Commit 8a69b198 authored by Graham McVicker's avatar Graham McVicker
Browse files

Removed Exon::contig and BaseAlignFeature::contig methods.

These were causing infinite recursion due to new superclass implementation of entire_seq, attach_seq, and contig methods
parent 2b27c8ea
......@@ -277,34 +277,6 @@ sub adaptor {
}
=head2 contig
Arg [1] : Bio::EnsEMBL::Slice or
Bio::EnsEMBL::RawContig $contig
Example : none
Description: The sequnence where the coordinates make sense. Channeled to
attach_seq/entire_seq from BioPerl
Returntype : Slice/RawContig
Exceptions : none
Caller : general
=cut
sub contig {
my $self = shift;
if( @_ ) {
my $value = shift;
#print "setting exons contig to ".$value." \n";
$self->attach_seq($value);
}
else {
return $self->entire_seq();
}
}
=head2 _parse_cigar
Args : none
......
......@@ -222,33 +222,6 @@ sub adaptor {
}
=head2 contig
Arg [1] : Bio::EnsEMBL::RawContig/Slice $contig
Example : none
Description: get/set for attribute contig. Is channeled to the bioperl
comliant entire_seq/attach_seq calls.
Returntype : Bio::EnsEMBL::RawContig/Slice
Exceptions : none
Caller : general
=cut
sub contig {
my $self = shift;
my $seq = shift;
if( $seq ) {
$self->attach_seq($seq);
}
return $self->entire_seq();
}
=head2 transform
Arg 1 : Bio::EnsEMBL::Slice $slice
......
......@@ -293,14 +293,20 @@ sub frame {
=cut
sub primary_tag{
my ($self,$arg) = @_;
my ($self,$arg) = @_;
if (defined($arg)) {
# throw warnings about setting primary tag
my ($p,$f,$l) = caller;
$self->warn("$f:$l setting primary_tag now deprecated." .
"Primary tag is delegated to analysis object");
}
if (defined($arg)) {
# throw warnings about setting primary tag
my ($p,$f,$l) = caller;
$self->warn("$f:$l setting primary_tag now deprecated. Primary tag is delegated to analysis object");
}
return $self->analysis->gff_feature();
unless($self->analysis) {
return '';
}
return $self->analysis->gff_feature();
}
=head2 source_tag
......@@ -322,7 +328,12 @@ sub source_tag{
if (defined($arg)) {
# throw warnings about setting primary tag
my ($p,$f,$l) = caller;
$self->warn("$f:$l setting source_tag now deprecated. Source tag is delegated to analysis object");
$self->warn("$f:$l setting source_tag now deprecated. " .
"Source tag is delegated to analysis object");
}
unless($self->analysis) {
return "";
}
return $self->analysis->gff_source();
......
......@@ -345,7 +345,7 @@ sub get_all_RepeatFeatures{
sub get_all_Genes{
my ($self, $empty_flag) = @_;
#caching is performed on a per slice basis in the GeneAdaptor
my $gene_adaptor = $self->adaptor->db->get_GeneAdaptor();
return $gene_adaptor->fetch_by_Slice($self, $empty_flag);
......
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