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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/variant_effect_predictor/Bio/EnsEMBL/Funcgen/ResultFeature.pm	Thu Apr 11 02:01:53 2013 -0400
@@ -0,0 +1,258 @@
+#
+# Ensembl module for Bio::EnsEMBL::Funcgen::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::ResultFeature - A module to represent a lightweight ResultFeature object
+
+=head1 SYNOPSIS
+
+use Bio::EnsEMBL::Funcgen::ResultFeature;
+
+my $rfeature = Bio::EnsEMBL::Funcgen::ResultFeature->new_fast([$start, $end, $score ]);
+
+my @rfeatures = @{$rset->get_displayable_ResultFeature_by_Slice($slice)};
+
+foreach my $rfeature (@rfeatures){
+    my $score = $rfeature->score();
+    my $rf_start = $rfeature->start();
+    my $rf_end = $rfeature->end();
+}
+
+=head1 DESCRIPTION
+
+This is a very sparse class designed to be as lightweight as possible to enable fast rendering in the web browser.
+As such only the information absolutely required is contained.  Any a piori information is omitted e.g. seq_region_id, 
+this will already be known as ResultFeatures are retrieved via a Slice method in ResultSet via the ResultSetAdaptor, 
+likewise with analysis and experimental_chip information.  ResultFeatures are transient objects, in that they are not 
+stored in the DB, but are a very small subset of information from the result and oligo_feature tables. ResultFeatures 
+should only be generated by the ResultSetAdaptor as there is no parameter checking in place.
+
+=cut
+
+use strict;
+use warnings;
+
+#Could set global named vars here for element names. Would take more memory
+
+package Bio::EnsEMBL::Funcgen::ResultFeature;
+
+use base ('Bio::EnsEMBL::Feature');
+
+=head2 new_fast
+
+  Args       : Array with attributes start, end, strand, score, probe, result_set_id, winow_size  IN THAT ORDER.
+               WARNING: None of these are validated, hence can omit some where not needed
+  Example    : none
+  Description: Fast and list version of new. Only works if the code is very disciplined.
+  Returntype : Bio::EnsEMBL::Funcgen::ResultFeature
+  Exceptions : None
+  Caller     : ResultSetAdaptor
+  Status     : At Risk
+
+=cut
+
+sub new_fast {
+  my ($class, @args)  = @_;
+  #return bless ($arrayref, $class);
+
+  #Passing arrayref here may cause problems with changing vars after obj creation
+
+  #warn "in new fast with @args";
+
+  bless \@args, $class;
+}
+
+
+
+
+=head2 start
+
+  Example    : my $start = $rf->start();
+  Description: Getter of the start attribute for ResultFeature
+               objects.
+  Returntype : int
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk - Now also sets to enable projection
+
+=cut
+
+sub start {  
+  $_[0]->[0] =  $_[1] if $_[1];
+  $_[0]->[0];
+}
+
+
+=head2 end
+
+  Example    : my $start = $rf->end();
+  Description: Getter of the end attribute for ResultFeature
+               objects.
+  Returntype : int
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk - Now also sets to enable projection
+
+=cut
+
+sub end {  
+  $_[0]->[1] =  $_[1] if $_[1];
+  $_[0]->[1];
+}
+
+
+#Do we need to chacnge this to strand and have slice strand context, as with start and end
+
+sub strand {  $_[0]->[2];}
+
+=head2 score
+
+  Example    : my $score = $rf->score();
+  Description: Getter of the score attribute for ResultFeature
+               objects
+  Returntype : string/float/double?
+  Exceptions : None
+  Caller     : General
+  Status     : At Risk
+
+=cut
+
+sub score {  $_[0]->[3];}
+
+
+=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 {  $_[0]->[4];}
+
+
+#The following are only used for storage and retrieval, hence why they are not included in new_fast which is streamlined
+#for performance
+#These have no validation so all thi smust be done in the caller/storer i.e. the adaptor
+
+sub result_set_id {  $_[0]->[5];}
+sub window_size {  $_[0]->[6];}
+
+#May not ever need this
+#We pass the slice to store
+#Don't normally want to remap, so don't need furing fetch
+#Now also sets for to enable projection
+
+sub slice {  
+  $_[0]->[7] =  $_[1] if $_[1];
+  $_[0]->[7];
+}
+
+
+#Had to reimplement these as they used direct hash calls rather than acessor
+#redefined to use accessors to array
+
+sub length {
+  my $self = shift;
+  return $self->end - $self->start + 1;
+}
+
+=head2 move
+
+  Arg [1]    : int start
+  Arg [2]    : int end
+  Arg [3]    : (optional) int strand
+  Example    : None
+  Description: Sets the start, end and strand in one call rather than in 
+               3 seperate calls to the start(), end() and strand() methods.
+               This is for convenience and for speed when this needs to be
+               done within a tight loop.
+  Returntype : none
+  Exceptions : Thrown is invalid arguments are provided
+  Caller     : general
+  Status     : Stable
+
+=cut
+
+sub move {
+  my $self = shift;
+
+  throw('start and end arguments are required') if(@_ < 2);
+
+  my $start  = shift;
+  my $end    = shift;
+  my $strand = shift;
+
+  if(defined($start) && defined($end) && $end < $start) {
+    throw('start must be less than or equal to end');
+  }
+  if(defined($strand) && $strand != 0 && $strand != -1 && $strand != 1) {
+    throw('strand must be 0, -1 or 1');
+  }
+
+  $self->[0] = $start;
+  $self->[1] = $end;
+  $self->[2] = $strand if(defined($strand));
+}
+
+
+
+=head2 feature_Slice
+
+  Args       : none
+  Example    : $slice = $feature->feature_Slice()
+  Description: Reimplementation of Bio::EnsEMBL::Feature method to enable
+               assembly mapping
+  Returntype : Bio::EnsEMBL::Slice or undef if this feature has no attached
+               Slice.
+  Exceptions : warning if Feature does not have attached slice.
+  Caller     : web drawing code
+  Status     : Stable
+
+=cut
+
+
+sub feature_Slice {
+  my ($self) = @_;
+
+  my $slice = $self->[7];
+
+  if(!$slice) {
+    warning('Cannot obtain Feature_Slice for feature without attached slice');
+    return undef;
+  }
+
+  return $slice->sub_Slice($self->[0], $self->[1]); 
+}
+
+
+
+1;
+