src/objects/seqsplit/seqsplit.asn
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--$Revision: 67040 $
--********************************************************************
--
-- Network Id server network access
-- Vasilchenko 2003
--
--
--*********************************************************************
--
-- seqsplit.asn
--
-- representation of split sequences
--
--*********************************************************************
NCBI-Seq-split DEFINITIONS ::=
BEGIN
EXPORTS ID2S-Chunk-Id, ID2S-Seq-annot-Info;
IMPORTS Seq-id FROM NCBI-Seqloc
Seq-entry FROM NCBI-Seqset
Bioseq, Seq-annot, Seq-descr, Seq-literal FROM NCBI-Sequence
Seq-align FROM NCBI-Seqalign;
----------------------------------------------------------------------------
-- Blob split info types
----------------------------------------------------------------------------
----------------------------------------------------------------------------
-- Chunks split description
ID2S-Split-Info ::= SEQUENCE {
bioseqs-info SET OF ID2S-Bioseqs-Info OPTIONAL,
chunks SET OF ID2S-Chunk-Info,
skeleton Seq-entry OPTIONAL
}
ID2S-Bioseqs-Info ::= SEQUENCE {
info ID2S-Bioseq-Info,
bioseqs ID2S-Bioseq-Ids
}
ID2S-Bioseq-Info ::= SEQUENCE {
gap-count INTEGER OPTIONAL,
seq-map-has-ref BOOLEAN OPTIONAL
}
ID2S-Chunk-Info ::= SEQUENCE {
id ID2S-Chunk-Id,
content SET OF ID2S-Chunk-Content
}
-- Description of information in this chunk
-- Place means id of Bioseq or Bioseq-set
ID2S-Chunk-Content ::= CHOICE {
-- place of Seq-descrs
seq-descr ID2S-Seq-descr-Info,
-- locations and types of annotations
seq-annot ID2S-Seq-annot-Info,
-- place of assembly history
seq-assembly ID2S-Seq-assembly-Info,
-- place of sequence map
seq-map ID2S-Seq-map-Info,
-- place of sequence data
seq-data ID2S-Seq-data-Info,
-- place of Seq-annots
seq-annot-place ID2S-Seq-annot-place-Info,
-- place of Bioseqs
bioseq-place SET OF ID2S-Bioseq-place-Info,
-- ids of features
feat-ids SET OF ID2S-Seq-feat-Ids-Info
}
ID2S-Seq-descr-Info ::= SEQUENCE {
type-mask INTEGER, -- mask of Seq-descr types,
bioseqs ID2S-Bioseq-Ids OPTIONAL,
bioseq-sets ID2S-Bioseq-set-Ids OPTIONAL
}
ID2S-Seq-annot-Info ::= SEQUENCE {
-- name is set if this is named annot
-- name may be empty which differ from unnamed annot
name VisibleString OPTIONAL,
align NULL OPTIONAL,
graph NULL OPTIONAL,
feat SET OF ID2S-Feat-type-Info OPTIONAL,
seq-loc ID2S-Seq-loc OPTIONAL
}
ID2S-Seq-annot-place-Info ::= SEQUENCE {
name VisibleString OPTIONAL,
bioseqs ID2S-Bioseq-Ids OPTIONAL,
bioseq-sets ID2S-Bioseq-set-Ids OPTIONAL
}
ID2S-Seq-feat-Ids-Info ::= SEQUENCE {
feat-types SET OF ID2S-Feat-type-Info OPTIONAL,
xref-types SET OF ID2S-Feat-type-Info OPTIONAL,
local-ids SET OF INTEGER OPTIONAL,
local-str-ids SET OF VisibleString OPTIONAL
}
ID2S-Feat-type-Info ::= SEQUENCE {
type INTEGER,
subtypes SET OF INTEGER OPTIONAL
}
ID2S-Seq-assembly-Info ::= SEQUENCE {
bioseqs ID2S-Bioseq-Ids
}
ID2S-Seq-map-Info ::= ID2S-Seq-loc
ID2S-Seq-data-Info ::= ID2S-Seq-loc
ID2S-Bioseq-place-Info ::= SEQUENCE {
bioseq-set INTEGER,
seq-ids ID2S-Bioseq-Ids
}
ID2S-Chunk ::= SEQUENCE {
data SET OF ID2S-Chunk-Data
}
ID2S-Chunk-Data ::= SEQUENCE {
-- place of data to insert
id CHOICE {
-- Bioseq-set id
bioseq-set INTEGER,
-- Bioseq id
gi INTEGER,
-- Bioseq id
seq-id Seq-id
},
-- Seq-descr, for Bioseq and Bioseq-set
descr Seq-descr OPTIONAL,
-- Seq-annot, for Bioseq and Bioseq-set
annots SET OF Seq-annot OPTIONAL,
-- assembly history Seq-align, for Bioseq
assembly SET OF Seq-align OPTIONAL,
-- sequence map, for Bioseq
seq-map SEQUENCE OF ID2S-Sequence-Piece OPTIONAL,
-- sequence data, for Bioseq
seq-data SEQUENCE OF ID2S-Sequence-Piece OPTIONAL,
-- Bioseq, for Bioseq-set
bioseqs SET OF Bioseq OPTIONAL
}
ID2S-Sequence-Piece ::= SEQUENCE {
start INTEGER, -- start position on sequence
data SEQUENCE OF Seq-literal
}
----------------------------------------------------------------------------
-- utility types
----------------------------------------------------------------------------
ID2S-Chunk-Id ::= INTEGER
ID2S-Bioseq-set-Ids ::= SET OF INTEGER
ID2S-Bioseq-Ids ::= SET OF CHOICE {
gi INTEGER,
seq-id Seq-id,
gi-range ID2S-Gi-Range
}
ID2S-Gi-Range ::= SEQUENCE {
start INTEGER, -- start gi in this gi range
count INTEGER DEFAULT 1 -- number of sequential gis
}
-- ID2S-Seq-loc is used to represent unordered and unstranded
-- set of intervals on set of sequences.
-- It's optimized for compact encoding of several common cases:
-- Seq-ids of type gi,
-- intervals covering whole sequences,
-- whole sequences with sequential gis,
-- set of intervals on the same sequence (Seq-id sharing).
ID2S-Seq-loc ::= CHOICE {
whole-gi INTEGER, -- whole sequence by gi
whole-seq-id Seq-id, -- whole sequence by Seq-id
whole-gi-range ID2S-Gi-Range, -- set of whole sequences by gis
gi-interval ID2S-Gi-Interval, -- interval on sequence by gi
seq-id-interval ID2S-Seq-id-Interval,-- interval on sequence by Seq-id
gi-ints ID2S-Gi-Ints, -- set of intervals on the same gi
seq-id-ints ID2S-Seq-id-Ints, -- set of intervals on the same id
loc-set SET OF ID2S-Seq-loc -- combination of locations
}
ID2S-Gi-Interval ::= SEQUENCE {
gi INTEGER,
start INTEGER,
length INTEGER DEFAULT 1
}
ID2S-Seq-id-Interval ::= SEQUENCE {
seq-id Seq-id,
start INTEGER,
length INTEGER DEFAULT 1
}
ID2S-Interval ::= SEQUENCE {
start INTEGER,
length INTEGER DEFAULT 1
}
ID2S-Gi-Ints ::= SEQUENCE {
gi INTEGER,
ints SET OF ID2S-Interval
}
ID2S-Seq-id-Ints ::= SEQUENCE {
seq-id Seq-id,
ints SET OF ID2S-Interval
}
END