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Commit 1d5ee781 authored by Daniel Rios's avatar Daniel Rios
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modified to use new_fast method in the constructor for speed purposes

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modules/Bio/EnsEMBL/DBSQL/SliceAdaptor.pm
+ 50
− 48
View file @ 1d5ee781
......@@ -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") );
......
modules/Bio/EnsEMBL/Slice.pm
+ 18
− 2
View file @ 1d5ee781
......@@ -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,
......
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