diff variant_effect_predictor/Bio/EnsEMBL/Funcgen/Set.pm @ 0:1f6dce3d34e0

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/Set.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,348 @@
+
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::Set
+#
+
+=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::Funcgen::Set - A module to represent a base Set object.
+ 
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::Set;
+
+@INC = qw (Bio::EnsEMBL::Funcgen::Set)
+
+sub new {
+  my $caller = shift;
+	
+  my $class = ref($caller) || $caller;
+	
+  my $self = $class->SUPER::new(@_);
+
+  
+}
+
+=head1 DESCRIPTION
+
+A base Set object which provides access common methods available across all Funcgen Set classes.
+
+
+=cut
+
+use strict;
+use warnings;
+
+package Bio::EnsEMBL::Funcgen::Set;
+
+use Bio::EnsEMBL::Utils::Argument qw( rearrange );
+use Bio::EnsEMBL::Utils::Exception qw( throw warning deprecate);
+use Bio::EnsEMBL::Funcgen::Storable;
+
+use vars qw(@ISA);
+@ISA = qw(Bio::EnsEMBL::Funcgen::Storable);
+
+
+=head2 new
+
+  Example    : my $self = $class->SUPER::new(@_);
+  Description: Constructor for Set objects.
+  Returntype : Bio::EnsEMBL::Funcgen::Set
+  Exceptions : None
+  Caller     : General
+  Status     : At risk
+
+=cut
+
+sub new {
+  my $caller = shift;
+	
+  my $class = ref($caller) || $caller;
+	
+  my $self = $class->SUPER::new(@_);
+  
+  #TYPE was never parsed here?
+  #Only in inheritants that used it i.e. FeatureSet
+
+  my ($name, $anal, $ftype, $ctype, $set_type, $fclass, $type)
+    = rearrange(['NAME', 'ANALYSIS', 'FEATURE_TYPE', 'CELL_TYPE', 'SET_TYPE', 'FEATURE_CLASS', 'TYPE'], @_);
+  
+  throw('Need to specify a name') if ! defined $name;
+
+  $self->set_type($set_type);
+  $self->feature_class($fclass);
+  $self->feature_class($type) if $type;#Remove this when fully implemented
+  $self->{'name'} = $name;
+  $self->cell_type($ctype) if $ctype;
+  $self->feature_type($ftype) if $ftype;
+
+  if(defined $anal){
+	$self->analysis($anal);
+  }elsif($self->set_type ne 'input'){
+	#Could move this to child Sets and just set analysis here
+	#As with ftype
+	throw('Must pass a valid -analysis parameter for a '.ref($self));
+  }
+
+  return $self;
+}
+
+
+
+
+
+
+=head2 name
+
+  Example    : my $set->name('SET1');
+  Description: Getter/Setter for the name of this Set.
+  Returntype : string
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub name {
+  my $self = shift;
+
+  return $self->{'name'};
+}
+
+=head2 cell_type
+
+  Example    : my $dset_ctype_name = $dset->cell_type->name();
+  Description: Getter for the cell_type for this DataSet.
+  Returntype : Bio::EnsEMBL::Funcgen::CellType
+  Exceptions : throws if arg not valid
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub cell_type {
+  my ($self, $ctype) = @_;
+
+  if(defined $ctype){
+
+	if(! (ref($ctype) eq 'Bio::EnsEMBL::Funcgen::CellType'
+		  && $ctype->dbID())){ 
+	  throw('Must pass a valid stored Bio::EnsEMBL::Funcgen::CellType');
+	}
+	$self->{'cell_type'} = $ctype;
+  }
+
+  return $self->{'cell_type'};
+}
+
+=head2 feature_type
+
+  Example    : my $dset_ftype_name = $dset->feature_type->name();
+  Description: Getter for the feature_type for this DataSet.
+  Returntype : Bio::EnsEMBL::Funcgen::FeatureType
+  Exceptions : Throws if arg not valid
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub feature_type {
+  my ($self, $ftype) = @_;
+   
+  if(defined $ftype){
+
+	if(! (ref($ftype) eq 'Bio::EnsEMBL::Funcgen::FeatureType'
+		  && $ftype->dbID())){ 
+	  throw('Must pass a valid stored Bio::EnsEMBL::Funcgen::FeatureType');
+	}
+	$self->{'feature_type'} = $ftype;
+  }
+
+  		  
+  return $self->{'feature_type'};
+}
+
+
+=head2 feature_class
+
+  Arg[0]     : string - feature class e.g. result, annotated, regulatory or external.
+  Example    : my $fclass = $dset->feature_class;
+  Description: Getter for the feature_type for this Set.
+  Returntype : string 
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+#Supercededs type method in FeatureSet
+
+sub feature_class {
+  my ($self, $fclass) = @_;
+   
+  if(defined $fclass){
+
+	#Leave this an implement in inheritants
+	#if(! grep /^${fclass}$/, ('annotated', 'result', 'external', 'regulatory')){
+	#  throw("You have no supplied a valid feature class:\t$fclass");
+	#}
+
+	$self->{'feature_class'} = $fclass;
+  }
+
+  return $self->{'feature_class'};
+}
+
+
+
+=head2 analysis
+
+  Example    : my $anal_name = $set->analysis->logic_name();
+  Description: Getter for the analysis attribute for this Set.
+  Returntype : Bio::EnsEMBL::Analysis
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub analysis {
+  my $self = shift;
+
+  if(@_){
+	throw('Must pass a valid stored Analysis') if (! (ref($_[0]) eq 'Bio::EnsEMBL::Analysis'
+													  && $_[0]->dbID()));
+	$self->{'analysis'} = shift;
+  }
+  
+ 
+  return $self->{'analysis'};
+}
+
+=head2 display_label
+
+  Example    : print $set->display_label();
+  Description: Getter for the display_label attribute for this Set.
+               This is more appropriate for teh predicted_features of the set.
+               Use the individual display_labels for each raw result set.
+  Returntype : str
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub display_label {
+  my $self = shift;
+
+ 
+  #Add display label in table?
+  #Can we aborc ResultSet method into this?
+
+  if(! $self->{'display_label'}){
+
+	#if($self->product_FeatureSet->feature_type->class() eq 'Regulatory Feature'){
+	#  $self->{'display_label'} = 'Regulatory Features';
+	#}
+	#else{
+
+	#This only works for annotated/regulatory_feature sets and result sets
+	#Move to other Set classes?
+
+	$self->{'display_label'} = $self->feature_type->name()." -";
+	$self->{'display_label'} .= " ".($self->cell_type->display_label() || 
+									 $self->cell_type->description()   ||
+									 $self->cell_type()->name());
+	
+
+	if($self->set_type eq 'result'){
+	  $self->{'display_label'} .= " signal";
+	}
+	else{
+	  $self->{'display_label'} .= " enriched sites";
+	}
+  }
+ 
+  return $self->{'display_label'};
+}
+
+
+
+=head2 set_type
+
+  Example    : my $set_type = $set->set_type;
+  Description: Getter for the Set type for this Set.
+  Returntype : string e.g. result, feature, data, input
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub set_type {
+  my ($self, $set_type) = @_;
+   
+  if(defined $set_type){
+	$self->{'_set_type'} = $set_type;
+  }
+  elsif(! defined $self->{'_set_type'}){
+	my @namespace = split/\:\:/, ref($self);
+	($self->{'_set_type'} = lc($namespace[$#namespace])) =~ s/set//;
+	
+  }
+
+  return $self->{'_set_type'};
+}
+
+=head2 type
+
+  Example    : my $type = $set->type;
+  Description: Getter for the type for this Set.
+               e.g. annotated, external, regulatory for FeatureSets
+                    or 
+                    array, sequencing for InputSets
+               Currently not applicable to DataSets or ResultSets
+  Exceptions : None
+  Returntype : string 
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub type {
+  my $self = shift;
+   
+  deprecate("Please use feature_class instead");
+  
+  return $self->feature_class(@_);
+
+  #$self->{'feature_class'} = shift if @_;
+  
+  #return $self->{'feature_class'};
+}
+
+
+
+1;
+