blast.asn

ncbi源码

--  ----------------------------------------------------------------------------
--
--                            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