[Bioperl-guts-l] [14788] bioperl-live/trunk/Bio/Assembly: Used weak references (Scalar::Util ::weaken) in a circular reference to fix memory leak

[Florent E Angly]

Revision: 14788
Author:   fangly
Date:     2008-08-05 18:48:06 -0400 (Tue, 05 Aug 2008)

Log Message:
-----------
Used weak references (Scalar::Util::weaken) in a circular reference to fix memory leak

Modified Paths:
--------------
    bioperl-live/trunk/Bio/Assembly/Contig.pm
    bioperl-live/trunk/Bio/Assembly/Scaffold.pm

Modified: bioperl-live/trunk/Bio/Assembly/Contig.pm
===================================================================
--- bioperl-live/trunk/Bio/Assembly/Contig.pm	2008-08-05 22:07:49 UTC (rev 14787)
+++ bioperl-live/trunk/Bio/Assembly/Contig.pm	2008-08-05 22:48:06 UTC (rev 14788)
@@ -210,6 +210,8 @@
 use Bio::SeqFeature::Collection;
 use Bio::Seq::PrimaryQual;
 
+use Scalar::Util qw(weaken);
+
 use base qw(Bio::Root::Root Bio::Align::AlignI);
 
 =head1 Object creator
@@ -304,8 +306,11 @@
 
     $self->throw("Using non Bio::Assembly::Scaffold object when assign contig to assembly")
     if (defined $assembly && ! $assembly->isa("Bio::Assembly::Scaffold"));
+    # We create a circular reference to a Scaffold object. It is made weak
+    # to prevent memory leaks.
+    $self->{'_assembly'} = $assembly if (defined $assembly); 
+    weaken($self->{'_assembly'});
 
-    $self->{'_assembly'} = $assembly if (defined $assembly);
     return $self->{'_assembly'};
 }
 
@@ -2105,4 +2110,5 @@
     return scalar(@{$dbref});
 }
 
+
 1;

Modified: bioperl-live/trunk/Bio/Assembly/Scaffold.pm
===================================================================
--- bioperl-live/trunk/Bio/Assembly/Scaffold.pm	2008-08-05 22:07:49 UTC (rev 14787)
+++ bioperl-live/trunk/Bio/Assembly/Scaffold.pm	2008-08-05 22:48:06 UTC (rev 14788)
@@ -65,7 +65,6 @@
 package Bio::Assembly::Scaffold;
 
 use strict;
-
 use Bio::Annotation::Collection;
 
 use base qw(Bio::Root::Root Bio::Assembly::ScaffoldI);
@@ -398,7 +397,7 @@
     $self->warn("Replacing contig $contigID with a new contig object")
         if (exists $self->{'_contigs'}{$contigID});
     $self->{'_contigs'}{$contigID} = $contig;
-    $contig->assembly($self);
+    $contig->assembly($self); # weak circular reference
 
     # Put contig sequences in the list of sequences belonging to the scaffold
     foreach my $seqID ($contig->get_seq_ids()) {
@@ -443,7 +442,7 @@
     $self->warn("Replacing singlet $singletID with a new singlet object")
         if (exists $self->{'_singlets'}{$singletID});
     $self->{'_singlets'}{$singletID} = $singlet;
-    $singlet->assembly($self);
+    $singlet->assembly($self); # weak circular reference
 
     # Put singlet sequence in the list of sequences belonging to the scaffold
     my $seqID = $singlet->seqref()->id();
@@ -686,4 +685,5 @@
     return @singlets;
 }
 
+
 1;