=head1 LICENSE Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute Copyright [2016-2019] 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 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License. =cut =head1 CONTACT Please email comments or questions to the public Ensembl developers list at . Questions may also be sent to the Ensembl help desk at . =cut =head1 NAME Bio::EnsEMBL::Analysis.pm - Stores details of an analysis run =head1 SYNOPSIS my $obj = new Bio::EnsEMBL::Analysis( -id => $id, -logic_name => 'SWIRBlast', -db => $db, -db_version => $db_version, -db_file => $db_file, -program => $program, -program_version => $program_version, -program_file => $program_file, -gff_source => $gff_source, -gff_feature => $gff_feature, -module => $module, -module_version => $module_version, -parameters => $parameters, -created => $created, -description => 'some warm words about this analysis', -display_label => 'UNIprot alignment', -displayable => '1', -web_data => 'web metadata info' ); =head1 DESCRIPTION Object to store details of an analysis run. =head1 METHODS =cut package Bio::EnsEMBL::Analysis; use vars qw(@ISA); use strict; use Bio::EnsEMBL::Storable; use Bio::EnsEMBL::Utils::Exception qw(throw); use Bio::EnsEMBL::Utils::Argument qw(rearrange); use base 'Bio::EnsEMBL::Storable'; =head2 new Arg [..] : Takes a set of named arguments Example : $analysis = new Bio::EnsEMBL::Analysis::Analysis( -id => $id, -logic_name => 'SWIRBlast', -db => $db, -db_version => $db_version, -db_file => $db_file, -program => $program, -program_version => $program_version, -program_file => $program_file, -gff_source => $gff_source, -gff_feature => $gff_feature, -module => $module, -module_version => $module_version, -parameters => $parameters, -created => $created ); Description: Creates a new Analysis object Returntype : Bio::EnsEMBL::Analysis Exceptions : none Caller : general Status : Stable =cut sub new { my($class,@args) = @_; my $self = bless {},$class; my ($id, $adaptor, $db, $db_version, $db_file, $program, $program_version, $program_file, $gff_source, $gff_feature, $module, $module_version, $parameters, $created, $logic_name, $description, $display_label, $displayable, $web_data) = rearrange([qw(ID ADAPTOR DB DB_VERSION DB_FILE PROGRAM PROGRAM_VERSION PROGRAM_FILE GFF_SOURCE GFF_FEATURE MODULE MODULE_VERSION PARAMETERS CREATED LOGIC_NAME DESCRIPTION DISPLAY_LABEL DISPLAYABLE WEB_DATA )],@args); $displayable ||= 0; $self->dbID ($id); $self->adaptor ($adaptor); $self->db ($db); $self->db_version ($db_version); $self->db_file ($db_file); $self->program ($program); $self->program_version($program_version); $self->program_file ($program_file); $self->module ($module); $self->module_version ($module_version); $self->gff_source ($gff_source); $self->gff_feature ($gff_feature); $self->parameters ($parameters); $self->created ($created); $self->logic_name ( $logic_name ); $self->description( $description ); $self->display_label( $display_label ); $self->displayable( $displayable ); $self->web_data ( $web_data ); return $self; # success - we hope! } =head2 db Arg [1] : string $db Description: get/set for the attribute db Returntype : string Exceptions : none Caller : general Status : Stable =cut sub db { my ($self,$arg) = @_; if (defined($arg)) { $self->{_db} = $arg; } return $self->{_db}; } =head2 db_version Arg [1] : string $db_version Description: get/set for attribute db_version Returntype : string Exceptions : none Caller : general Status : Stable =cut sub db_version { my ($self,$arg) = @_; if (defined($arg)) { $self->{_db_version} = $arg; } return $self->{_db_version}; } =head2 db_file Arg [1] : string $db_file Description: get/set for attribute db_file Returntype : string Exceptions : none Caller : general Status : Stable =cut sub db_file { my ($self,$arg) = @_; if (defined($arg)) { $self->{_db_file} = $arg; } return $self->{_db_file}; } =head2 program Arg [1] : string $program Description: get/set for attribute program Returntype : string Exceptions : none Caller : general Status : Stable =cut sub program { my ($self,$arg) = @_; if (defined($arg)) { $self->{_program} = $arg; } return $self->{_program}; } =head2 program_version Arg [1] : string $program_version Description: get/set for attribute program_version Returntype : string Exceptions : none Caller : general Status : Stable =cut sub program_version { my ($self,$arg) = @_; if (defined($arg)) { $self->{_program_version} = $arg; } return $self->{_program_version}; } =head2 program_file Arg [1] : string $program_file Description: get/set for attribute program_file Returntype : string Exceptions : none Caller : general Status : Stable =cut sub program_file { my ($self,$arg) = @_; if (defined($arg)) { $self->{_program_file} = $arg; } return $self->{_program_file}; } =head2 module Arg [1] : string $module Description: get/set for attribute module. Usually a RunnableDB perl module that executes this analysis job. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub module { my ($self,$arg) = @_; if (defined($arg)) { $self->{_module} = $arg; } return $self->{_module}; } =head2 module_version Arg [1] : string $module_version Description: get/set for attribute module_version Returntype : string Exceptions : none Caller : general Status : Stable =cut sub module_version { my ($self,$arg) = @_; if (defined($arg)) { $self->{_module_version} = $arg; } return $self->{_module_version}; } =head2 gff_source Arg [1] : string $gff_source Description: get/set for attribute gff_source Returntype : string Exceptions : none Caller : general Status : Stable =cut sub gff_source { my ($self,$arg) = @_; if (defined($arg)) { $self->{_gff_source} = $arg; } return $self->{_gff_source}; } =head2 gff_feature Arg [1] : string $gff_feature Description: get/set for attribute gff_feature Returntype : string Exceptions : none Caller : general Status : Stable =cut sub gff_feature { my ($self,$arg) = @_; if (defined($arg)) { $self->{_gff_feature} = $arg; } return $self->{_gff_feature}; } =head2 parameters Arg [1] : string $parameters Description: get/set for attribute parameters. This should be evaluated by the module if given or the program that is specified. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub parameters { my ($self,$arg) = @_; if (defined($arg)) { $self->{_parameters} = $arg; } return $self->{_parameters}; } =head2 created Arg [1] : string $created Description: get/set for attribute created time. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub created { my ($self,$arg) = @_; if (defined($arg)) { $self->{_created} = $arg; } return $self->{_created}; } =head2 logic_name Arg [1] : string $logic_name Description: Get/set method for the logic_name, the name under which this typical analysis is known. Returntype : string Exceptions : none Caller : general Status : Stable =cut sub logic_name { my ($self, $arg ) = @_; ( defined $arg ) && ($self->{_logic_name} = $arg); $self->{_logic_name}; } =head2 has_database Args : none Description: tests if the db attribute is set, returns 1 if so, 0 if not. Returntype : int 0,1 Exceptions : none Caller : general Status : Stable =cut sub has_database{ my ($self,@args) = @_; if( defined $self->db ){ return 1; } return 0; } =head2 description Arg [1] : string $description Example : none Description: get/set for attribute description Returntype : string Exceptions : none Caller : general Status : Stable =cut sub description { my ($self,$arg) = @_; if (defined($arg)) { $self->{_description} = $arg; } return $self->{_description}; } =head2 display_label Arg [1] : string $display_label Description: get/set for attribute display_label Returntype : string Exceptions : none Caller : general Status : Stable =cut sub display_label { my ($self,$arg) = @_; if (defined($arg)) { $self->{_display_label} = $arg; } return $self->{_display_label}; } =head2 displayable Arg [1] : string $displayable Description: get/set for attribute displayable Returntype : string Exceptions : none Caller : general Status : Stable =cut sub displayable { my ($self,$arg) = @_; if (defined($arg)) { $self->{_displayable} = $arg; } return $self->{_displayable}; } =head2 web_data Arg [1] : string $web_data Description: get/set for attribute web_data Returntype : string Exceptions : none Caller : general Status : Stable =cut # See also _objFromHashref in AnalysisAdaptor for context. sub web_data { my ($self,$arg) = @_; if (defined($arg)) { $self->{_web_data} = $arg; } return $self->{_web_data}; } =head2 compare Arg 1 : Bio::EnsEMBL::Analysis $ana The analysis to compare to Description: returns 1 if this analysis is special case of given analysis returns 0 if they are equal returns -1 if they are completely different Returntype : int -1,0,1 Exceptions : none Caller : unknown Status : Stable =cut sub compare { my ($self, $ana ) = @_; throw("Object is not a Bio::EnsEMBL::Analysis") unless $ana->isa("Bio::EnsEMBL::Analysis"); my $detail = 0; foreach my $methodName ( 'program', 'program_version', 'program_file', 'db','db_version','db_file','gff_source','gff_feature', 'module', 'module_version', 'parameters','logic_name' ) { if( defined $self->$methodName() && ! $ana->can($methodName )) { $detail = 1; } if( defined $self->$methodName() && ! defined $ana->$methodName() ) { $detail = 1; } # if given anal is different from this, defined or not, then its different if( defined($ana->$methodName()) && defined($self->$methodName()) && ( $self->$methodName() ne $ana->$methodName() )) { return -1; } } if( $detail == 1 ) { return 1 }; return 0; } 1;