From d6a5411e5dc2b99ecca4d4b73a2a422377fce30a Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Andreas=20Kusalananda=20K=C3=A4h=C3=A4ri?=
<ak4@sanger.ac.uk>
Date: Mon, 7 Jan 2008 11:07:02 +0000
Subject: [PATCH] Make the current slice a class variable rather than an object
attribute. Also store the projection segments and the mapping from
seq_region_ids to the projection segments in the class.
---
modules/Bio/EnsEMBL/Collection.pm | 86 +++++++++++++++++++------------
1 file changed, 53 insertions(+), 33 deletions(-)
diff --git a/modules/Bio/EnsEMBL/Collection.pm b/modules/Bio/EnsEMBL/Collection.pm
index 4d66b48c1f..61ed4a8c6c 100644
--- a/modules/Bio/EnsEMBL/Collection.pm
+++ b/modules/Bio/EnsEMBL/Collection.pm
@@ -206,6 +206,8 @@ use Bio::EnsEMBL::Utils::Exception qw( throw );
use base qw( Bio::EnsEMBL::DBSQL::BaseAdaptor );
+# Here are some class constants and class variables.
+
# Symbolic constants that acts as indices into the individual feature
# collection entries. These must be in sync with the columns returned
# by the _columns() method.
@@ -215,6 +217,18 @@ use constant { ENTRY_DBID => 0,
ENTRY_SEQREGIONEND => 3,
ENTRY_SEQREGIONSTRAND => 4 };
+# We'll keep the current slice and the projection segments of all slices
+# on the various coordinate systems as class variables rather than
+# as object attributes. This way, the Ensembl drawing code can have
+# several collection objects attached to one web view (e.g. one per
+# track in ContigView), all sharing the same projection segments. These
+# structures may be emptied using the flush() method (TODO: implement
+# the flush() method).
+
+our $SLICE;
+our %SEGMENTS;
+our %SEQ_REG_MAP;
+
=head1 METHODS (constructor)
=head2 new
@@ -261,9 +275,9 @@ sub new {
SELECT cs.name, mc.max_length, m.meta_value
FROM coord_system cs,
meta_coord mc
- LEFT JOIN meta m ON m.meta_key = ?
- WHERE mc.table_name = ?
- AND mc.coord_system_id = cs.coord_system_id
+ LEFT JOIN meta m ON m.meta_key = ?
+ WHERE mc.table_name = ?
+ AND mc.coord_system_id = cs.coord_system_id
);
my $sth = $this->prepare($sql);
@@ -323,17 +337,21 @@ sub slice {
my ( $this, $slice ) = @_;
if ( defined($slice) ) {
- my %seqreg_map;
- my @all_segments;
+ my $slice_name = $slice->name();
foreach
my $cs_name ( keys( %{ $this->__attrib('coordinate_systems') } ) )
{
+ if ( exists( $SEGMENTS{$slice_name}{$cs_name} ) ) { next }
+
my @segments = @{ $slice->project($cs_name) };
foreach my $segment (@segments) {
- $seqreg_map{ $segment->to_Slice()->get_seq_region_id() } =
- $segment;
+ # This is a simple map between seq_region_id and a
+ # ProjectionSegment, used in the mapping done by the
+ # _objs_from_sth() method.
+ $SEQ_REG_MAP{$slice_name}
+ { $segment->to_Slice()->get_seq_region_id() } = $segment;
}
@segments = ( undef, [@segments] );
@@ -348,26 +366,21 @@ sub slice {
pop(@segments);
}
- push( @all_segments, @segments );
- }
-
- # The 'segments' list is a list of ProjectionSegment objects and of
- # arrays of ProjectionSegment objects. For segments in arrays, no
- # constraint on seq_region_start or seq_region_end is needed.
- $this->__attrib( 'segments', \@all_segments );
+ # This list is a list of ProjectionSegment objects and of arrays
+ # of ProjectionSegment objects. For segments in arrays, no
+ # constraint on seq_region_start or seq_region_end is needed.
+ $SEGMENTS{$slice_name}{$cs_name} = \@segments;
- # This is a simple map between seq_region_id and a
- # ProjectionSegment, used in the mapping done by the
- # _objs_from_sth() method.
- $this->__attrib( 'seqreg_map', \%seqreg_map );
+ } ## end foreach my $cs_name ( keys(...
$this->entries( [] );
$this->__attrib( 'is_populated', 0 );
- $this->__attrib( 'slice', $slice );
+ $SLICE = $slice;
+
} ## end if ( defined($slice) )
- return $this->__attrib('slice');
+ return $SLICE;
} ## end sub slice
=head2 entries
@@ -473,14 +486,20 @@ sub populate {
my @entries;
- foreach my $segment ( @{ $this->__attrib('segments') } ) {
- if ( defined($segment)
- && ( ref($segment) ne 'ARRAY'
- || scalar( @{$segment} ) > 0 ) )
- {
- push( @entries,
- @{ $this->generic_fetch( $this->__constraint($segment) ) }
- );
+ my $slice_name = $this->slice()->name();
+
+ foreach
+ my $cs_name ( keys( %{ $this->__attrib('coordinate_systems') } ) )
+ {
+ foreach my $segment ( @{ $SEGMENTS{$slice_name}{$cs_name} } ) {
+ if ( defined($segment)
+ && ( ref($segment) ne 'ARRAY'
+ || scalar( @{$segment} ) > 0 ) )
+ {
+ push( @entries,
+ @{$this->generic_fetch( $this->__constraint($segment) ) }
+ );
+ }
}
}
@@ -1034,21 +1053,22 @@ sub _default_where_clause {
sub _objs_from_sth {
my ( $this, $sth ) = @_;
- my $seqreg_map = $this->__attrib('seqreg_map');
-
my @features;
my ( $segment, $segment_slice, $segment_slice_start,
$segment_slice_strand, $segment_offset );
+ my $slice_name = $this->slice()->name();
my $slice_start = $this->slice()->start();
while ( my $entry = $sth->fetchrow_arrayref() ) {
if ( !defined($segment)
- || $segment != $seqreg_map->{ $entry->[ENTRY_SEQREGIONID] } )
+ || $segment !=
+ $SEQ_REG_MAP{$slice_name}{ $entry->[ENTRY_SEQREGIONID] } )
{
- $segment = $seqreg_map->{ $entry->[ENTRY_SEQREGIONID] };
- $segment_slice = $segment->to_Slice();
+ $segment =
+ $SEQ_REG_MAP{$slice_name}{ $entry->[ENTRY_SEQREGIONID] };
+ $segment_slice = $segment->to_Slice();
$segment_slice_start = $segment_slice->start();
$segment_slice_strand = $segment_slice->strand();
--
GitLab