view variant_effect_predictor/Bio/EnsEMBL/Analysis.pm @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

=head1 LICENSE

  Copyright (c) 1999-2012 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

    http://www.ensembl.org/info/about/code_licence.html

=head1 CONTACT

  Please email comments or questions to the public Ensembl
  developers list at <[e-mail]>.

  Questions may also be sent to the Ensembl help desk at
  <[e-mail]>.

=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 Scalar::Util qw/isweak weaken/;

@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 new_fast

  Arg [1]    : HashRef $hashref
               Value to bless
  Description: Bless a hash into this object type
  Exceptions : none
  Returntype : Bio::EnsEMBL::Analysis
  Caller     : general, subclass constructors

=cut

sub new_fast {
  my ($class, $hashref) = @_;
  my $self = bless $hashref, ref($class) || $class;
  weaken($self->{adaptor})  if ( ! isweak($self->{adaptor}) );
  return $self;
}

=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

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;