Methods now return empty array ref instead of undef. Removed annoying warning.

modules/Bio/EnsEMBL/StrainSlice.pm

@@ -126,14 +126,14 @@ sub new{
 
             if (defined $individual){
                 my $allele_features = $af_adaptor->fetch_all_by_Slice($self,$individual);
-                warning("No strain genotype data available for Slice ".$self->name." and Strain ".$individual->name) if ! defined $allele_features->[0];
+                #warning("No strain genotype data available for Slice ".$self->name." and Strain ".$individual->name) if ! defined $allele_features->[0];
                 my $vf_ids = {}; #hash containing the relation vf_id->af
 		$self->{'_strain'} = $individual;		
 		map {defined $_->{'_variation_feature_id'} ? $vf_ids->{$_->{'_variation_feature_id'}} = $_ : ''
 } @{$allele_features};
 #		my $new_allele_features = $self->_filter_af_by_coverage($allele_features);
 #		$self->{'alleleFeatures'} = $new_allele_features;
-		$self->{'alleleFeatures'} = $allele_features;
+		$self->{'alleleFeatures'} = $allele_features || [];
 		$self->{'_vf_ids'} = $vf_ids;
 		return $self;
 	    }
@@ -391,10 +391,10 @@ sub get_all_AlleleFeatures_Slice{
     $with_coverage ||= 0; #by default, get all AlleleFeatures
     if ($with_coverage == 1){
 	my $new_allele_features = $self->_filter_af_by_coverage($self->{'alleleFeatures'});
-	return $new_allele_features;
+	return $new_allele_features || [];
     }
 
-    return $self->{'alleleFeatures'};
+    return $self->{'alleleFeatures'} || [];
 }
 
 =head2 get_all_differences_StrainSlice
@@ -797,131 +797,4 @@ sub remove_indels {
 	$self->{'alleleFeatures'} = \@new_afs;
 }
 
-
-=head2 _get_ReadCoverage
-
-	Args		: none
-	Example		: $ss->_get_ReadCoverage()
-	Description	: Internal method to add read coverage info to this strain slice
-	ReturnType	: none
-	Exceptions	: none
-	Caller		: Internal
-
-=cut
-
-sub _get_ReadCoverage {
-	my $self = shift;
-	
-	# check we have an adaptor
-	unless(defined $self->adaptor) {
-		warning('Cannot get Read Coverage info without attached adaptor');
-		return '';
-	}	
-	
-	# try and get a var DB connection
-	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 '';
-    }
-	
-	# try and get a RC adaptor
-	my $rc_adaptor = $variation_db->get_ReadCoverageAdaptor();
-	
-	unless($rc_adaptor) {
-		warning("Could not get ReadCoverageAdaptor");
-		return '';
-    }
-	
-	# try and get an individual adatpor
-	my $ind_adaptor = $variation_db->get_IndividualAdaptor;
-
-	unless($ind_adaptor){
-		warning("Could not get IndividualAdaptor");
-		return '';
-	}
-	
-	# get the individual object
-	my $ind = shift @{$ind_adaptor->fetch_all_by_name($self->{'strain_name'})};
-	
-	# get all read coverage units for this individual and slice
-	my @rcs = @{$rc_adaptor->fetch_all_by_Slice_Sample_depth($self, $ind)};
-	
-	# get indels
-	my @indels_ordered = sort {$b->start() <=> $a->start()} @{$self->{'alignIndels'}} if (defined $self->{'alignIndels'});
-	
-	# get length differences
-	my %length_changes;
-    foreach my $af (@indels_ordered) {
-		$length_changes{$af->start} = $af->length_diff;
-	}
-	
-	my @new_rcs;
-	
-	# change RC coordinates according to length diffs
-	foreach my $rc(@rcs) {
-		foreach my $pos(keys %length_changes) {
-			if($rc->start > $pos) {
-				$rc->start($rc->start + $length_changes{$pos});
-			}
-			
-			if($rc->end > $pos) {
-				$rc->end($rc->end + $length_changes{$pos});
-			}
-		}
-		
-		push @new_rcs, $rc;
-	}
-	
-	$self->{'_read_coverage'} = \@new_rcs;
-	
-	return $self->{'_read_coverage'};
-}
-
-
-=head2 masked_seq
-
-	Args		: none
-	Example		: my $seq = $ss->masked_seq()
-	Description	: Returns the sequence of this Strain Slice with "N"s in place
-				  of the sequence where there is no read coverage.
-	ReturnType	: none
-	Exceptions	: none
-	Caller		: General
-
-=cut
-
-sub masked_seq {
-	my $self = shift;
-	
-	# get the sequence of the strain
-	my $seq = $self->seq();
-	
-	# make an equivalent fully masked string
-	my $masked = "N" x length($seq);
-	
-	# make sure read coverage has been retrieved
-	if(!defined($self->{'_read_coverage'})) {
-		$self->_get_ReadCoverage();
-	}
-	
-	# iterate through read coverage units
-	foreach my $rc(@{$self->{'_read_coverage'}}) {
-		next unless $rc->level() >= 1;
-		
-		my ($start, $end) = ($rc->start, $rc->end);
-		
-		# adjust coords to within string bounds
-		$start = 1 if $start < 1;
-		$end = length($seq) if $end > length($seq);
-		
-		# unmask sequence over region of coverage
-		substr($masked, $start - 1, ($end - $start) + 1) = substr($seq, $start - 1, ($end - $start) + 1);
-	}
-	
-	return $masked;
-}
-
 1;