src/objects/blast/blast.asn
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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,
Blast4-value,
Blast4-parameter,
Blast4-parameters;
IMPORTS
Bioseq FROM NCBI-Sequence
Seq-data FROM NCBI-Sequence
Bioseq-set FROM NCBI-Seqset
PssmWithParameters FROM NCBI-ScoreMat
Seq-id,
Seq-interval,
Seq-loc FROM NCBI-Seqloc
Seq-align,
Seq-align-set FROM NCBI-Seqalign;
-- --------------------------------------------------------------------
--
-- Requests
--
-- --------------------------------------------------------------------
Blast4-request ::= SEQUENCE {
-- Client identifier (email address, organization name, program/script
-- name, or any other form of contacting the owner of this request)
ident VisibleString OPTIONAL,
-- Payload of the request
body Blast4-request-body
}
-- An archive format for results. the results can be reformatted from
-- this format also.
Blast4-archive ::= SEQUENCE {
-- Query and options
request Blast4-request,
-- Results of search
results Blast4-get-search-results-reply,
messages SEQUENCE OF Blast4-error OPTIONAL
}
Blast4-request-body ::= CHOICE {
finish-params Blast4-finish-params-request,
-- Get all available BLAST databases
get-databases NULL,
-- Get supported scoring matrices
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,
get-request-info Blast4-get-request-info-request,
get-sequence-parts Blast4-get-seq-parts-request,
get-windowmasked-taxids NULL,
-- Get version and info about some extended methods
get-protocol-info Blast4-get-protocol-info-request,
-- Get search info: status, title and etc.
get-search-info Blast4-get-search-info-request,
-- OLD OK get-databases-ex NULL
get-databases-ex Blast4-get-databases-ex-request
}
Blast4-get-databases-ex-request ::= SEQUENCE {
params Blast4-parameters OPTIONAL
}
-- END ADD EXT INFO
Blast4-finish-params-request ::= SEQUENCE {
program VisibleString,
service VisibleString,
paramset VisibleString OPTIONAL,
params Blast4-parameters OPTIONAL
}
-- This type allows the specification of what result types are desired
Blast4-result-types ::= ENUMERATED {
-- Default retrieves the following result types (if available): alignments,
-- phi-alignments masks, ka-blocks, search-stats and pssm
default (63),
alignments (1),
phi-alignments (2),
masks (4),
ka-blocks (8),
search-stats (16),
pssm (32),
simple-results (64)
}
Blast4-get-search-results-request ::= SEQUENCE {
-- The request ID of the BLAST search
request-id VisibleString,
-- Logical OR of Blast4-result-types, assumes default if absent
result-types INTEGER OPTIONAL
}
-- 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 PssmWithParameters,
seq-loc-list SEQUENCE OF Seq-loc,
bioseq-set Bioseq-set
}
-- Options have been broken down into three groups as part of the BLAST
-- API work. The algorithm options essentially correspond to those
-- options available via the CBlastOptions class.
-- For definitions of the names used in the Blast4-parameter structures, see
-- c++/{include,src}/objects/blast/names.[hc]pp in the NCBI C++ toolkit.
-- algorithm-options: Options for BLAST (ie. seq comparison) algorithm.
-- program-options: Options for controlling program execution and/or
-- database filtering
-- format-options: Options for formatting BLAST results, clients should
-- use this only if applicable, otherwise they should be
-- ignored
Blast4-queue-search-request ::= SEQUENCE {
program VisibleString,
service VisibleString,
queries Blast4-queries,
subject Blast4-subject,
-- This field contains a task description
paramset VisibleString OPTIONAL,
algorithm-options Blast4-parameters OPTIONAL,
program-options Blast4-parameters OPTIONAL,
format-options Blast4-parameters OPTIONAL
}
-- Request to retrieve the status of a given search
Blast4-get-search-status-request ::= SEQUENCE {
request-id VisibleString
}
-- Reply to retrieve the status of a given search
Blast4-get-search-status-reply ::= SEQUENCE {
status VisibleString
}
-- Fetch information about the search request.
Blast4-get-request-info-request ::= SEQUENCE {
request-id VisibleString
}
Blast4-get-request-info-reply ::= SEQUENCE {
database Blast4-database,
program VisibleString,
service VisibleString,
created-by VisibleString,
queries Blast4-queries,
algorithm-options Blast4-parameters,
program-options Blast4-parameters,
format-options Blast4-parameters OPTIONAL,
subjects Blast4-subject OPTIONAL
}
-- Fetch the search strategy (i.e.: object used to submit the search)
Blast4-get-search-strategy-request ::= SEQUENCE {
request-id VisibleString
}
-- Return the search strategy (i.e.: Blast4-request containing a
-- Blast4-queue-search-request, an object used to submit the search)
Blast4-get-search-strategy-reply ::= Blast4-request
-- Fetch sequence data from a BLAST database
Blast4-get-sequences-request ::= SEQUENCE {
-- Name of the BLAST database from which to retrieve the sequence data
database Blast4-database,
-- Sequence identifiers for the sequence to get
seq-ids SEQUENCE OF Seq-id,
-- Determines whether the returned Bioseqs should contain the sequence data
-- or not
skip-seq-data BOOLEAN DEFAULT FALSE,
-- Determines whether or not the defline of the returned Bioseqs should
-- contain only the requested seq id. This optional field only applies
-- to non-redundant BLAST database
target-only BOOLEAN OPTIONAL
}
-- Fetch parts of sequences from a BLAST database
Blast4-get-seq-parts-request ::= SEQUENCE {
-- Name of the BLAST database from which to retrieve the sequence data
database Blast4-database,
-- Allows the specification of ranges of sequence data needed.
-- If the sequence(s) interval's end is 0, no data will be fetched.
-- If end is past the length of the sequence, it will be adjusted to the
-- end of the sequence (this allows fetching of the first chunk in
-- cases where the length is not yet known).
seq-locations SEQUENCE OF Seq-interval
}
-- support for version and checking availability of methods
Blast4-get-protocol-info-request ::= Blast4-parameters
-- variose search information
Blast4-get-search-info-request ::= SEQUENCE {
request-id VisibleString,
info 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,
get-queries Blast4-get-queries-reply,
get-request-info Blast4-get-request-info-reply,
get-sequence-parts Blast4-get-seq-parts-reply,
get-windowmasked-taxids Blast4-get-windowmasked-taxids-reply,
get-protocol-info Blast4-get-protocol-info-reply,
get-search-info Blast4-get-search-info-reply,
get-databases-ex Blast4-get-databases-ex-reply
}
Blast4-finish-params-reply ::= Blast4-parameters
Blast4-get-windowmasked-taxids-reply ::= SEQUENCE OF INTEGER
Blast4-get-databases-reply ::= SEQUENCE OF Blast4-database-info
Blast4-get-databases-ex-reply ::= SEQUENCE OF Blast4-database-info
Blast4-get-matrices-reply ::= SEQUENCE OF Blast4-matrix-id
Blast4-get-parameters-reply ::= SEQUENCE OF Blast4-parameter-info
-- Note: Paramsets and tasks represent the same concept: a human readable
-- description that represents a set of parameters with specific values
-- to accomplish a given task
Blast4-get-paramsets-reply ::= SEQUENCE OF Blast4-task-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,
-- Masking locations for the query sequence(s). Each element of this set
-- corresponds to a single query's translation frame as appropriate.
masks SEQUENCE OF Blast4-mask OPTIONAL,
ka-blocks SEQUENCE OF Blast4-ka-block OPTIONAL,
search-stats SEQUENCE OF VisibleString OPTIONAL,
pssm PssmWithParameters OPTIONAL,
simple-results Blast4-simple-results OPTIONAL
}
Blast4-get-sequences-reply ::= SEQUENCE OF Bioseq
-- Bundles Seq-ids and sequence data to fulfill requests of type
-- Blast4-get-seq-parts-request
Blast4-seq-part-data ::= SEQUENCE {
-- Sequence identifier
id Seq-id,
-- Its sequence data (may be partial)
data Seq-data
}
Blast4-get-seq-parts-reply ::= SEQUENCE OF Blast4-seq-part-data
Blast4-queue-search-reply ::= SEQUENCE {
request-id VisibleString OPTIONAL
}
Blast4-get-queries-reply ::= SEQUENCE {
queries Blast4-queries
}
Blast4-get-protocol-info-reply ::= Blast4-parameters
Blast4-get-search-info-reply ::= SEQUENCE {
request-id VisibleString,
info Blast4-parameters OPTIONAL
}
-- --------------------------------------------------------------------
--
-- Errors
--
-- --------------------------------------------------------------------
Blast4-error ::= SEQUENCE {
-- This is an integer to allow for flexibility, but the values assigned
-- should be of type Blast4-error-code
code INTEGER,
message VisibleString OPTIONAL
}
-- This enumeration defines values that are intended to be used with the
-- Blast4-error::code in a logical AND operation to easily determine whether a
-- given Blast4-error object contains either a warning or an error
Blast4-error-flags ::= ENUMERATED {
warning (1024),
error (2048)
}
-- Defines values for use in Blast4-error::code.
-- Note: warnings should have values greater than 1024 and less than 2048,
-- errors should have values greater than 2048.
Blast4-error-code ::= INTEGER {
-- A conversion issue was found when converting to/from blast3 from/to
-- blast4 protocol in the blast4 server
conversion-warning (1024),
-- Indicates internal errors in the blast4 server
internal-error (2048),
-- Request type is not implemented in the blast4 server
not-implemented (2049),
-- Request type is not allowed in the blast4 server
not-allowed (2050),
-- Malformed/invalid requests (e.g.: parsing errors or invalid data in request)
bad-request (2051),
-- The RID requested is unknown or it has expired
bad-request-id (2052),
-- The search is pending
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,
extended Blast4-parameters OPTIONAL
}
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
}
-- Masking locations for a query's frame. The locations field is a single
-- Seq-loc of type Packed-int, which contains all the masking locations for the
-- translation frame specified by the frame field.
-- Notes:
-- On input (i.e.: when the client specifies masking locations as a
-- Blast4-parameter), in the case of protein queries, the frame field must
-- always be notset, in the case of nucleotide queries (regardless of whether
-- the search will translate these or not), the frame must be plus1. Masking
-- locations in the translated encoding are not permitted.
-- On output (i.e.: when blast 4 server encodes these as part of the
-- Blast4-get-search-results-reply), the same conventions as above apply for
-- non-translated protein and nucleotide queries, but in the case of translated
-- nucleotide queries, the frame field can be specified in any of the
-- translation frames as appropriate.
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
}
-- Self documenting task structure
Blast4-task-info ::= SEQUENCE {
-- Name of this task
name VisibleString,
-- Description of the task
documentation 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,
seq-loc-list SEQUENCE OF Seq-loc
}
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 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