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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/Collection/ResultFeature.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,169 @@
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::Collection::ResultFeature
+#
+=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::Collection::ResultFeature - A module to represent a lightweight ResultFeature collection
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::Collection::ResultFeature;
+
+my $rfeature = Bio::EnsEMBL::Funcgen::Collection::ResultFeature->new_fast({
+   start  => $start, 
+   end    => $end, 
+   scores => [ $score ]
+});
+
+my @rfeatures = @{$rset->get_displayable_ResultFeatures_by_Slice($slice)};
+
+foreach my $rfeature (@rfeatures){
+    my $score = $rfeature->score();
+    my $rf_start = $rfeature->start();
+    my $rf_end = $rfeature->end();
+}
+
+=head1 DESCRIPTION
+
+This is a Collection feature which is designed to store compressed/collected 
+feature information for a defined window/bin size over a complete seq_region.
+Or alternatively a single feature at the natural resolution i.e. window_size == 0.
+The complete seq_region collections are cropped to provide a ResultFeature on any
+given Slice. ResultFeatures are primarily stored in the result_feature table, 
+but can also be generated on the fly from unprocessed data in the array result
+tables.
+
+
+=head1 SEE ALSO
+
+Bio::EnsEMBL::Funcgen::DBSQL::ResultFeatureAdaptor
+Bio::EnsEMBL::Funcgen::Collector::ResultFeature
+
+=cut
+
+
+#This is distinct from a normal feature as the collection may have differen attributes and methods from the normal feature
+#implementation.  For example a Bio::EnsEMBL::Collection::Gene would only have summary information over several genes.
+#Altho', unlikely that we'll ever collect genes.
+
+use strict;
+use warnings;
+
+
+package Bio::EnsEMBL::Funcgen::Collection::ResultFeature;
+use base ('Bio::EnsEMBL::Feature');#@ISA
+
+#This needs to inherit from Bio::EnsEMBL::Collection
+#Which can host some of the below methods
+
+#Reverted to hash implementation as we no longer deal with 
+#huge amounts of features due to collections.
+#This enables use of transform/seq_region_start/end methods
+#and enable us to store on slices that do not begin at 1
+#Altho need to remove code stipulating this
+
+
+
+#To do
+#Can we move any of these methods to a base Collection class?
+#Should probably now use normal new method with validation?
+
+=head2 new_fast
+
+  Args       : Array with attributes start, end, strand, scores, probe, result_set_id, window_size, slice  IN THAT ORDER.
+               WARNING: None of these are validated, hence can omit some where not needed
+  Example    : none
+  Description: Fast and list version of new. Only works if the code is very disciplined.
+  Returntype : Bio::EnsEMBL::Funcgen::ResultFeature
+  Exceptions : None
+  Caller     : ResultSetAdaptor
+  Status     : At Risk
+
+=cut
+
+sub new_fast {
+  #This is agnostic towards to type of reference
+  return bless ($_[1], $_[0]);
+
+}
+
+
+
+=head2 scores
+
+  Example    : my $score = $rf->score();
+  Description: Getter of the scores attribute for ResultFeature
+               objects
+  Returntype : Arrayref.
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub scores {  
+  return $_[0]->{scores};
+}
+
+
+
+=head2 probe
+
+  Example    : my $probe = $rf->probe();
+  Description: Getter of the probe attribute for ResultFeature
+               objects
+  Returntype : Bio::EnsEMBL::Funcgen::Probe
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk - This can only be used for Features with window 0.
+
+=cut
+
+#probe_id is currently not available in the result_feature table, so this would be a result/probe_feature query.
+
+sub probe {  
+  return $_[0]->{probe};
+}
+
+
+sub result_set_id {  
+  return $_[0]->{result_set_id};
+}
+
+sub window_size {  
+  return $_[0]->{window_size};
+}
+
+
+sub get_min_max_scores{
+  
+  if(! defined $_[0]->{'min_max_scores'}){
+	my @sorted_scores = sort { $a <=> $b } @{$_[0]->{'scores'}};
+	$_[0]->{'min_max_scores'} = [$sorted_scores[0], $sorted_scores[$#sorted_scores]];
+  }
+
+  return $_[0]->{'min_max_scores'};
+}
+
+
+1;
+