diff --git a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
index 9589bd22323f9c6165a89f4c2cda491ea7f2e4ca..8b3a5d474e50f51923e01d04d6a7d6f2ab95e42d 100644
--- a/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+++ b/modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
@@ -389,13 +389,14 @@ sub fetch_by_region {
}
return
- Bio::EnsEMBL::Slice->new( -COORD_SYSTEM => $cs,
- -SEQ_REGION_NAME => $seq_region_name,
- -SEQ_REGION_LENGTH => $length,
- -START => $start,
- -END => $end,
- -STRAND => $strand,
- -ADAPTOR => $self );
+ Bio::EnsEMBL::Slice->new_fast({
+ 'coord_system' => $cs,
+ 'seq_region_name' => $seq_region_name,
+ 'seq_region_length' => $length,
+ 'start' => $start,
+ 'end' => $end,
+ 'strand' => $strand,
+ 'adaptor' => $self} );
} ## end sub fetch_by_region
@@ -506,13 +507,14 @@ sub fetch_by_seq_region_id {
}
return
- Bio::EnsEMBL::Slice->new( -COORD_SYSTEM => $cs,
- -SEQ_REGION_NAME => $name,
- -SEQ_REGION_LENGTH => $length,
- -START => $start || 1,
- -END => $end || $length,
- -STRAND => $strand || 1,
- -ADAPTOR => $self );
+ Bio::EnsEMBL::Slice->new_fast({
+ 'coord_system' => $cs,
+ 'seq_region_name' => $name,
+ 'seq_region_length'=> $length,
+ 'start' => $start || 1,
+ 'end' => $end || $length,
+ 'strand' => $strand || 1,
+ 'adaptor' => $self} );
} ## end sub fetch_by_seq_region_id
@@ -732,14 +734,14 @@ sub fetch_all {
$cache_count++;
}
- my $slice = Bio::EnsEMBL::Slice->new
- (-START => 1,
- -END => $length,
- -STRAND => 1,
- -SEQ_REGION_NAME => $name,
- -SEQ_REGION_LENGTH => $length,
- -COORD_SYSTEM => $cs,
- -ADAPTOR => $self);
+ my $slice = Bio::EnsEMBL::Slice->new_fast({
+ 'start' => 1,
+ 'end' => $length,
+ 'strand' => 1,
+ 'seq_region_name' => $name,
+ 'seq_region_length'=> $length,
+ 'coord_system' => $cs,
+ 'adaptor' => $self});
if(!defined($include_duplicates) or !$include_duplicates){
# test if this slice *could* have a duplicate (exception) region
@@ -1085,14 +1087,14 @@ sub fetch_by_Feature{
$size = int( ($1-100)/200 * ($fend-$fstart+1) ) if( $size =~/([\d+\.]+)%/ );
#return a new slice covering the region of the feature
- my $S = Bio::EnsEMBL::Slice->new
- (-seq_region_name => $slice->seq_region_name,
- -seq_region_length => $slice->seq_region_length,
- -coord_system => $slice->coord_system,
- -start => $fstart - $size,
- -end => $fend + $size,
- -strand => 1,
- -adaptor => $self);
+ my $S = Bio::EnsEMBL::Slice->new_fast({
+ 'seq_region_name' => $slice->seq_region_name,
+ 'seq_region_length' => $slice->seq_region_length,
+ 'coord_system' => $slice->coord_system,
+ 'start' => $fstart - $size,
+ 'end' => $fend + $size,
+ 'strand' => 1,
+ 'adaptor' => $self});
$S->{'_raw_feature_strand'} = $feature->strand * $slice_strand if $feature->can('strand');
return $S;
}
@@ -1258,28 +1260,28 @@ sub fetch_normalized_slice_projection {
my @out;
for my $coord ( @linked ) {
if( $coord->isa( "Bio::EnsEMBL::Mapper::Gap" )) {
- my $exc_slice = Bio::EnsEMBL::Slice->new
- (-START => $coord->start(),
- -END => $coord->end(),
- -STRAND => $slice->strand(),
- -COORD_SYSTEM => $slice->coord_system(),
- -ADAPTOR => $self,
- -SEQ_REGION_NAME => $slice->seq_region_name(),
- -SEQ_REGION_LENGTH => $slice->seq_region_length());
+ my $exc_slice = Bio::EnsEMBL::Slice->new_fast({
+ 'start' => $coord->start(),
+ 'end' => $coord->end(),
+ 'strand' => $slice->strand(),
+ 'coord_system' => $slice->coord_system(),
+ 'adaptor' => $self,
+ 'seq_region_name' => $slice->seq_region_name(),
+ 'seq_region_length' => $slice->seq_region_length()});
push( @out, bless ( [ $rel_start, $coord->length()+$rel_start-1,
$exc_slice ], "Bio::EnsEMBL::ProjectionSegment") );
} else {
my $exc_slice = $self->fetch_by_seq_region_id( $coord->id() );
- my $exc2_slice = Bio::EnsEMBL::Slice->new
- (
- -START => $coord->start(),
- -END => $coord->end(),
- -STRAND => $coord->strand(),
- -SEQ_REGION_NAME => $exc_slice->seq_region_name(),
- -SEQ_REGION_LENGTH => $exc_slice->seq_region_length(),
- -COORD_SYSTEM => $exc_slice->coord_system(),
- -ADAPTOR => $self
- );
+ my $exc2_slice = Bio::EnsEMBL::Slice->new_fast({
+
+ 'start' => $coord->start(),
+ 'end' => $coord->end(),
+ 'strand' => $coord->strand(),
+ 'seq_region_name' => $exc_slice->seq_region_name(),
+ 'seq_region_length' => $exc_slice->seq_region_length(),
+ 'coord_system' => $exc_slice->coord_system(),
+ 'adaptor' => $self
+ });
push( @out, bless( [ $rel_start, $coord->length() + $rel_start - 1,
$exc2_slice ], "Bio::EnsEMBL::ProjectionSegment") );
diff --git a/modules/Bio/EnsEMBL/Slice.pm b/modules/Bio/EnsEMBL/Slice.pm
index 6605cfa257a0bcb8a26634d775a098f3f42c4682..8659500266ccb06ae4536e79bb3d4b7270a08ef3 100644
--- a/modules/Bio/EnsEMBL/Slice.pm
+++ b/modules/Bio/EnsEMBL/Slice.pm
@@ -194,6 +194,23 @@ sub new {
'adaptor' => $adaptor}, $class;
}
+=head2 new_fast
+
+ Arg [1] : hashref to be blessed
+ Description: Construct a new Bio::EnsEMBL::Slice using the hashref.
+ Exceptions : none
+ Returntype : Bio::EnsEMBL::Slice
+ Caller : general
+ Status : Stable
+
+=cut
+
+
+sub new_fast {
+ my $class = shift;
+ my $hashref = shift;
+ return bless $hashref, $class;
+}
=head2 adaptor
@@ -782,8 +799,7 @@ sub project {
# trim off regions which are not defined
return $self->_constrain_to_region();
}
-
- #create slices for the mapped-to coord system
+ #create slices for the mapped-to coord system
my $slice = $slice_adaptor->fetch_by_seq_region_id(
$coord->id(),
$coord_start,