[Bioperl-guts-l] bioperl-live/Bio/DB/SeqFeature/Store berkeleydb.pm, 1.13, 1.14 memory.pm, 1.9, 1.10

Lincoln Stein lstein at dev.open-bio.org
Tue Jan 23 15:04:39 EST 2007


Update of /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store
In directory dev.open-bio.org:/tmp/cvs-serv25888/Bio/DB/SeqFeature/Store

Modified Files:
	berkeleydb.pm memory.pm 
Log Message:
use Bio::DB::SeqFeatureI methods rather than generic methods

Index: memory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/memory.pm,v
retrieving revision 1.9
retrieving revision 1.10
diff -C2 -d -r1.9 -r1.10
*** memory.pm	28 Sep 2006 15:42:48 -0000	1.9
--- memory.pm	23 Jan 2007 20:04:37 -0000	1.10
***************
*** 289,294 ****
    my ($obj,$id) = @_;
  
!   for my $tag ($obj->all_tags) {
!     for my $value ($obj->each_tag_value($tag)) {
        $self->{_index}{attribute}{lc $tag}{lc $value}{$id} = undef;
      }
--- 289,294 ----
    my ($obj,$id) = @_;
  
!   for my $tag ($obj->get_all_tags) {
!     for my $value ($obj->get_tag_values($tag)) {
        $self->{_index}{attribute}{lc $tag}{lc $value}{$id} = undef;
      }

Index: berkeleydb.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/DB/SeqFeature/Store/berkeleydb.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** berkeleydb.pm	22 Nov 2006 20:25:27 -0000	1.13
--- berkeleydb.pm	23 Jan 2007 20:04:37 -0000	1.14
***************
*** 579,584 ****
      or $self->throw("Couldn't find 'attributes' index file");
  
!   for my $tag ($obj->all_tags) {
!     for my $value ($obj->each_tag_value($tag)) {
        my $key = "\L${tag}:${value}\E";
        $self->update_or_delete($delete,$db,$key,$id);
--- 579,584 ----
      or $self->throw("Couldn't find 'attributes' index file");
  
!   for my $tag ($obj->get_all_tags) {
!     for my $value ($obj->get_tag_values($tag)) {
        my $key = "\L${tag}:${value}\E";
        $self->update_or_delete($delete,$db,$key,$id);



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