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Bio-EnsEMBL-112.0_54
River stage zero No dependents
/ Bio::EnsEMBL::DBSQL::AnalysisAdaptor

LICENSE

Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2024] EMBL-European Bioinformatics Institute

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

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NAME

Bio::EnsEMBL::DBSQL::AnalysisAdaptor

SYNOPSIS

use Bio::EnsEMBL::Registry;

Bio::EnsEMBL::Registry->load_registry_from_db(
  -host => 'ensembldb.ensembl.org',
  -user => 'anonymous'
);

$analysis_adaptor =
  Bio::EnsEMBL::Registry->get_adaptor( "human", "core", "analysis" );

my $analysis = $analysis_adaptor->fetch_by_logic_name('genscan');

DESCRIPTION

Module to encapsulate all db access for persistent class Analysis.
There should be just one per application and database connection.

METHODS

new

Args       : Bio::EnsEMBL::DBSQL::DBAdaptor
Example    : my $aa = new Bio::EnsEMBL::DBSQL::AnalysisAdaptor();
Description: Creates a new Bio::EnsEMBL::DBSQL::AnalysisAdaptor object and
             internally loads and caches all the Analysis objects from the 
             database.
Returntype : Bio::EnsEMBL::DBSQL::AnalysisAdaptor
Exceptions : none
Caller     : Bio::EnsEMBL::DBSQL::DBAdaptor
Status     : Stable

fetch_all

Args       : none
Example    : my @analysis = @{$analysis_adaptor->fetch_all()};
Description: fetches all of the Analysis objects from the database and caches
             them internally.
Returntype : listref of Bio::EnsEMBL::Analysis retrieved from the database
Exceptions : none
Caller     : AnalysisAdaptor::new
Status     : Stable

fetch_all_by_feature_class

Arg [1]    : string $feature_cless - The name of the feature class
Example    : my @analyses = @{$analysis_adaptor->fetch_all_by_feature_class('Gene');
Description: Returns all analyses that correspond to a given 
             feature class; see feature_classes method for a list.
Returntype : Listref of Bio::EnsEMBL::Analysis
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_dbID

Arg [1]    : int $internal_analysis_id - the database id of the analysis 
             record to retrieve
Example    : my $analysis = $analysis_adaptor->fetch_by_dbID(1);
Description: Retrieves an Analysis object from the database via its internal
             id.
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller     : general
Status     : Stable

fetch_by_logic_name

Arg [1]    : string $logic_name the logic name of the analysis to retrieve
Example    : my $analysis = $a_adaptor->fetch_by_logic_name('Eponine');
Description: Retrieves an analysis object from the database using its unique
             logic name.
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller     : general
Status     : Stable

store

Arg [1]    : Bio:EnsEMBL::Analysis $analysis
Example    : $analysis_adaptor->store($analysis);
Description: Stores $analysis in db.  If the analysis is already stored in
             the database its dbID and adaptor are updated, but the analysis
             is not stored a second time.
             Sets created date if not already set. Sets dbID and adaptor
             inside $analysis. Returns dbID.
Returntype : int - dbID of stored analysis
Exceptions : throw on incorrect argument
             throw if analysis argument does not have a logic name
Caller     : general
Status     : Stable

update

Arg [1]    : Bio::EnsEMBL::Analysis $anal
Example    : $adaptor->update($anal)
Description: Updates this analysis in the database
Returntype : int 1 if update is performed, undef if it is not
Exceptions : throw if arg is not an analysis object
Caller     : ?
Status     : Stable

remove

Arg [1]    : Bio::EnsEMBL::Analysis $anal
Example    : $adaptor->remove($anal)
Description: Removes this analysis from the database.  This is not really
             safe to execute in a multi process environment, so programs
             should not remove analysis while out on the farm.
Returntype : none
Exceptions : thrown if $anal arg is not an analysis object
Caller     : ?
Status     : Stable

exists

Arg [1]    : Bio::EnsEMBL::Analysis $anal
Example    : if($adaptor->exists($anal)) #do something
Description: Tests whether this Analysis already exists in the database
             by checking first if the adaptor and dbID are set and
             secondly by whether it is in this adaptors internal cache.
             Note that this will not actually check the database and will
             not find and analysis which were recently added by other
             processes.  You are better off simply trying to store an
             analysis which will reliably ensure that it is not stored twice
             in the database.
Returntype : int dbID if analysis is found, otherwise returns undef
Exceptions : thrown if $anal arg is not an analysis object
Caller     : store
Status     : Stable

_objFromHashref

Arg [1]    : hashref $rowHash
Description: Private helper function generates an Analysis object from a 
             mysql row hash reference.
Returntype : Bio::EnsEMBL::Analysis
Exceptions : none
Caller     : Bio::EnsEMBL::DBSQL::AnalsisAdaptor::fetch_* methods
Status     : Stable