blast.asn
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上传日期：2007-06-13
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- -- ----------------------------------------------------------------------------
- --
- -- PUBLIC DOMAIN NOTICE
- -- National Center for Biotechnology Information
- --
- -- This software/database is a "United States Government Work" under the terms
- -- of the United States Copyright Act. It was written as part of the author's
- -- official duties as a United States Government employee and thus cannot be
- -- copyrighted. This software/database is freely available to the public for
- -- use. The National Library of Medicine and the U.S. Government have not
- -- placed any restriction on its use or reproduction.
- --
- -- Although all reasonable efforts have been taken to ensure the accuracy and
- -- reliability of the software and data, the NLM and the U.S. Government do not
- -- and cannot warrant the performance or results that may be obtained by using
- -- this software or data. The NLM and the U.S. Government disclaim all
- -- warranties, express or implied, including warranties of performance,
- -- merchantability or fitness for any particular purpose.
- --
- -- Please cite the authors in any work or product based on this material.
- --
- -- ----------------------------------------------------------------------------
- --
- -- Authors: Tom Madden, Tim Boemker
- --
- -- ASN.1 interface to BLAST.
- --
- -- ----------------------------------------------------------------------------
- NCBI-Blast4 DEFINITIONS ::=
- BEGIN
- EXPORTS
- Blast4-ka-block;
- IMPORTS
- Bioseq FROM NCBI-Sequence
- Bioseq-set FROM NCBI-Seqset
- Score-matrix-parameters FROM NCBI-ScoreMat
- Seq-id,
- Seq-loc FROM NCBI-Seqloc
- Seq-align,
- Seq-align-set FROM NCBI-Seqalign;
- -- --------------------------------------------------------------------
- --
- -- Requests
- --
- -- --------------------------------------------------------------------
- Blast4-request ::= SEQUENCE {
- ident VisibleString OPTIONAL,
- body Blast4-request-body
- }
- Blast4-request-body ::= CHOICE {
- finish-params Blast4-finish-params-request,
- get-databases NULL,
- get-matrices NULL,
- get-parameters NULL,
- get-paramsets NULL,
- get-programs NULL,
- get-search-results Blast4-get-search-results-request,
- get-sequences Blast4-get-sequences-request,
- queue-search Blast4-queue-search-request
- }
- Blast4-finish-params-request ::= SEQUENCE {
- program VisibleString,
- service VisibleString,
- paramset VisibleString OPTIONAL,
- params Blast4-parameters OPTIONAL
- }
- Blast4-get-search-results-request ::= SEQUENCE {
- request-id VisibleString
- }
- Blast4-get-sequences-request ::= SEQUENCE {
- database Blast4-database,
- seq-ids SEQUENCE OF Seq-id
- }
- -- If a PSSM is used (ie. for PSI-Blast), it must contain a "query"
- -- for formatting purposes. Bioseq-set may contain any number of
- -- queries, specified as data. Seq-loc-list may contain only the
- -- "whole" or "interval" types. In the case of "whole", any number of
- -- queries may be used; in the case of "interval", there should be
- -- exactly one query. (This is limited by the BlastObject.)
- Blast4-queries ::= CHOICE {
- pssm Score-matrix-parameters,
- seq-loc-list SEQUENCE OF Seq-loc,
- bioseq-set Bioseq-set
- }
- -- Options have been broken down into two groups as part of the BLAST
- -- API work. The algorithm options essentially correspond to those
- -- options available via the CBlastOptions class.
- -- algorithm-options: Options for BLAST (ie. seq comparison) algorithm.
- -- program-options: Other options, such as which seqs. to compare.
- Blast4-queue-search-request ::= SEQUENCE {
- program VisibleString,
- service VisibleString,
- queries Blast4-queries,
- subject Blast4-subject,
- paramset VisibleString OPTIONAL,
- algorithm-options Blast4-parameters OPTIONAL,
- program-options Blast4-parameters OPTIONAL
- }
- -- --------------------------------------------------------------------
- --
- -- Replies
- --
- -- --------------------------------------------------------------------
- Blast4-reply ::= SEQUENCE {
- errors SEQUENCE OF Blast4-error OPTIONAL,
- body Blast4-reply-body
- }
- Blast4-reply-body ::= CHOICE {
- finish-params Blast4-finish-params-reply,
- get-databases Blast4-get-databases-reply,
- get-matrices Blast4-get-matrices-reply,
- get-parameters Blast4-get-parameters-reply,
- get-paramsets Blast4-get-paramsets-reply,
- get-programs Blast4-get-programs-reply,
- get-search-results Blast4-get-search-results-reply,
- get-sequences Blast4-get-sequences-reply,
- queue-search Blast4-queue-search-reply
- }
- Blast4-finish-params-reply ::= Blast4-parameters
- Blast4-get-databases-reply ::= SEQUENCE OF Blast4-database-info
- Blast4-get-matrices-reply ::= SEQUENCE OF Blast4-matrix-id
- Blast4-get-parameters-reply ::= SEQUENCE OF Blast4-parameter-info
- Blast4-get-paramsets-reply ::= SEQUENCE OF Blast4-paramset-info
- Blast4-get-programs-reply ::= SEQUENCE OF Blast4-program-info
- Blast4-get-search-results-reply ::= SEQUENCE {
- alignments Seq-align-set OPTIONAL,
- phi-alignments Blast4-phi-alignments OPTIONAL,
- mask Blast4-mask OPTIONAL,
- ka-blocks SEQUENCE OF Blast4-ka-block OPTIONAL,
- search-stats SEQUENCE OF VisibleString OPTIONAL,
- pssm Score-matrix-parameters OPTIONAL
- }
- Blast4-get-sequences-reply ::= SEQUENCE OF Bioseq
- Blast4-queue-search-reply ::= SEQUENCE {
- request-id VisibleString OPTIONAL
- }
- -- --------------------------------------------------------------------
- --
- -- Errors
- --
- -- --------------------------------------------------------------------
- Blast4-error ::= SEQUENCE {
- code INTEGER,
- message VisibleString OPTIONAL
- }
- Blast4-error-flags ::= ENUMERATED {
- warning (1024),
- error (2048)
- }
- Blast4-error-code ::= INTEGER {
- -- warnings
- conversion-warning (1024),
- -- errors
- internal-error (2048),
- not-implemented (2049),
- not-allowed (2050),
- bad-request (2051),
- bad-request-id (2052),
- search-pending (2053)
- }
- -- --------------------------------------------------------------------
- --
- -- Other types in alphabetical order
- --
- -- --------------------------------------------------------------------
- Blast4-cutoff ::= CHOICE {
- e-value REAL,
- raw-score INTEGER
- }
- Blast4-database ::= SEQUENCE {
- name VisibleString,
- type Blast4-residue-type
- }
- -- Borrowed from seq.asn
- Blast4-seqtech ::= INTEGER {
- unknown (0) ,
- standard (1) , -- standard sequencing
- est (2) , -- Expressed Sequence Tag
- sts (3) , -- Sequence Tagged Site
- survey (4) , -- one-pass genomic sequence
- genemap (5) , -- from genetic mapping techniques
- physmap (6) , -- from physical mapping techniques
- derived (7) , -- derived from other data, not a primary entity
- concept-trans (8) , -- conceptual translation
- seq-pept (9) , -- peptide was sequenced
- both (10) , -- concept transl. w/ partial pept. seq.
- seq-pept-overlap (11) , -- sequenced peptide, ordered by overlap
- seq-pept-homol (12) , -- sequenced peptide, ordered by homology
- concept-trans-a (13) , -- conceptual transl. supplied by author
- htgs-1 (14) , -- unordered High Throughput sequence contig
- htgs-2 (15) , -- ordered High Throughput sequence contig
- htgs-3 (16) , -- finished High Throughput sequence
- fli-cdna (17) , -- full length insert cDNA
- htgs-0 (18) , -- single genomic reads for coordination
- htc (19) , -- high throughput cDNA
- wgs (20) , -- whole genome shotgun sequencing
- other (255) -- use Source.techexp
- }
- Blast4-database-info ::= SEQUENCE {
- database Blast4-database,
- description VisibleString,
- last-updated VisibleString,
- total-length BigInt,
- num-sequences BigInt,
- seqtech Blast4-seqtech,
- taxid INTEGER
- }
- Blast4-frame-type ::= ENUMERATED {
- notset (0),
- plus1 (1),
- plus2 (2),
- plus3 (3),
- minus1 (4),
- minus2 (5),
- minus3 (6)
- }
- Blast4-ka-block ::= SEQUENCE {
- lambda REAL,
- k REAL,
- h REAL,
- gapped BOOLEAN
- }
- Blast4-mask ::= SEQUENCE {
- locations SEQUENCE OF Seq-loc,
- frame Blast4-frame-type
- }
- Blast4-matrix-id ::= SEQUENCE {
- residue-type Blast4-residue-type,
- name VisibleString
- }
- Blast4-parameter ::= SEQUENCE {
- name VisibleString,
- value Blast4-value
- }
- Blast4-parameter-info ::= SEQUENCE {
- name VisibleString,
- type VisibleString
- }
- Blast4-paramset-info ::= SEQUENCE {
- program VisibleString,
- name VisibleString
- }
- Blast4-program-info ::= SEQUENCE {
- program VisibleString,
- services SEQUENCE OF VisibleString
- }
- Blast4-residue-type ::= ENUMERATED {
- unknown (0),
- protein (1),
- nucleotide (2)
- }
- Blast4-strand-type ::= ENUMERATED {
- forward-strand (1),
- reverse-strand (2),
- both-strands (3)
- }
- Blast4-subject ::= CHOICE {
- database VisibleString,
- sequences SEQUENCE OF Bioseq
- }
- Blast4-parameters ::= SEQUENCE OF Blast4-parameter
- Blast4-phi-alignments ::= SEQUENCE {
- num-alignments INTEGER,
- seq-locs SEQUENCE OF Seq-loc
- }
- Blast4-value ::= CHOICE {
- -- scalar types
- big-integer BigInt,
- bioseq Bioseq,
- boolean BOOLEAN,
- cutoff Blast4-cutoff,
- integer INTEGER,
- matrix Score-matrix-parameters,
- real REAL,
- seq-align Seq-align,
- seq-id Seq-id,
- seq-loc Seq-loc,
- strand-type Blast4-strand-type,
- string VisibleString,
- -- lists of scalar types
- big-integer-list SEQUENCE OF BigInt,
- bioseq-list SEQUENCE OF Bioseq,
- boolean-list SEQUENCE OF BOOLEAN,
- cutoff-list SEQUENCE OF Blast4-cutoff,
- integer-list SEQUENCE OF INTEGER,
- matrix-list SEQUENCE OF Score-matrix-parameters,
- real-list SEQUENCE OF REAL,
- seq-align-list SEQUENCE OF Seq-align,
- seq-id-list SEQUENCE OF Seq-id,
- seq-loc-list SEQUENCE OF Seq-loc,
- strand-type-list SEQUENCE OF Blast4-strand-type,
- string-list SEQUENCE OF VisibleString,
- -- imported collection types
- bioseq-set Bioseq-set,
- seq-align-set Seq-align-set
- }
- END
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