deleted for release/95

modules/Bio/EnsEMBL/IndividualSliceFactory.pm

-=head1 LICENSE
-
-Copyright [1999-2015] Wellcome Trust Sanger Institute and the EMBL-European Bioinformatics Institute
-Copyright [2016-2018] EMBL-European Bioinformatics Institute
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-     http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
-
-=cut
-
-
-=head1 CONTACT
-
-  Please email comments or questions to the public Ensembl
-  developers list at <http://lists.ensembl.org/mailman/listinfo/dev>.
-
-  Questions may also be sent to the Ensembl help desk at
-  <http://www.ensembl.org/Help/Contact>.
-
-=cut
-
-package Bio::EnsEMBL::IndividualSliceFactory;
-
-use strict;
-use Bio::EnsEMBL::Utils::Argument qw(rearrange);
-use Bio::EnsEMBL::Utils::Sequence qw(reverse_comp);
-use Bio::EnsEMBL::Slice;
-use Bio::EnsEMBL::Mapper;
-use Bio::EnsEMBL::Utils::Exception qw(throw deprecate warning);
-use Scalar::Util qw(weaken);
-
-=head2 new
-=cut
-
-sub new{
-    my $caller = shift;
-    deprecate("new is deprecated and will be removed in e95.");
-    my $class = ref($caller) || $caller;
-
-    #creates many IndividualSlice objects from the Population
-
-    my ($population_name, $coord_system, $start, $end, $strand, $seq_region_name, $seq_region_length, $adaptor) = rearrange(['POPULATION', 'COORD_SYSTEM','START','END','STRAND','SEQ_REGION_NAME','SEQ_REGION_LENGTH', 'ADAPTOR'],@_);
-
-    my $self = bless {
-	population_name => $population_name,
-	coord_system => $coord_system,
-	start => $start,
-	end => $end,
-	strand => $strand,
-	seq_region_name => $seq_region_name,
-	seq_region_length => $seq_region_length},$class;
-
-    $self->adaptor($adaptor);
-    return $self;
-}
-
-sub adaptor {
-  my $self = shift;
-  deprecate("adaptor is deprecated and will be removed in e95.");
-
-  if(@_) {
-    my $ad = shift;
-    if($ad && (!ref($ad) || !$ad->isa('Bio::EnsEMBL::DBSQL::BaseAdaptor'))) {
-      throw('Adaptor argument must be a Bio::EnsEMBL::DBSQL::BaseAdaptor');
-    }
-    weaken($self->{'adaptor'} = $ad);
-  }
-
-  return $self->{'adaptor'}
-}
-
-sub get_all_IndividualSlice{
-    my $self = shift;
-    deprecate("get_all_IndividualSlice is deprecated and will be removed in e95.");
-
-    my $slice;
-    if(!$self->adaptor) {
-	warning('Cannot get IndividualSlice features without attached adaptor');
-	return '';
-    }
-    my $variation_db = $self->adaptor->db->get_db_adaptor('variation');
-
-    unless($variation_db) {
-	warning("Variation database must be attached to core database to " .
-		"retrieve variation information" );
-	return '';
-    }
-    #get the AlleleFeatures in the Population
-    my $af_adaptor = $variation_db->get_AlleleFeatureAdaptor;
-    
-    if( $af_adaptor ) {
-	#set the adaptor to retrieve data from genotype table
-	$af_adaptor->from_IndividualSlice(1);
-	#get the Individual for the given strain
-	my $population_adaptor = $variation_db->get_PopulationAdaptor;
-	my $individual_adaptor = $variation_db->get_IndividualAdaptor;
-	if ($population_adaptor && $individual_adaptor){
-	    $slice = Bio::EnsEMBL::Slice->new(-coord_system => $self->{'coord_system'},
-					      -start => $self->{'start'},
-					      -end => $self->{'end'},
-					      -strand => $self->{'strand'},
-					      -seq_region_name => $self->{'seq_region_name'},
-					      -seq_region_length => $self->{'seq_region_length'},
-					      -adaptor => $self->adaptor
-					      );
-	    my $population = $population_adaptor->fetch_by_name($self->{'population_name'}); 
-	    #check that there is such population in the database
-	    if (defined $population){
-		#get all the AlleleFeatures in the $population and the Slice given
-		my $allele_features = $af_adaptor->fetch_all_by_Slice($slice,$population);
-		#get Individuals in the Population
-		my $individuals = $individual_adaptor->fetch_all_by_Population($population);		
-		return $self->_rearrange_Individuals_Alleles($individuals,$allele_features);
-	    }
-	    else{ 
-		warning("Population not in the database");
-		return '';
- 
-	    }
-	}
-	else{
-	    warning("Not possible to retrieve PopulationAdaptor from the variation database");
-	    return '';
-	}	
-    }
-    
-    else{
-	warning("Not possible to retrieve AlleleFeatureAdaptor from variation database");
-	return '';
-    }
-}
-
-sub _rearrange_Individuals_Alleles{
-    my $self = shift;
-    deprecate("_rearrange_Individuals_Alleles is deprecated and will be removed in e95.");
-
-    my $individuals = shift;
-    my $allele_features;
-    my $individual_slice;
-    #create the hash with all the individuals
-    my %individuals_ids;
-    #foreach of the individual, create the IndividualSlice object and add it to the mapping hash
-    foreach my $individual (@{$individuals}){
-	$individual_slice = Bio::EnsEMBL::Variation::IndividualSlice->new(
-	    -coord_system => $self->{'coord_system'},
-	    -start => $self->{'$start'},
-	    -end  => $self->{'end'},
-	    -strand => $self->{'strand'},
-	    -seq_region_name => $self->{'seq_region_name'},
-	    -seq_region_length => $self->{'seq_region_length'},
-	    -individual => $individual->name);
-	
-	$individuals_ids{$individual->dbID} = $individual_slice;
-    }
-
-    #and rearrange all the AlleleFeatures to the individuals
-    foreach my $allele_feature (@{$allele_features}){
-	$individuals_ids{$allele_feature->{'_sample_id'}}->add_AlleleFeature($allele_feature);
-    }
-    my @result = values %individuals_ids;
-    return \@result;
-}
-
-
-1;