diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/FeatureSet.pm @ 0:21066c0abaf5 draft

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/FeatureSet.pm	Fri Aug 03 10:04:48 2012 -0400
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+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::FeatureSet
+#
+
+=head1 LICENSE
+
+  Copyright (c) 1999-2011 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]>.
+
+
+=head1 NAME
+
+Bio::EnsEMBL::FeatureSet - A module to represent FeatureSet.
+ 
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::FeatureSet;
+
+my $result_set = Bio::EnsEMBL::Funcgen::FeatureSet->new(
+
+); 
+
+
+
+=head1 DESCRIPTION
+
+A FeatureSet object provides access to a set of feature predictions and their details, which may have been generated from a 
+single or multiple Experiments with potentially differing analyses.  The FeatureSet itself will only have a single analysis 
+which may be one or a combination of programs but will be represented by one analysis record.
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Funcgen::FeatureSet;
+
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate);
+use Bio::EnsEMBL::Funcgen::Set;
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Funcgen::Set);
+
+my %valid_classes = ( annotated    => undef,
+                      regulatory   => undef,
+                      external     => undef,
+                      segmentation => undef, );
+
+=head2 new
+
+    -name          => $name,
+    -feature_type  => $ftype,
+                                                                    -cell_type     => $ctype,
+                                                                    -name          => $name,
+              -description   => 'Release 3.1',
+                                                           -display_label => 'Short name',
+  -analysis      => $analysis,
+  Arg [-EXPERIMENT_ID]     : Experiment dbID
+  -dbid          => $dbid,
+Arg [-ADAPTOR]
+
+  Example    : my $feature = Bio::EnsEMBL::Funcgen::FeatureSet->new(
+                                                                    -dbid          => $dbid,
+                                                                    -analysis      => $analysis,
+                                                                    -feature_type  => $ftype,
+                                                                    -cell_type     => $ctype,
+                                                                    -name          => $name,
+                                                                    -feature_class => 'annotated',
+                                                                    -description   => 'Release 3.1',
+                                                                    -display_label => 'Short name',
+                                                                    -input_set     => $iset,
+			                                                       ); 
+  Description: Constructor for FeatureSet objects.
+  Returntype : Bio::EnsEMBL::Funcgen::FeatureSet
+  Exceptions : Throws if FeatureType defined
+  Caller     : General
+  Status     : At risk
+
+=cut
+
+sub new {
+  my $caller = shift;
+  my $class  = ref($caller) || $caller;
+  my $self   = $class->SUPER::new(@_);
+
+  my ( $desc, $dlabel, $iset_id, $iset, $exp_id, $exp ) =
+    rearrange( [ 
+                'DESCRIPTION',   'DISPLAY_LABEL',
+                'INPUT_SET_ID', 'INPUT_SET', 'EXPERIMENT_ID', 'EXPERIMENT'
+               ],
+               @_ );
+
+
+  if($exp_id || $exp){
+    throw('Passing an Experiment or an experiment_id is now deprecated,'.
+          ' please use -input_set or -input_set_id instead');
+  }
+
+  #Allow exp or exp_id to be passed to support storing and lazy loading
+
+  #Mandatory params checks here (setting done in Set.pm)
+  throw('Must provide a FeatureType')
+    if ( !defined $self->feature_type );
+
+ #explicit type check here to avoid invalid types being imported as NULL
+ #subsequently throwing errors on retrieval
+  my $type = $self->feature_class;
+
+  if ( !( $type && exists $valid_classes{$type} ) ) {
+    throw( 'You must define a valid FeatureSet type e.g. ' .
+           join( ', ', keys %valid_classes ) );
+  }
+
+  #Direct assignment to prevent need for set arg test in method
+
+  $self->{'description'}   = $desc   if defined $desc;
+  $self->{'display_label'} = $dlabel if defined $dlabel;
+  $self->{'input_set_id'} = $iset_id if defined $iset_id;
+
+  if ( defined $iset ) {
+    #Exp obj is only passed during object storing
+    #so let the adaptor do is_stored_and_valid
+    $self->{'input_set'} = $iset;
+  }
+
+  return $self;
+} ## end sub new
+
+
+
+=head2 new_fast
+
+  Args       : Hashref with all internal attributes set
+  Example    : none
+  Description: Quick and dirty version of new. Only works if the code is very
+               disciplined.
+  Returntype : Bio::EnsEMBL::Funcgen::FeatureSet
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+
+sub new_fast {
+  return bless ($_[1], $_[0]);
+}
+
+
+=head2 description
+
+  Example    : print "Feature set description is:\t".$fset->description."\n";
+  Description: Getter for the description of this FeatureSet. e.g. Release 3.1
+  Returntype : String
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub description {
+  return $_[0]->{'description'};
+}
+
+
+
+=head2 display_label
+
+  Example    : print $rset->display_label;
+  Description: Getter for the display_label attribute for this FeatureSet.
+  Returntype : String
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub display_label {
+  my $self = shift;
+
+  if ( !$self->{'display_label'} ) {
+
+    if ( $self->feature_type->class() eq 'Regulatory Feature' ) {
+      $self->{'display_label'} = $self->name;
+    }
+    else {
+      #This still fails here if we don't have a class or a cell_type set
+
+      $self->{'display_label'} =
+        $self->feature_type->name() . " - " . $self->cell_type->name() .
+        " Enriched Sites";
+    }
+  }
+
+  return $self->{'display_label'};
+}
+
+
+
+
+=head2 get_FeatureAdaptor
+
+  Example    : 
+  Description: Retrieves and caches FeatureAdaptor of feature_set type 
+  Returntype : Bio::EnsEMBL::Funcgen::DBSQL::ucfirst($self->feature_class())FeatureAdaptor
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+
+sub get_FeatureAdaptor{
+  my $self = shift;
+
+  if(! exists $self->{'adaptor_refs'}){
+
+	foreach my $valid_class(keys %valid_classes){
+	  my $method = 'get_'.ucfirst($valid_class).'FeatureAdaptor';
+
+	  $self->{'adaptor_refs'}{$valid_class} =  $self->adaptor->db->$method;
+	}
+  }
+  
+  return $self->{'adaptor_refs'}->{$self->feature_class()};
+
+}
+
+
+
+=head2 get_Features_by_Slice
+
+  Example    : my @features = @{$FeatureSet->get_Features_by_Slice($slice)};
+  Description: Retrieves all Features for this FeatureSet for a given Slice
+  Returntype : ARRAYREF containing Features of the feature_set type i.e. Annotated, Regulatory or Supporting;
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_Features_by_Slice{
+  my ($self, $slice) = @_;
+
+  return $self->get_FeatureAdaptor->fetch_all_by_Slice_FeatureSets($slice, [$self]);
+}
+
+
+=head2 get_Features_by_FeatureType
+
+  Arg[0]     : Bio::EnsEMBL::Funcgen::FeatureType
+  Example    : my @features = @{$FeatureSet->get_Features_by_FeatureType($ftype)};
+  Description: Retrieves all Features for this FeatureSet for a given FeatureType
+               or associated FeatureType. This is mainly used by external FeatureSets
+               which can sometimes have more than one associated FeatureType.
+  Returntype : ARRAYREF
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+
+sub get_Features_by_FeatureType{
+  my ($self, $type) = @_;
+
+  return $self->get_FeatureAdaptor->fetch_all_by_FeatureType_FeatureSets($type, [$self]);
+}
+
+
+=head2 get_all_Features
+
+  Example    : my @features = @{$FeatureSet->get_all_Features};
+  Description: Retrieves all Features for this FeatureSet
+  Returntype : ARRAYREF
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_all_Features{
+  my $self = shift;
+
+  return $self->get_FeatureAdaptor->fetch_all_by_FeatureSets([$self]);
+}
+
+
+
+
+=head2 is_focus_set
+
+  Args       : None
+  Example    : if($fset->is_focus_set){ ... }
+  Description: Returns true if FeatureSet is a focus set used in the RegulatoryBuild
+  Returntype : Boolean
+  Exceptions : Throws if meta entry not present
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub is_focus_set{
+  my $self = shift;
+
+  if(! defined $self->{focus_set}){
+
+	if(! defined $self->cell_type){
+	  warn "FeatureSet without an associated CellType cannot be a focus set:\t".$self->name;
+	  $self->{focus_set} = 0;
+	}
+	else{
+	   $self->{focus_set} = $self->adaptor->fetch_focus_set_config_by_FeatureSet($self);
+	 }
+  }
+
+  return $self->{focus_set};
+}
+
+
+=head2 is_attribute_set
+
+  Args       : None
+  Example    : if($fset->is_attribute_set){ ... }
+  Description: Returns true if FeatureSet is a supporting/attribute(focus or not) set used in the RegulatoryBuild
+  Returntype : Boolean
+  Exceptions : Throws if meta entry not present
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub is_attribute_set{
+  my $self = shift;
+
+  if(! defined $self->{attribute_set}){
+
+	if(! defined $self->cell_type){
+	  warn "FeatureSet without an associated CellType cannot be a attribute set:\t".$self->name;
+	  $self->{attribute_set} = 0;
+	}
+	else{
+	   $self->{attribute_set} = $self->adaptor->fetch_attribute_set_config_by_FeatureSet($self);
+	 }
+  }
+
+  return $self->{attribute_set};
+}
+
+
+=head2 get_InputSet
+
+  Example    : my $input_set = $FeatureSet->get_InputSet;
+  Description: Retrieves the InputSet for this FeatureSet
+  Returntype : Bio::EnsEMBL::Funcgen::InputSet
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub get_InputSet{
+  my $self = shift;
+
+  if( (! defined $self->{input_set}) &&
+	  (defined $self->{input_set_id}) ){
+	$self->{input_set} = $self->adaptor->db->get_InputSetAdaptor->fetch_by_dbID($self->{input_set_id});
+  }
+
+  return $self->{input_set};
+}
+
+
+
+=head2 source_label
+
+  Example    : my $source_label = $fset->source_label;
+  Description: Retrieves the source label this FeatureSet, used in zmenus
+  Returntype : Arrayref of Strings
+  Exceptions : None
+  Caller     : Webcode zmenus
+  Status     : At Risk - remove, to be done by webcode?
+
+=cut
+
+#These are used to link through to the experiment view based on feature_set_id
+
+sub source_label{
+  my $self = shift;
+
+  if (! defined $self->{source_label}) {
+    my $input_set = $self->get_InputSet;
+    my @source_labels;
+
+    if ($input_set) {
+
+
+      foreach my $isset(@{$input_set->get_InputSubsets}){
+
+        if(defined $isset->archive_id){
+          push @source_labels, $isset->archive_id;
+        }
+        #Archive IDs e.g. SRX identifiers or undef.
+      }
+
+      #Append project name
+      my $exp_group = $input_set->get_Experiment->experimental_group;
+	   
+      if ($exp_group && 
+          $exp_group->is_project) {
+        push @source_labels, $exp_group->name;
+      }
+    }
+  
+ 
+    $self->{source_label} = join(' ', @source_labels);
+  }
+
+  return $self->{source_label};
+}
+
+
+
+
+### DEPRECATED ###
+
+=head2 get_Experiment
+#
+#  Example    : my $exp = $FeatureSet->get_Experiment;
+#  Description: Retrieves the Experiment for this FeatureSet
+#  Returntype : Bio::EnsEMBL::Funcgen::Experiment
+#  Exceptions : None
+#  Caller     : General
+  Status     : DEPRECATED
+
+=cut
+
+sub get_Experiment{
+  throw('FeatureSet::get_Experiment is not longer supported, please use FeatureSet::get_InputSet');
+}
+
+
+1;