diff variant_effect_predictor/Bio/EnsEMBL/Analysis.pm @ 0:2bc9b66ada89 draft default tip

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Analysis.pm	Thu Apr 11 06:29:17 2013 -0400
@@ -0,0 +1,621 @@
+=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;
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