diff --git a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
index 65bb56a4f0baedf1b2cb1ca383610972050b6c78..c7a437e8e4e903d98978e4d200b93954223b3b2f 100644
--- a/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/ExonAdaptor.pm
@@ -515,7 +515,7 @@ sub list_stable_ids {
# Caller : internal
sub _objs_from_sth {
- my ($self, $sth, $mapper, $dest_slice) = @_;
+ my ( $self, $sth, $mapper, $dest_slice ) = @_;
#
# This code is ugly because an attempt has been made to remove as many
@@ -530,21 +530,17 @@ sub _objs_from_sth {
my %sr_name_hash;
my %sr_cs_hash;
- my (
- $exon_id, $seq_region_id, $seq_region_start,
- $seq_region_end, $seq_region_strand, $phase,
- $end_phase, $is_current, $is_constitutive,
- $stable_id, $version, $created_date,
- $modified_date
- );
+ my ( $exon_id, $seq_region_id, $seq_region_start,
+ $seq_region_end, $seq_region_strand, $phase,
+ $end_phase, $is_current, $is_constitutive,
+ $stable_id, $version, $created_date,
+ $modified_date );
- $sth->bind_columns(
- \$exon_id, \$seq_region_id, \$seq_region_start,
- \$seq_region_end, \$seq_region_strand, \$phase,
- \$end_phase, \$is_current, \$is_constitutive,
- \$stable_id, \$version, \$created_date,
- \$modified_date
- );
+ $sth->bind_columns( \( $exon_id, $seq_region_id, $seq_region_start,
+ $seq_region_end, $seq_region_strand, $phase,
+ $end_phase, $is_current, $is_constitutive,
+ $stable_id, $version, $created_date,
+ $modified_date ) );
my $asm_cs;
my $cmp_cs;
@@ -552,9 +548,10 @@ sub _objs_from_sth {
my $asm_cs_name;
my $cmp_cs_vers;
my $cmp_cs_name;
- if($mapper) {
- $asm_cs = $mapper->assembled_CoordSystem();
- $cmp_cs = $mapper->component_CoordSystem();
+
+ if ($mapper) {
+ $asm_cs = $mapper->assembled_CoordSystem();
+ $cmp_cs = $mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
@@ -569,38 +566,42 @@ sub _objs_from_sth {
my $dest_slice_sr_name;
my $dest_slice_sr_id;
my $asma;
- if($dest_slice) {
- $dest_slice_start = $dest_slice->start();
- $dest_slice_end = $dest_slice->end();
- $dest_slice_strand = $dest_slice->strand();
- $dest_slice_length = $dest_slice->length();
- $dest_slice_cs = $dest_slice->coord_system();
+
+ if ($dest_slice) {
+ $dest_slice_start = $dest_slice->start();
+ $dest_slice_end = $dest_slice->end();
+ $dest_slice_strand = $dest_slice->strand();
+ $dest_slice_length = $dest_slice->length();
+ $dest_slice_cs = $dest_slice->coord_system();
$dest_slice_sr_name = $dest_slice->seq_region_name();
- $dest_slice_sr_id = $dest_slice->get_seq_region_id();
- $asma = $self->db->get_AssemblyMapperAdaptor();
+ $dest_slice_sr_id = $dest_slice->get_seq_region_id();
+ $asma = $self->db->get_AssemblyMapperAdaptor();
}
- FEATURE: while($sth->fetch()) {
+FEATURE: while ( $sth->fetch() ) {
#need to get the internal_seq_region, if present
$seq_region_id = $self->get_seq_region_id_internal($seq_region_id);
- my $slice = $slice_hash{"ID:".$seq_region_id};
+ my $slice = $slice_hash{ "ID:" . $seq_region_id };
my $dest_mapper = $mapper;
- if(!$slice) {
+ if ( !$slice ) {
$slice = $sa->fetch_by_seq_region_id($seq_region_id);
- $slice_hash{"ID:".$seq_region_id} = $slice;
- $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
- $sr_cs_hash{$seq_region_id} = $slice->coord_system();
+ $slice_hash{ "ID:" . $seq_region_id } = $slice;
+ $sr_name_hash{$seq_region_id} = $slice->seq_region_name();
+ $sr_cs_hash{$seq_region_id} = $slice->coord_system();
}
#obtain a mapper if none was defined, but a dest_seq_region was
- if(!$dest_mapper && $dest_slice &&
- !$dest_slice_cs->equals($slice->coord_system)) {
- $dest_mapper = $asma->fetch_by_CoordSystems($dest_slice_cs,
- $slice->coord_system);
- $asm_cs = $dest_mapper->assembled_CoordSystem();
- $cmp_cs = $dest_mapper->component_CoordSystem();
+ if ( !$dest_mapper
+ && $dest_slice
+ && !$dest_slice_cs->equals( $slice->coord_system ) )
+ {
+ $dest_mapper =
+ $asma->fetch_by_CoordSystems( $dest_slice_cs,
+ $slice->coord_system );
+ $asm_cs = $dest_mapper->assembled_CoordSystem();
+ $cmp_cs = $dest_mapper->component_CoordSystem();
$asm_cs_name = $asm_cs->name();
$asm_cs_vers = $asm_cs->version();
$cmp_cs_name = $cmp_cs->name();
@@ -630,57 +631,126 @@ sub _objs_from_sth {
}
#
- # If a destination slice was provided convert the coords
- # If the dest_slice starts at 1 and is foward strand, nothing needs doing
+ # If a destination slice was provided convert the coords. If the
+ # dest_slice starts at 1 and is foward strand, nothing needs doing.
#
- if($dest_slice) {
- if($dest_slice_start != 1 || $dest_slice_strand != 1) {
- if($dest_slice_strand == 1) {
- $seq_region_start = $seq_region_start - $dest_slice_start + 1;
- $seq_region_end = $seq_region_end - $dest_slice_start + 1;
- } else {
- my $tmp_seq_region_start = $seq_region_start;
- $seq_region_start = $dest_slice_end - $seq_region_end + 1;
- $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
- $seq_region_strand *= -1;
- }
- }
-
- #throw away features off the end of the requested slice
- if($seq_region_end < 1 || $seq_region_start > $dest_slice_length ||
- ( $dest_slice_sr_id != $seq_region_id )) {
- next FEATURE;
+ if ( defined($dest_slice) ) {
+ if ( $dest_slice_strand == 1 ) {
+ # On the positive strand.
+
+ $seq_region_start = $seq_region_start - $dest_slice_start + 1;
+ $seq_region_end = $seq_region_end - $dest_slice_start + 1;
+
+ # Handle circular chromosomes.
+ if ( $dest_slice->is_circular() ) {
+ if ( $seq_region_start > $seq_region_end ) {
+ # Looking at a feature overlapping the chromsome origin.
+
+ if ( $seq_region_end > $dest_slice_start ) {
+ # Looking at the region in the beginning of the
+ # chromosome.
+ $seq_region_start -= $dest_slice->seq_region_length();
+ }
+
+ if ( $seq_region_end < 0 ) {
+ $seq_region_end += $dest_slice->seq_region_length();
+ }
+
+ } elsif ( $dest_slice_start > $dest_slice_end
+ && $seq_region_end < 0 )
+ {
+ # Looking at the region overlapping the chromosome
+ # origin and a feature which is at the beginning of the
+ # chromosome.
+ $seq_region_start += $dest_slice->seq_region_length();
+ $seq_region_end += $dest_slice->seq_region_length();
+ }
+ }
+
+ } else {
+ # On the negative strand.
+
+ # Handle circular chromosomes.
+ if ( $dest_slice->is_circular() ) {
+ if ( $seq_region_start > $seq_region_end ) {
+
+ if ( $dest_slice_start > $dest_slice_end ) {
+ my $tmp_seq_region_start = $seq_region_start;
+ $seq_region_start = $dest_slice_end - $seq_region_end + 1;
+ $seq_region_end =
+ $dest_slice_end +
+ $dest_slice->seq_region_length -
+ $tmp_seq_region_start + 1;
+ } else {
+
+ if ( $seq_region_end > $dest_slice_start ) {
+ # Looking at the region in the beginning of the
+ # chromosome.
+ $seq_region_start =
+ $dest_slice_end - $seq_region_end + 1;
+ $seq_region_end =
+ $seq_region_end -
+ $dest_slice->seq_region_length -
+ $dest_slice_start + 1;
+ } else {
+ my $tmp_seq_region_start = $seq_region_start;
+ $seq_region_start =
+ $dest_slice_end -
+ $seq_region_end -
+ $dest_slice->seq_region_length + 1;
+ $seq_region_end =
+ $dest_slice_end - $tmp_seq_region_start + 1;
+ }
+
+ }
+
+ } ## end if ( $seq_region_start...)
+ } else {
+ # Non-circular chromosome.
+ my $tmp_seq_region_start = $seq_region_start;
+ $seq_region_start = $dest_slice_end - $seq_region_end + 1;
+ $seq_region_end = $dest_slice_end - $tmp_seq_region_start + 1;
+ }
+
+ $seq_region_strand = -$seq_region_strand;
+
+ } ## end else [ if ( $dest_slice_strand...)]
+
+ # Throw away features off the end of the requested slice.
+ if ( $seq_region_end < 1
+ || $seq_region_start > $dest_slice_length
+ || ( $dest_slice_sr_id != $seq_region_id ) )
+ {
+ next FEATURE;
}
$slice = $dest_slice;
- }
+ } ## end if ( defined($dest_slice...))
# Finally, create the new exon.
- push(
- @exons,
- $self->_create_feature_fast(
- 'Bio::EnsEMBL::Exon',
- {
- 'start' => $seq_region_start,
- 'end' => $seq_region_end,
- 'strand' => $seq_region_strand,
- 'adaptor' => $self,
- 'slice' => $slice,
- 'dbID' => $exon_id,
- 'stable_id' => $stable_id,
- 'version' => $version,
- 'created_date' => $created_date || undef,
- 'modified_date' => $modified_date || undef,
- 'phase' => $phase,
- 'end_phase' => $end_phase,
- 'is_current' => $is_current,
- 'is_constitutive' => $is_constitutive
- } ) );
-
- }
+ push( @exons,
+ $self->_create_feature_fast(
+ 'Bio::EnsEMBL::Exon', {
+ 'start' => $seq_region_start,
+ 'end' => $seq_region_end,
+ 'strand' => $seq_region_strand,
+ 'adaptor' => $self,
+ 'slice' => $slice,
+ 'dbID' => $exon_id,
+ 'stable_id' => $stable_id,
+ 'version' => $version,
+ 'created_date' => $created_date || undef,
+ 'modified_date' => $modified_date || undef,
+ 'phase' => $phase,
+ 'end_phase' => $end_phase,
+ 'is_current' => $is_current,
+ 'is_constitutive' => $is_constitutive } )
+ );
+
+ } ## end while ( $sth->fetch() )
return \@exons;
-}
+} ## end sub _objs_from_sth
=head1 DEPRECATED METHODS