remove Tiny

.includepath

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <includepath>
   <includepathentry path="lib" />
-  <includepathentry path="${workspace_loc}/Bio-Tiny-Util-AA/lib" />
-  <includepathentry path="${workspace_loc}/Bio-Tiny-Util-DNA/lib" />
+  <includepathentry path="${workspace_loc}/Bio-Util-AA/lib" />
+  <includepathentry path="${workspace_loc}/Bio-Util-DNA/lib" />
 </includepath>
 

.project

@@ -1,10 +1,10 @@
 <?xml version="1.0" encoding="UTF-8"?>
 <projectDescription>
-	<name>Bio-Tiny-Translator</name>
+	<name>Bio-Translator</name>
 	<comment></comment>
 	<projects>
-		<project>Bio-Tiny-Util-AA</project>
-		<project>Bio-Tiny-Util-DNA</project>
+		<project>Bio-Util-AA</project>
+		<project>Bio-Util-DNA</project>
 	</projects>
 	<buildSpec>
 		<buildCommand>

Build.PL

@@ -3,18 +3,18 @@ use warnings;
 use Module::Build;
 
 my $builder = Module::Build->new(
-    module_name         => 'Bio::Tiny::Translator',
+    module_name         => 'Bio::Translator',
     license             => 'perl',
     dist_author         => 'Kevin Galinsky <kgalinsky plus cpan at gmail dot com>',
-    dist_version_from   => 'lib/Bio/Tiny/Translator.pm',
+    dist_version_from   => 'lib/Bio/Translator.pm',
     build_requires => {
         'Test::More' => 0,
     },
     requires => {
-        'Bio::Tiny::Util::AA' => '>= 0.1.0',
-        'Bio::Tiny::Util::DNA' => '>= 0.2.0'
+        'Bio::Util::AA' => '>= 0.1.0',
+        'Bio::Util::DNA' => '>= 0.2.0'
     },
-    add_to_cleanup      => [ 'Bio-Tiny-Translator-*' ],
+    add_to_cleanup      => [ 'Bio-Translator-*' ],
     create_makefile_pl => 'traditional',
 );
 

Changes

@@ -1,4 +1,4 @@
-Revision history for Bio::Tiny::Translator
+Revision history for Bio::Translator
 
 0.5.7   May 10 2011
   - Changed namespace
@@ -28,7 +28,7 @@ Revision history for Bio::Tiny::Translator
 
 0.5.1   Apr 13 2009
   - Better documentation in Utils
-  - Fixed bugs in Bio::Tiny::Translator::Utils::regex and find
+  - Fixed bugs in Bio::Translator::Utils::regex and find
   - Fixed load test and added new tests
 
 0.5.0   Apr 2 2009

MANIFEST.SKIP

@@ -70,7 +70,7 @@
 ^MANIFEST\.SKIP
 
 # Avoid archives of this distribution
-\bBio-Tiny-Translator-[\d\.\_]+
+\bBio-Translator-[\d\.\_]+
 
 # Avoid tests that aren't useful for end-user
 ^t/kwalitee

README

@@ -1,4 +1,4 @@
-Bio::Tiny::Translator tries to be a robust translator object featuring translation
+Bio::Translator tries to be a robust translator object featuring translation
 tables based off the the ones provided by NCBI
 (http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi).
 Key features include the ability to handle degenerate nucleotides and to
@@ -18,21 +18,21 @@ SUPPORT AND DOCUMENTATION
 
 After installing, you can find documentation for this module with the perldoc command.
 
-    perldoc Bio::Tiny::Translator
+    perldoc Bio::Translator
 
 You can also look for information at:
 
     Search CPAN
-        http://search.cpan.org/dist/Bio-Tiny-Translator
+        http://search.cpan.org/dist/Bio-Translator
 
     CPAN Request Tracker:
-        http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Tiny-Translator
+        http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Translator
 
     AnnoCPAN, annotated CPAN documentation:
-        http://annocpan.org/dist/Bio-Tiny-Translator
+        http://annocpan.org/dist/Bio-Translator
 
     CPAN Ratings:
-        http://cpanratings.perl.org/d/Bio-Tiny-Translator
+        http://cpanratings.perl.org/d/Bio-Translator
 
 COPYRIGHT AND LICENCE
 

bin/translate_fasta.pl

@@ -8,11 +8,11 @@
 use strict;
 #use warnings;
 
-use Bio::Tiny::Translator;
+use Bio::Translator;
 use Getopt::Euclid ':vars';
 
 # Instantiate the translator
-my $t = Bio::Tiny::Translator->new($ARGV_translation_table);
+my $t = Bio::Translator->new($ARGV_translation_table);
 
 # Build the list of file handles or standard input
 

lib/Bio/Translator.pm

@@ -1,4 +1,4 @@
-package Bio::Tiny::Translator;
+package Bio::Translator;
 
 use strict;
 use warnings;
@@ -7,35 +7,35 @@ use version; our $VERSION = qv('0.6.0');
 
 =head1 NAME
 
-Bio::Tiny::Translator - Translate DNA sequences
+Bio::Translator - Translate DNA sequences
 
 =head1 SYNOPSIS
 
-    use Bio::Tiny::Translator;
+    use Bio::Translator;
 
-    my $translator = new Bio::Tiny::Translator();
-    my $translator = new Bio::Tiny::Translator(11);
-    my $translator = new Bio::Tiny::Translator( 12, 'id' );
-    my $translator = new Bio::Tiny::Translator( 'Yeast Mitochondrial', 'name' );
-    my $translator = new Bio::Tiny::Translator( 'mito', 'name' );
+    my $translator = new Bio::Translator();
+    my $translator = new Bio::Translator(11);
+    my $translator = new Bio::Translator( 12, 'id' );
+    my $translator = new Bio::Translator( 'Yeast Mitochondrial', 'name' );
+    my $translator = new Bio::Translator( 'mito', 'name' );
 
-    my $translator = custom Bio::Tiny::Translator( \$custom_table );
-    my $translator = custom Bio::Tiny::Translator( \$custom_table, 1 );
+    my $translator = custom Bio::Translator( \$custom_table );
+    my $translator = custom Bio::Translator( \$custom_table, 1 );
 
     $translator->translate( \$seq );
     $translator->translate( \$seq, { strand => 1 } );
     $translator->translate( \$seq, { strand => -1 } );
 
 =head1 DESCRIPTION
 
-C<Bio::Tiny::Translator> tries to be a robust translator object featuring
+C<Bio::Translator> tries to be a robust translator object featuring
 translation tables based off the the ones provided by
 L<NCBI|http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi>.
 Key features include the ability to handle degenerate nucleotides and to
 translate to ambiguous amino acids.
 
 First, create a new translator object using one of the included tables or a
-custom one (see C<Bio::Tiny::Translator::Table> for table formats), and then
+custom one (see C<Bio::Translator::Table> for table formats), and then
 passing your DNA sequences to your translator object.
 
 The translator uses interbase coordinates. See below for the difference between
@@ -63,10 +63,10 @@ __PACKAGE__->mk_accessors('table');
 use Carp;
 use Params::Validate;
 
-use Bio::Tiny::Translator::Table;
-use Bio::Tiny::Translator::Validations ':validations';
+use Bio::Translator::Table;
+use Bio::Translator::Validations ':validations';
 
-use Bio::Tiny::Util::DNA qw/ $all_nucleotide_match /;
+use Bio::Util::DNA qw/ $all_nucleotide_match /;
 
 =head1 CONSTRUCTORS
 
@@ -76,18 +76,18 @@ sub _new { shift->SUPER::new( { table => shift } ) }
 
 =head2 new
 
-    my $translator = new Bio::Tiny::Translator();
-    my $translator = new Bio::Tiny::Translator( $id );
-    my $translator = new Bio::Tiny::Translator( $id, \%params );
+    my $translator = new Bio::Translator();
+    my $translator = new Bio::Translator( $id );
+    my $translator = new Bio::Translator( $id, \%params );
 
 Create a translator with a translation table provided by $id. Please see
-Bio::Tiny::Translator::Table for the full list of options.
+Bio::Translator::Table for the full list of options.
 
 =cut
 
 sub new {
     my $class = shift;
-    my $table = Bio::Tiny::Translator::Table->new(@_) or return;
+    my $table = Bio::Translator::Table->new(@_) or return;
     $class->_new($table);
 }
 
@@ -97,13 +97,13 @@ sub new {
     my $translator = $translator->custom( $table_ref, \%params );
 
 Create a translator with a custom translation table. Please see
-Bio::Tiny::Translator::Table for the full list of options.
+Bio::Translator::Table for the full list of options.
 
 =cut
 
 sub custom {
     my $class = shift;
-    my $table = Bio::Tiny::Translator::Table->custom(@_) or return;
+    my $table = Bio::Translator::Table->custom(@_) or return;
     $class->_new($table);
 }
 
@@ -358,36 +358,36 @@ Kevin Galinsky, C<kgalinsky plus cpan at gmail dot com>
 =head1 BUGS
 
 Please report any bugs or feature requests to
-C<bug-bio-tiny-translator at rt.cpan.org>, or through the web interface at
-L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Tiny-Translator>.
+C<bug-bio-translator at rt.cpan.org>, or through the web interface at
+L<http://rt.cpan.org/NoAuth/ReportBug.html?Queue=Bio-Translator>.
 I will be notified, and then you'll automatically be notified of progress on
 your bug as I make changes.
 
 =head1 SUPPORT
 
 You can find documentation for this module with the perldoc command.
 
-    perldoc Bio::Tiny::Translator
+    perldoc Bio::Translator
 
 You can also look for information at:
 
 =over 4
 
 =item * AnnoCPAN: Annotated CPAN documentation
 
-L<http://annocpan.org/dist/Bio-Tiny-Translator>
+L<http://annocpan.org/dist/Bio-Translator>
 
 =item * CPAN Ratings
 
-L<http://cpanratings.perl.org/d/Bio-Tiny-Translator>
+L<http://cpanratings.perl.org/d/Bio-Translator>
 
 =item * RT: CPAN's request tracker
 
-L<http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Tiny-Translator>
+L<http://rt.cpan.org/NoAuth/Bugs.html?Dist=Bio-Translator>
 
 =item * Search CPAN
 
-L<http://search.cpan.org/dist/Bio-Tiny-Translator>
+L<http://search.cpan.org/dist/Bio-Translator>
 
 =back