608 lines
22 KiB
Groff
608 lines
22 KiB
Groff
-- ----------------------------------------------------------------------------
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--
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-- PUBLIC DOMAIN NOTICE
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-- National Center for Biotechnology Information
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--
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-- This software/database is a "United States Government Work" under the terms
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-- of the United States Copyright Act. It was written as part of the author's
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-- official duties as a United States Government employee and thus cannot be
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-- copyrighted. This software/database is freely available to the public for
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-- use. The National Library of Medicine and the U.S. Government have not
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-- placed any restriction on its use or reproduction.
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--
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-- Although all reasonable efforts have been taken to ensure the accuracy and
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-- reliability of the software and data, the NLM and the U.S. Government do not
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-- and cannot warrant the performance or results that may be obtained by using
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-- this software or data. The NLM and the U.S. Government disclaim all
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-- warranties, express or implied, including warranties of performance,
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-- merchantability or fitness for any particular purpose.
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--
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-- Please cite the authors in any work or product based on this material.
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--
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-- ----------------------------------------------------------------------------
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--
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-- Authors: Tom Madden, Tim Boemker
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--
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-- ASN.1 interface to BLAST.
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--
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-- ----------------------------------------------------------------------------
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NCBI-Blast4 DEFINITIONS ::=
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BEGIN
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EXPORTS
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Blast4-ka-block,
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Blast4-value,
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Blast4-parameter,
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Blast4-parameters;
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IMPORTS
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Bioseq FROM NCBI-Sequence
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Seq-data FROM NCBI-Sequence
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Bioseq-set FROM NCBI-Seqset
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PssmWithParameters FROM NCBI-ScoreMat
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Seq-id,
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Seq-interval,
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Seq-loc FROM NCBI-Seqloc
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Seq-align,
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Seq-align-set FROM NCBI-Seqalign;
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-- pycrate patch, taken from general.asn
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BigInt ::= [APPLICATION 2] IMPLICIT INTEGER
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-- --------------------------------------------------------------------
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--
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-- Requests
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--
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-- --------------------------------------------------------------------
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Blast4-request ::= SEQUENCE {
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-- Client identifier (email address, organization name, program/script
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-- name, or any other form of contacting the owner of this request)
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ident VisibleString OPTIONAL,
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-- Payload of the request
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body Blast4-request-body
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}
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-- An archive format for results. the results can be reformatted from
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-- this format also.
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Blast4-archive ::= SEQUENCE {
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-- Query and options
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request Blast4-request,
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-- Results of search
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results Blast4-get-search-results-reply,
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messages SEQUENCE OF Blast4-error OPTIONAL
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}
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Blast4-request-body ::= CHOICE {
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finish-params Blast4-finish-params-request,
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-- Get all available BLAST databases
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get-databases NULL,
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-- Get supported scoring matrices
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get-matrices NULL,
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get-parameters NULL,
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get-paramsets NULL,
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get-programs NULL,
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get-search-results Blast4-get-search-results-request,
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get-sequences Blast4-get-sequences-request,
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queue-search Blast4-queue-search-request,
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get-request-info Blast4-get-request-info-request,
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get-sequence-parts Blast4-get-seq-parts-request,
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get-windowmasked-taxids NULL,
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-- Get version and info about some extended methods
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get-protocol-info Blast4-get-protocol-info-request,
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-- Get search info: status, title and etc.
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get-search-info Blast4-get-search-info-request,
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-- OLD OK get-databases-ex NULL
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get-databases-ex Blast4-get-databases-ex-request
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}
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Blast4-get-databases-ex-request ::= SEQUENCE {
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params Blast4-parameters OPTIONAL
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}
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-- END ADD EXT INFO
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Blast4-finish-params-request ::= SEQUENCE {
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program VisibleString,
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service VisibleString,
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paramset VisibleString OPTIONAL,
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params Blast4-parameters OPTIONAL
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}
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-- This type allows the specification of what result types are desired
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Blast4-result-types ::= ENUMERATED {
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-- Default retrieves the following result types (if available): alignments,
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-- phi-alignments masks, ka-blocks, search-stats and pssm
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default (63),
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alignments (1),
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phi-alignments (2),
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masks (4),
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ka-blocks (8),
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search-stats (16),
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pssm (32),
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simple-results (64)
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}
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Blast4-get-search-results-request ::= SEQUENCE {
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-- The request ID of the BLAST search
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request-id VisibleString,
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-- Logical OR of Blast4-result-types, assumes default if absent
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result-types INTEGER OPTIONAL
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}
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-- If a PSSM is used (ie. for PSI-Blast), it must contain a "query"
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-- for formatting purposes. Bioseq-set may contain any number of
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-- queries, specified as data. Seq-loc-list may contain only the
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-- "whole" or "interval" types. In the case of "whole", any number of
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-- queries may be used; in the case of "interval", there should be
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-- exactly one query. (This is limited by the BlastObject.)
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Blast4-queries ::= CHOICE {
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pssm PssmWithParameters,
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seq-loc-list SEQUENCE OF Seq-loc,
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bioseq-set Bioseq-set
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}
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-- Options have been broken down into three groups as part of the BLAST
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-- API work. The algorithm options essentially correspond to those
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-- options available via the CBlastOptions class.
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-- For definitions of the names used in the Blast4-parameter structures, see
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-- c++/{include,src}/objects/blast/names.[hc]pp in the NCBI C++ toolkit.
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-- algorithm-options: Options for BLAST (ie. seq comparison) algorithm.
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-- program-options: Options for controlling program execution and/or
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-- database filtering
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-- format-options: Options for formatting BLAST results, clients should
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-- use this only if applicable, otherwise they should be
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-- ignored
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Blast4-queue-search-request ::= SEQUENCE {
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program VisibleString,
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service VisibleString,
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queries Blast4-queries,
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subject Blast4-subject,
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-- This field contains a task description
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paramset VisibleString OPTIONAL,
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algorithm-options Blast4-parameters OPTIONAL,
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program-options Blast4-parameters OPTIONAL,
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format-options Blast4-parameters OPTIONAL
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}
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-- Request to retrieve the status of a given search
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Blast4-get-search-status-request ::= SEQUENCE {
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request-id VisibleString
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}
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-- Reply to retrieve the status of a given search
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Blast4-get-search-status-reply ::= SEQUENCE {
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status VisibleString
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}
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-- Fetch information about the search request.
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Blast4-get-request-info-request ::= SEQUENCE {
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request-id VisibleString
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}
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Blast4-get-request-info-reply ::= SEQUENCE {
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database Blast4-database,
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program VisibleString,
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service VisibleString,
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created-by VisibleString,
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queries Blast4-queries,
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algorithm-options Blast4-parameters,
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program-options Blast4-parameters,
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format-options Blast4-parameters OPTIONAL,
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subjects Blast4-subject OPTIONAL
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}
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-- Fetch the search strategy (i.e.: object used to submit the search)
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Blast4-get-search-strategy-request ::= SEQUENCE {
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request-id VisibleString
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}
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-- Return the search strategy (i.e.: Blast4-request containing a
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-- Blast4-queue-search-request, an object used to submit the search)
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Blast4-get-search-strategy-reply ::= Blast4-request
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-- Fetch sequence data from a BLAST database
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Blast4-get-sequences-request ::= SEQUENCE {
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-- Name of the BLAST database from which to retrieve the sequence data
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database Blast4-database,
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-- Sequence identifiers for the sequence to get
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seq-ids SEQUENCE OF Seq-id,
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-- Determines whether the returned Bioseqs should contain the sequence data
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-- or not
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skip-seq-data BOOLEAN DEFAULT FALSE,
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-- Determines whether or not the defline of the returned Bioseqs should
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-- contain only the requested seq id. This optional field only applies
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-- to non-redundant BLAST database
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target-only BOOLEAN OPTIONAL
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}
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-- Fetch parts of sequences from a BLAST database
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Blast4-get-seq-parts-request ::= SEQUENCE {
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-- Name of the BLAST database from which to retrieve the sequence data
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database Blast4-database,
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-- Allows the specification of ranges of sequence data needed.
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-- If the sequence(s) interval's end is 0, no data will be fetched.
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-- If end is past the length of the sequence, it will be adjusted to the
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-- end of the sequence (this allows fetching of the first chunk in
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-- cases where the length is not yet known).
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seq-locations SEQUENCE OF Seq-interval
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}
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-- support for version and checking availability of methods
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Blast4-get-protocol-info-request ::= Blast4-parameters
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-- variose search information
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Blast4-get-search-info-request ::= SEQUENCE {
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request-id VisibleString,
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info Blast4-parameters OPTIONAL
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}
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-- --------------------------------------------------------------------
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--
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-- Replies
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--
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-- --------------------------------------------------------------------
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Blast4-reply ::= SEQUENCE {
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errors SEQUENCE OF Blast4-error OPTIONAL,
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body Blast4-reply-body
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}
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Blast4-reply-body ::= CHOICE {
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finish-params Blast4-finish-params-reply,
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get-databases Blast4-get-databases-reply,
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get-matrices Blast4-get-matrices-reply,
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get-parameters Blast4-get-parameters-reply,
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get-paramsets Blast4-get-paramsets-reply,
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get-programs Blast4-get-programs-reply,
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get-search-results Blast4-get-search-results-reply,
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get-sequences Blast4-get-sequences-reply,
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queue-search Blast4-queue-search-reply,
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get-queries Blast4-get-queries-reply,
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get-request-info Blast4-get-request-info-reply,
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get-sequence-parts Blast4-get-seq-parts-reply,
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get-windowmasked-taxids Blast4-get-windowmasked-taxids-reply,
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get-protocol-info Blast4-get-protocol-info-reply,
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get-search-info Blast4-get-search-info-reply,
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get-databases-ex Blast4-get-databases-ex-reply
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}
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Blast4-finish-params-reply ::= Blast4-parameters
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Blast4-get-windowmasked-taxids-reply ::= SEQUENCE OF INTEGER
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Blast4-get-databases-reply ::= SEQUENCE OF Blast4-database-info
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Blast4-get-databases-ex-reply ::= SEQUENCE OF Blast4-database-info
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Blast4-get-matrices-reply ::= SEQUENCE OF Blast4-matrix-id
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Blast4-get-parameters-reply ::= SEQUENCE OF Blast4-parameter-info
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-- Note: Paramsets and tasks represent the same concept: a human readable
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-- description that represents a set of parameters with specific values
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-- to accomplish a given task
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Blast4-get-paramsets-reply ::= SEQUENCE OF Blast4-task-info
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Blast4-get-programs-reply ::= SEQUENCE OF Blast4-program-info
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Blast4-get-search-results-reply ::= SEQUENCE {
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alignments Seq-align-set OPTIONAL,
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phi-alignments Blast4-phi-alignments OPTIONAL,
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-- Masking locations for the query sequence(s). Each element of this set
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-- corresponds to a single query's translation frame as appropriate.
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masks SEQUENCE OF Blast4-mask OPTIONAL,
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ka-blocks SEQUENCE OF Blast4-ka-block OPTIONAL,
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search-stats SEQUENCE OF VisibleString OPTIONAL,
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pssm PssmWithParameters OPTIONAL,
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simple-results Blast4-simple-results OPTIONAL
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}
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Blast4-get-sequences-reply ::= SEQUENCE OF Bioseq
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-- Bundles Seq-ids and sequence data to fulfill requests of type
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-- Blast4-get-seq-parts-request
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Blast4-seq-part-data ::= SEQUENCE {
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-- Sequence identifier
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id Seq-id,
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-- Its sequence data (may be partial)
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data Seq-data
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}
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Blast4-get-seq-parts-reply ::= SEQUENCE OF Blast4-seq-part-data
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Blast4-queue-search-reply ::= SEQUENCE {
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request-id VisibleString OPTIONAL
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}
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Blast4-get-queries-reply ::= SEQUENCE {
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queries Blast4-queries
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}
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Blast4-get-protocol-info-reply ::= Blast4-parameters
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Blast4-get-search-info-reply ::= SEQUENCE {
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request-id VisibleString,
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info Blast4-parameters OPTIONAL
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}
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-- --------------------------------------------------------------------
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--
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-- Errors
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--
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-- --------------------------------------------------------------------
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Blast4-error ::= SEQUENCE {
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-- This is an integer to allow for flexibility, but the values assigned
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-- should be of type Blast4-error-code
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code INTEGER,
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message VisibleString OPTIONAL
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}
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-- This enumeration defines values that are intended to be used with the
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-- Blast4-error::code in a logical AND operation to easily determine whether a
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-- given Blast4-error object contains either a warning or an error
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Blast4-error-flags ::= ENUMERATED {
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warning (1024),
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error (2048)
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}
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-- Defines values for use in Blast4-error::code.
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-- Note: warnings should have values greater than 1024 and less than 2048,
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-- errors should have values greater than 2048.
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Blast4-error-code ::= INTEGER {
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-- A conversion issue was found when converting to/from blast3 from/to
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-- blast4 protocol in the blast4 server
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conversion-warning (1024),
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-- Indicates internal errors in the blast4 server
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internal-error (2048),
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-- Request type is not implemented in the blast4 server
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not-implemented (2049),
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-- Request type is not allowed in the blast4 server
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not-allowed (2050),
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-- Malformed/invalid requests (e.g.: parsing errors or invalid data in request)
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bad-request (2051),
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-- The RID requested is unknown or it has expired
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bad-request-id (2052),
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-- The search is pending
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search-pending (2053)
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}
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-- --------------------------------------------------------------------
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--
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-- Other types in alphabetical order
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--
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-- --------------------------------------------------------------------
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Blast4-cutoff ::= CHOICE {
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e-value REAL,
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raw-score INTEGER
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}
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Blast4-database ::= SEQUENCE {
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name VisibleString,
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type Blast4-residue-type
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}
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-- Borrowed from seq.asn
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Blast4-seqtech ::= INTEGER {
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unknown (0) ,
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standard (1) , -- standard sequencing
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est (2) , -- Expressed Sequence Tag
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sts (3) , -- Sequence Tagged Site
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survey (4) , -- one-pass genomic sequence
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genemap (5) , -- from genetic mapping techniques
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physmap (6) , -- from physical mapping techniques
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derived (7) , -- derived from other data, not a primary entity
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concept-trans (8) , -- conceptual translation
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seq-pept (9) , -- peptide was sequenced
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both (10) , -- concept transl. w/ partial pept. seq.
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seq-pept-overlap (11) , -- sequenced peptide, ordered by overlap
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seq-pept-homol (12) , -- sequenced peptide, ordered by homology
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concept-trans-a (13) , -- conceptual transl. supplied by author
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htgs-1 (14) , -- unordered High Throughput sequence contig
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htgs-2 (15) , -- ordered High Throughput sequence contig
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htgs-3 (16) , -- finished High Throughput sequence
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fli-cdna (17) , -- full length insert cDNA
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htgs-0 (18) , -- single genomic reads for coordination
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htc (19) , -- high throughput cDNA
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wgs (20) , -- whole genome shotgun sequencing
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other (255) -- use Source.techexp
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}
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Blast4-database-info ::= SEQUENCE {
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database Blast4-database,
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description VisibleString,
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last-updated VisibleString,
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total-length BigInt,
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num-sequences BigInt,
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seqtech Blast4-seqtech,
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taxid INTEGER,
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extended Blast4-parameters OPTIONAL
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}
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Blast4-frame-type ::= ENUMERATED {
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notset (0),
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plus1 (1),
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plus2 (2),
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plus3 (3),
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minus1 (4),
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minus2 (5),
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minus3 (6)
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}
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Blast4-ka-block ::= SEQUENCE {
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lambda REAL,
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k REAL,
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h REAL,
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gapped BOOLEAN
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}
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-- Masking locations for a query's frame. The locations field is a single
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-- Seq-loc of type Packed-int, which contains all the masking locations for the
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-- translation frame specified by the frame field.
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-- Notes:
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-- On input (i.e.: when the client specifies masking locations as a
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-- Blast4-parameter), in the case of protein queries, the frame field must
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-- always be notset, in the case of nucleotide queries (regardless of whether
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-- the search will translate these or not), the frame must be plus1. Masking
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-- locations in the translated encoding are not permitted.
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-- On output (i.e.: when blast 4 server encodes these as part of the
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-- Blast4-get-search-results-reply), the same conventions as above apply for
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-- non-translated protein and nucleotide queries, but in the case of translated
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-- nucleotide queries, the frame field can be specified in any of the
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-- translation frames as appropriate.
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Blast4-mask ::= SEQUENCE {
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locations SEQUENCE OF Seq-loc,
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frame Blast4-frame-type
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}
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Blast4-matrix-id ::= SEQUENCE {
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residue-type Blast4-residue-type,
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name VisibleString
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}
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Blast4-parameter ::= SEQUENCE {
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name VisibleString,
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value Blast4-value
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}
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Blast4-parameter-info ::= SEQUENCE {
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name VisibleString,
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type VisibleString
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}
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-- Self documenting task structure
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Blast4-task-info ::= SEQUENCE {
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-- Name of this task
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name VisibleString,
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-- Description of the task
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documentation VisibleString
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}
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Blast4-program-info ::= SEQUENCE {
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program VisibleString,
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services SEQUENCE OF VisibleString
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}
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Blast4-residue-type ::= ENUMERATED {
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unknown (0),
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protein (1),
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nucleotide (2)
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}
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Blast4-strand-type ::= ENUMERATED {
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forward-strand (1),
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reverse-strand (2),
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both-strands (3)
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}
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Blast4-subject ::= CHOICE {
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database VisibleString,
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sequences SEQUENCE OF Bioseq,
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seq-loc-list SEQUENCE OF Seq-loc
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}
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Blast4-parameters ::= SEQUENCE OF Blast4-parameter
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Blast4-phi-alignments ::= SEQUENCE {
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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 PssmWithParameters,
|
|
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 PssmWithParameters,
|
|
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,
|
|
|
|
-- Intended to represent user-provided masking locations for a single query
|
|
-- sequence (name field in Blast4-parameter should be "LCaseMask").
|
|
-- Multiple Blast4-parameters of this type are needed to specify masking
|
|
-- locations for multiple queries.
|
|
query-mask Blast4-mask
|
|
}
|
|
|
|
-- Complete set of simple Blast results
|
|
Blast4-simple-results ::= SEQUENCE {
|
|
all-alignments SEQUENCE OF Blast4-alignments-for-query
|
|
}
|
|
|
|
-- Alignments for one query, compiled from the raw SeqAlign results
|
|
Blast4-alignments-for-query ::= SEQUENCE {
|
|
|
|
-- Query sequence identifier
|
|
-- (present if query is not a local id in the SeqAlign)
|
|
query-id VisibleString,
|
|
|
|
-- All the alignments for this query
|
|
alignments SEQUENCE OF Blast4-simple-alignment
|
|
}
|
|
|
|
-- A single alignment
|
|
Blast4-simple-alignment ::= SEQUENCE {
|
|
|
|
-- Subject sequence identifier
|
|
-- (normally a GI from the SeqAlign)
|
|
subject-id VisibleString,
|
|
|
|
-- E-Value
|
|
e-value REAL,
|
|
|
|
-- Bit score
|
|
bit-score REAL,
|
|
|
|
-- Number of identities
|
|
num-identities INTEGER OPTIONAL,
|
|
|
|
-- Number of insertions/deletions
|
|
num-indels INTEGER OPTIONAL,
|
|
|
|
-- Full query range covered by this HSP
|
|
full-query-range Blast4-range,
|
|
|
|
-- Full subject range covered by this HSP
|
|
full-subject-range Blast4-range
|
|
}
|
|
|
|
-- Range on a sequence - zero offset
|
|
Blast4-range ::= SEQUENCE {
|
|
start INTEGER OPTIONAL,
|
|
end INTEGER OPTIONAL,
|
|
-- The frame of the range (absent for proteins; -1/1 for nucleotides;
|
|
-- -1,-2,-3,1,2,3 for translated sequences)
|
|
strand INTEGER OPTIONAL
|
|
}
|
|
|
|
END
|