SEQUENCE {
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id ID2S-Chunk-Id,
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content SET OF ID2S-Chunk-Content
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}
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-- Description of information in this chunk
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-- Place means id of Bioseq or Bioseq-set
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ID2S-Chunk-Content ::= CHOICE {
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-- place of Seq-descrs
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seq-descr ID2S-Seq-descr-Info,
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-- locations and types of annotations
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seq-annot ID2S-Seq-annot-Info,
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-- place of assembly history
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seq-assembly ID2S-Seq-assembly-Info,
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-- place of sequence map
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seq-map ID2S-Seq-map-Info,
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-- place of sequence data
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seq-data ID2S-Seq-data-Info,
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-- place of Seq-annots
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seq-annot-place ID2S-Seq-annot-place-Info,
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-- place of Bioseqs
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bioseq-place SET OF ID2S-Bioseq-place-Info,
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-- ids of features
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feat-ids SET OF ID2S-Seq-feat-Ids-Info
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}
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ID2S-Seq-descr-Info ::= SEQUENCE {
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type-mask INTEGER, -- mask of Seq-descr types,
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bioseqs ID2S-Bioseq-Ids OPTIONAL,
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bioseq-sets ID2S-Bioseq-set-Ids OPTIONAL
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}
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ID2S-Seq-annot-Info ::= SEQUENCE {
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-- name is set if this is named annot
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-- name may be empty which differ from unnamed annot
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name VisibleString OPTIONAL,
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align NULL OPTIONAL,
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graph NULL OPTIONAL,
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feat SET OF ID2S-Feat-type-Info OPTIONAL,
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seq-loc ID2S-Seq-loc OPTIONAL
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}
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ID2S-Seq-annot-place-Info ::= SEQUENCE {
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name VisibleString OPTIONAL,
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bioseqs ID2S-Bioseq-Ids OPTIONAL,
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bioseq-sets ID2S-Bioseq-set-Ids OPTIONAL
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}
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ID2S-Seq-feat-Ids-Info ::= SEQUENCE {
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feat-types SET OF ID2S-Feat-type-Info OPTIONAL,
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xref-types SET OF ID2S-Feat-type-Info OPTIONAL,
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local-ids SET OF INTEGER OPTIONAL,
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local-str-ids SET OF VisibleString OPTIONAL
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}
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ID2S-Feat-type-Info ::= SEQUENCE {
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type INTEGER,
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subtypes SET OF INTEGER OPTIONAL
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}
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ID2S-Seq-assembly-Info ::= SEQUENCE {
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bioseqs ID2S-Bioseq-Ids
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}
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ID2S-Seq-map-Info ::= ID2S-Seq-loc
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ID2S-Seq-data-Info ::= ID2S-Seq-loc
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ID2S-Bioseq-place-Info ::= SEQUENCE {
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bioseq-set INTEGER,
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seq-ids ID2S-Bioseq-Ids
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}
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ID2S-Chunk ::= SEQUENCE {
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data SET OF ID2S-Chunk-Data
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}
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ID2S-Chunk-Data ::= SEQUENCE {
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-- place of data to insert
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id CHOICE {
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-- Bioseq-set id
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bioseq-set INTEGER,
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-- Bioseq id
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gi INTEGER,
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-- Bioseq id
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seq-id Seq-id
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},
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-- Seq-descr, for Bioseq and Bioseq-set
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descr Seq-descr OPTIONAL,
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-- Seq-annot, for Bioseq and Bioseq-set
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annots SET OF Seq-annot OPTIONAL,
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-- assembly history Seq-align, for Bioseq
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assembly SET OF Seq-align OPTIONAL,
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-- sequence map, for Bioseq
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seq-map SEQUENCE OF ID2S-Sequence-Piece OPTIONAL,
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-- sequence data, for Bioseq
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seq-data SEQUENCE OF ID2S-Sequence-Piece OPTIONAL,
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-- Bioseq, for Bioseq-set
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bioseqs SET OF Bioseq OPTIONAL
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}
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ID2S-Sequence-Piece ::= SEQUENCE {
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start INTEGER, -- start position on sequence
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data SEQUENCE OF Seq-literal
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}
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----------------------------------------------------------------------------
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-- utility types
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----------------------------------------------------------------------------
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ID2S-Chunk-Id ::= INTEGER
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ID2S-Bioseq-set-Ids ::= SET OF INTEGER
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ID2S-Bioseq-Ids ::= SET OF CHOICE {
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gi INTEGER,
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seq-id Seq-id,
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gi-range ID2S-Gi-Range
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}
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ID2S-Gi-Range ::= SEQUENCE {
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start INTEGER, -- start gi in this gi range
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count INTEGER DEFAULT 1 -- number of sequential gis
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}
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-- ID2S-Seq-loc is used to represent unordered and unstranded
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-- set of intervals on set of sequences.
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-- It's optimized for compact encoding of several common cases:
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-- Seq-ids of type gi,
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-- intervals covering whole sequences,
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-- whole sequences with sequential gis,
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-- set of intervals on the same sequence (Seq-id sharing).
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ID2S-Seq-loc ::= CHOICE {
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whole-gi INTEGER, -- whole sequence by gi
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whole-seq-id Seq-id, -- whole sequence by Seq-id
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whole-gi-range ID2S-Gi-Range, -- set of whole sequences by gis
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gi-interval ID2S-Gi-Interval, -- interval on sequence by gi
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seq-id-interval ID2S-Seq-id-Interval,-- interval on sequence by Seq-id
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gi-ints ID2S-Gi-Ints, -- set of intervals on the same gi
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seq-id-ints ID2S-Seq-id-Ints, -- set of intervals on the same id
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loc-set SET OF ID2S-Seq-loc -- combination of locations
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}
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ID2S-Gi-Interval ::= SEQUENCE {
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gi INTEGER,
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start INTEGER,
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length INTEGER DEFAULT 1
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}
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ID2S-Seq-id-Interval ::= SEQUENCE {
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seq-id Seq-id,
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start INTEGER,
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length INTEGER DEFAULT 1
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}
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ID2S-Interval ::= SEQUENCE {
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start INTEGER,
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length INTEGER DEFAULT 1
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}
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ID2S-Gi-Ints ::= SEQUENCE {
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gi INTEGER,
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ints SET OF ID2S-Interval
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}
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ID2S-Seq-id-Ints ::= SEQUENCE {
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seq-id Seq-id,
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ints SET OF ID2S-Interval
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}
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END
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