bump alpha to test ODBA-related bug fix

svn path=/bioperl-live/branches/branch-1-6/; revision=16191
bioperl · Sep 28, 2009 · 744beb7 · 744beb7
1 parent 2834e5b
commit 744beb7
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Showing 5 changed files with 20 additions and 6 deletions.
diff --git a/Bio/DB/Flat/BDB/fasta.pm b/Bio/DB/Flat/BDB/fasta.pm
@@ -81,5 +81,19 @@ sub seq_to_ids {
   \%ids;
 }
 
+sub parse_one_record {
+    my $self  = shift;
+    my $fh    = shift;
+
+    # fasta parses by changing $/ to '\n>', need to adjust accordingly
+    my $adj = ( $^O =~ /mswin/i ) ? -2 : -1; 
+    my $parser =
+      $self->{cached_parsers}{fileno($fh)}
+        ||= Bio::SeqIO->new(-fh=>$fh,-format=>$self->default_file_format);
+    my $seq = $parser->next_seq or return;
+    $self->{flat_alphabet} ||= $seq->alphabet;
+    my $ids = $self->seq_to_ids($seq);
+    return ($ids, $adj);
+}
 
 1;
diff --git a/Bio/Root/Build.pm b/Bio/Root/Build.pm
@@ -85,7 +85,7 @@ BEGIN {
 use strict;
 use warnings;
 
-our $VERSION = '1.006000_005';
+our $VERSION = '1.006000_006';
 our @extra_types = qw(options excludes_os feature_requires test); # test must always be last in the list!
 our $checking_types = "requires|conflicts|".join("|", @extra_types);
 

diff --git a/Bio/Root/Version.pm b/Bio/Root/Version.pm
@@ -98,7 +98,7 @@ methods. Internal methods are usually preceded with a _
 package Bio::Root::Version;
 use strict;
 
-our $VERSION = '1.006000_005';
+our $VERSION = '1.006000_006';
 $VERSION = eval $VERSION;
 
 sub import {

diff --git a/t/LocalDB/Index.t b/t/LocalDB/Index.t
@@ -95,7 +95,7 @@ is ($seq->display_id(), 'ROA1_HUMAN');
 
 # test id_parser
 $ind = Bio::Index::Swissprot->new(-filename   => 'Wibbl4',
-											 -write_flag => 1);
+								-write_flag => 1);
 $ind->id_parser(\&get_id);
 $ind->make_index(test_input_file('roa1.swiss'));
 ok ( -e "Wibbl4" || -e "Wibbl4.pag" );

diff --git a/t/LocalDB/Registry.t b/t/LocalDB/Registry.t
@@ -31,7 +31,7 @@ SKIP: {
 	is $entries, 7;
 
 	SKIP: {
-		test_skip(-tests => 2, -requires_modules => [qw(DB_File BerkeleyDB)]);
+		test_skip(-tests => 2, -requires_modules => [qw(DB_File)]);
 
 		my $bdb = Bio::DB::Flat->new(-directory  => $tmpdir,
 					 -dbname     => 'testbdb',
@@ -45,7 +45,7 @@ SKIP: {
 
 	SKIP: {
 		test_skip(-tests => 9,
-                  -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common BerkeleyDB)],
+                  -requires_modules => [qw(LWP::UserAgent HTTP::Request::Common)],
                   -requires_networking => 1);
 
 		my $registry = Bio::DB::Registry->new();
@@ -61,7 +61,7 @@ SKIP: {
 		is $sequence, "MAHARVLLLALAVLATAAVAVASSSSFADSNPIRPVTDRAASTLESAVLGALGRTRHALRFARFAVRYGKSYESAAEVRRRFRIFSESLEEVRSTNRKGLPYRLGINRFSDMSWEEFQATRLGAAQTCSATLAGNHLMRDAAALPETKDWREDGIVSPVKNQAHCGSCWTFSTTGALEAAYTQATGKNISLSEQQLVDCAGGFNNFGCNGGLPSQAFEYIKYNGGIDTEESYPYKGVNGVCHYKAENAAVQVLDSVNITLNAEDELKNAVGLVRPVSVAFQVIDGFRQYKSGVYTSDHCGTTPDDVNHAVLAVGYGVENGVPYWLIKNSWGADWGDNGYFKMEMGKNMCAIATCASYPVVAA";
 
 		SKIP: {
-			test_skip(-tests => 4, -requires_modules => [qw(DB_File BerkeleyDB)]);
+			test_skip(-tests => 4, -requires_modules => [qw(DB_File)]);
 
 			ok grep /testbdb/,@available_services;
 			$db = $registry->get_database('testbdb');