[Bioperl-guts-l] [14801] bioperl-live/trunk/Bio/DB/SeqFeature: made -gff an alias for -dsn in Bio::DB::Seqfeature::Store:: memory adaptor new() call, since people are having trouble adapting to shift between Bio::DB:: GFF and Bio::Db::SeqFeature::Store

[Lincoln Stein]

Revision: 14801
Author:   lstein
Date:     2008-08-14 11:23:24 -0400 (Thu, 14 Aug 2008)

Log Message:
-----------
made -gff an alias for -dsn in Bio::DB::Seqfeature::Store::memory adaptor new() call, since people are having trouble adapting to shift between Bio::DB::GFF and Bio::Db::SeqFeature::Store

Modified Paths:
--------------
    bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm
    bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm

Modified: bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm
===================================================================
--- bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm	2008-08-14 08:14:57 UTC (rev 14800)
+++ bioperl-live/trunk/Bio/DB/SeqFeature/Store/memory.pm	2008-08-14 15:23:24 UTC (rev 14801)
@@ -109,6 +109,9 @@
   $db  = Bio::DB::SeqFeature::Store->new( -adaptor => 'memory',
                                           -dsn     => '/usr/annotations/worm.gff3.gz');
 
+For compatibility with the Bio::DB::GFF memory adapter, -gff is
+recognized as an alias for -dsn.
+
 See L<Bio::DB::SeqFeature::Store> for all the access methods supported
 by this adaptor. The various methods for storing and updating features
 and sequences into the database are supported, including GFF3 loading
@@ -143,7 +146,7 @@
 
 sub post_init {
   my $self = shift;
-  my ($file_or_dir) = rearrange([['DIR','DSN','FILE']], at _);
+  my ($file_or_dir) = rearrange([['DIR','DSN','FILE','GFF']], at _);
   return unless $file_or_dir;
 
   my $loader = Bio::DB::SeqFeature::Store::GFF3Loader->new(-store    => $self,

Modified: bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm
===================================================================
--- bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm	2008-08-14 08:14:57 UTC (rev 14800)
+++ bioperl-live/trunk/Bio/DB/SeqFeature/Store.pm	2008-08-14 15:23:24 UTC (rev 14801)
@@ -259,7 +259,7 @@
  -serializer        The name of the serializer class (default Storable)
 
  -index_subfeatures Whether or not to make subfeatures searchable
-                    (default true)
+                    (default false)
 
  -cache             Activate LRU caching feature -- size of cache