Updated trunk to 0.5.1

git-svn-id: https://jcvi-tools.svn.sourceforge.net/svnroot/jcvi-tools/JCVI-Translator/trunk@16 a16988d2-67c9-4db9-a897-0603be59747b

Changes

@@ -1,5 +1,10 @@
 Revision history for JCVI-Translator
 
+0.5.1   Apr 13 2009
+ - Better documentation in Utils
+ - Fixed bugs in JCVI::Translator::Utils::regex and find
+ - Fixed load test and added new tests
+
 0.5.0   Apr 2 2009
  - Split out the table into its own package
  - Split out helper translator functions into their own package

lib/JCVI/Translator.pm

@@ -67,7 +67,7 @@ use strict;
 use warnings;
 
 use version;
-our $VERSION = qv('0.5.0');
+our $VERSION = qv('0.5.1');
 
 use base qw(Class::Accessor::Fast);
 __PACKAGE__->mk_accessors(qw(table base));
@@ -618,14 +618,12 @@ sub translate_codon {
     my %p = validate(
         @p,
         {
-
             # Make sure strand is 1 or -1
             strand => {
                 default => 1,
                 regex   => qr/^[+-]?1$/,
                 type    => Params::Validate::SCALAR
             },
-
             # Make sure it is a boolean value
             start => {
                 default => 0,
@@ -636,8 +634,11 @@ sub translate_codon {
     );
 
     $codon = uc $codon;
-    my $rc = $p{strand} == 1 ? 0 : 1;
 
+    # Set up the translation table given the strand and whether this is
+    # searching for stop codons. Set up the not_found string by whether this
+    # is a start or not.
+    my $rc = $p{strand} == 1 ? 0 : 1;
     my ( $table, $not_found );
     unless ( $p{start} ) {
         $table     = $self->table->_forward->[$rc];