Raw content of Bio::EnsEMBL::Analysis
<![CDATA[=head1 LICENSE
Copyright (c) 1999-2009 The European Bioinformatics Institute and
Genome Research Limited. All rights reserved.
This software is distributed under a modified Apache license.
For license details, please see
/info/about/code_licence.html
=head1 CONTACT
Please email comments or questions to the public Ensembl
developers list at <ensembl-dev@ebi.ac.uk>.
Questions may also be sent to the Ensembl help desk at
<helpdesk@ensembl.org>.
=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);
@ISA = qw(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 $db
Example : none
Description: get/set for the attribute db
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub db {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_db} = $arg;
}
return $self->{_db};
}
=head2 db_version
Arg [1] : string $db_version
Example : none
Description: get/set for attribute db_version
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub db_version {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_db_version} = $arg;
}
return $self->{_db_version};
}
=head2 db_file
Arg [1] : string $db_file
Example : none
Description: get/set for attribute db_file
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub db_file {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_db_file} = $arg;
}
return $self->{_db_file};
}
=head2 program
Arg [1] : string $program
Example : none
Description: get/set for attribute program
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub program {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_program} = $arg;
}
return $self->{_program};
}
=head2 program_version
Arg [1] : string $program_version
Example : none
Description: get/set for attribute program_version
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub program_version {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_program_version} = $arg;
}
return $self->{_program_version};
}
=head2 program_file
Arg [1] : string $program_file
Example : none
Description: get/set for attribute program_file
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub program_file {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_program_file} = $arg;
}
return $self->{_program_file};
}
=head2 module
Arg [1] : string $module
Example : none
Description: get/set for attribute module. Usually a RunnableDB perl
module that executes this analysis job.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub module {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_module} = $arg;
}
return $self->{_module};
}
=head2 module_version
Arg [1] : string $module_version
Example : none
Description: get/set for attribute module_version
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub module_version {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_module_version} = $arg;
}
return $self->{_module_version};
}
=head2 gff_source
Arg [1] : string $gff_source
Example : none
Description: get/set for attribute gff_source
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub gff_source {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_gff_source} = $arg;
}
return $self->{_gff_source};
}
=head2 gff_feature
Arg [1] : string $gff_feature
Example : none
Description: get/set for attribute gff_feature
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub gff_feature {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_gff_feature} = $arg;
}
return $self->{_gff_feature};
}
=head2 parameters
Arg [1] : string $parameters
Example : none
Description: get/set for attribute parameters. This should be evaluated
by the module if given or the program that is specified.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub parameters {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_parameters} = $arg;
}
return $self->{_parameters};
}
=head2 created
Arg [1] : string $created
Example : none
Description: get/set for attribute created time.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub created {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_created} = $arg;
}
return $self->{_created};
}
=head2 logic_name
Arg [1] : string $logic_name
Example : none
Description: Get/set method for the logic_name, the name under
which this typical analysis is known.
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub logic_name {
my ($self, $arg ) = @_;
( defined $arg ) &&
($self->{_logic_name} = $arg);
$self->{_logic_name};
}
=head2 has_database
Args : none
Example : none
Description: tests if the db attribute is set, returns 1 if so,
0 if not.
Returntype : int 0,1
Exceptions : none
Caller : general
Status : Stable
=cut
sub has_database{
my ($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 $display_label
Example : none
Description: get/set for attribute display_label
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub display_label {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_display_label} = $arg;
}
return $self->{_display_label};
}
=head2 displayable
Arg [1] : string $displayable
Example : none
Description: get/set for attribute displayable
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub displayable {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_displayable} = $arg;
}
return $self->{_displayable};
}
=head2 web_data
Arg [1] : string $web_data
Example : none
Description: get/set for attribute web_data
Returntype : string
Exceptions : none
Caller : general
Status : Stable
=cut
sub web_data {
my ($self,$arg) = @_;
if (defined($arg)) {
$self->{_web_data} = $arg;
}
return $self->{_web_data};
}
=head2 compare
Arg 1 : Bio::EnsEMBL::Analysis $ana
The analysis to compare to
Example : none
Description: returns 1 if this analysis is special case of given analysis
returns 0 if they are equal
returns -1 if they are completely different
Returntype : int -1,0,1
Exceptions : none
Caller : unknown
Status : Stable
=cut
sub compare {
my ($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;
]]>