further move Bio::JBrowse::Script namespace to Bio::JBrowse::Cmd to a…

…ppease dzil
Arabidopsis-Information-Portal · Apr 13, 2012 · 9acfffc · 9acfffc
1 parent 6a56c1e
commit 9acfffc
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Showing 10 changed files with 22 additions and 22 deletions.
diff --git a/bin/flatfile-to-json.pl b/bin/flatfile-to-json.pl
@@ -4,9 +4,9 @@
 use lib "$RealBin/../lib";
 use JBlibs;
 
-use Bio::JBrowse::Script::FlatFileToJson;
+use Bio::JBrowse::Cmd::FlatFileToJson;
 
-exit Bio::JBrowse::Script::FlatFileToJson->new(@ARGV)->run;
+exit Bio::JBrowse::Cmd::FlatFileToJson->new(@ARGV)->run;
 
 __END__
 

diff --git a/bin/remove-track.pl b/bin/remove-track.pl
@@ -4,9 +4,9 @@
 use lib "$RealBin/../lib";
 use JBlibs;
 
-use Bio::JBrowse::Script::RemoveTrack;
+use Bio::JBrowse::Cmd::RemoveTrack;
 
-exit Bio::JBrowse::Script::RemoveTrack->new(@ARGV)->run;
+exit Bio::JBrowse::Cmd::RemoveTrack->new(@ARGV)->run;
 
 __END__
 

diff --git a/lib/Bio/JBrowse/Script.pm → lib/Bio/JBrowse/Cmd.pm b/lib/Bio/JBrowse/Script.pm → lib/Bio/JBrowse/Cmd.pm
@@ -1,4 +1,4 @@
-package Bio::JBrowse::Script;
+package Bio::JBrowse::Cmd;
 use strict;
 use warnings;
 

diff --git a/lib/Bio/JBrowse/Script/FlatFileToJson.pm → lib/Bio/JBrowse/Cmd/FlatFileToJson.pm b/lib/Bio/JBrowse/Script/FlatFileToJson.pm → lib/Bio/JBrowse/Cmd/FlatFileToJson.pm
@@ -10,12 +10,12 @@ Do C<perldoc bin/flatfile-to-json.pl> for most of the documentation.
 
 =cut
 
-package Bio::JBrowse::Script::FlatFileToJson;
+package Bio::JBrowse::Cmd::FlatFileToJson;
 
 use strict;
 use warnings;
 
-use base 'Bio::JBrowse::Script';
+use base 'Bio::JBrowse::Cmd';
 
 use ArrayRepr;
 use GenomeDB;
@@ -198,11 +198,11 @@ sub make_gff_stream {
     my $self = shift;
 
     require Bio::GFF3::LowLevel::Parser;
-    require Bio::JBrowse::Script::FlatFileToJson::FeatureStream::GFF3_LowLevel;
+    require Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::GFF3_LowLevel;
 
     my $p = Bio::GFF3::LowLevel::Parser->new( $self->opt('gff') );
 
-    return Bio::JBrowse::Script::FlatFileToJson::FeatureStream::GFF3_LowLevel->new(
+    return Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::GFF3_LowLevel->new(
         parser => $p,
         track_label => $self->opt('trackLabel')
      );
@@ -212,7 +212,7 @@ sub make_bed_stream {
     my ( $self, $config_hash ) = @_;
 
     require Bio::FeatureIO;
-    require Bio::JBrowse::Script::FlatFileToJson::FeatureStream::BioPerl;
+    require Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::BioPerl;
 
     my $io = Bio::FeatureIO->new(
         -format => 'bed',
@@ -221,7 +221,7 @@ sub make_bed_stream {
         ($self->opt('thickType') ? ("-thick_type" => $self->opt('thickType')) : ()),
         );
 
-    return Bio::JBrowse::Script::FlatFileToJson::FeatureStream::BioPerl->new(
+    return Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::BioPerl->new(
         stream => sub { $io->next_feature },
         track_label => $self->opt('trackLabel'),
     );

diff --git a/...se/Script/FlatFileToJson/FeatureStream.pm → ...rowse/Cmd/FlatFileToJson/FeatureStream.pm b/...se/Script/FlatFileToJson/FeatureStream.pm → ...rowse/Cmd/FlatFileToJson/FeatureStream.pm
@@ -5,7 +5,7 @@ used for handling features inside FlatFileToJson.pm
 
 =cut
 
-package Bio::JBrowse::Script::FlatFileToJson::FeatureStream;
+package Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream;
 use strict;
 use warnings;
 

diff --git a/...t/FlatFileToJson/FeatureStream/BioPerl.pm → ...d/FlatFileToJson/FeatureStream/BioPerl.pm b/...t/FlatFileToJson/FeatureStream/BioPerl.pm → ...d/FlatFileToJson/FeatureStream/BioPerl.pm
@@ -5,10 +5,10 @@ for working with BioPerl seqfeature objects
 
 =cut
 
-package Bio::JBrowse::Script::FlatFileToJson::FeatureStream::BioPerl;
+package Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::BioPerl;
 use strict;
 use warnings;
-use base 'Bio::JBrowse::Script::FlatFileToJson::FeatureStream';
+use base 'Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream';
 
 sub next_items {
     my ( $self ) = @_;

diff --git a/...FileToJson/FeatureStream/GFF3_LowLevel.pm → ...FileToJson/FeatureStream/GFF3_LowLevel.pm b/...FileToJson/FeatureStream/GFF3_LowLevel.pm → ...FileToJson/FeatureStream/GFF3_LowLevel.pm
@@ -5,11 +5,11 @@ class for working with L<Bio::GFF3::LowLevel::Parser> features
 
 =cut
 
-package Bio::JBrowse::Script::FlatFileToJson::FeatureStream::GFF3_LowLevel;
+package Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::GFF3_LowLevel;
 use strict;
 use warnings;
 
-use base 'Bio::JBrowse::Script::FlatFileToJson::FeatureStream';
+use base 'Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream';
 
 sub next_items {
     while ( my $i = $_[0]->{parser}->next_item ) {

diff --git a/lib/Bio/JBrowse/Script/RemoveTrack.pm → lib/Bio/JBrowse/Cmd/RemoveTrack.pm b/lib/Bio/JBrowse/Script/RemoveTrack.pm → lib/Bio/JBrowse/Cmd/RemoveTrack.pm
@@ -8,7 +8,7 @@ Do C<perldoc bin/remove-track.pl> to see usage documentation.
 
 =cut
 
-package Bio::JBrowse::Script::RemoveTrack;
+package Bio::JBrowse::Cmd::RemoveTrack;
 use strict;
 use warnings;
 
@@ -17,7 +17,7 @@ use File::Path ();
 use File::Spec;
 
 use JsonFileStorage;
-use base 'Bio::JBrowse::Script';
+use base 'Bio::JBrowse::Cmd';
 
 sub option_defaults {
     ( dir => 'data/' )

diff --git a/tests/perl_tests/flatfile-to-json.pl.t b/tests/perl_tests/flatfile-to-json.pl.t
@@ -6,7 +6,7 @@ use JBlibs;
 use Test::More;
 use Test::Warn;
 
-use Bio::JBrowse::Script::FlatFileToJson;
+use Bio::JBrowse::Cmd::FlatFileToJson;
 
 use File::Spec::Functions qw( catfile catdir );
 use File::Temp ();
@@ -20,7 +20,7 @@ sub run_with(@) {
     #ok( ! $?, 'flatfile-to-json.pl ran ok' );
     my @args = @_;
     warnings_are {
-      Bio::JBrowse::Script::FlatFileToJson->new( @args )->run;
+      Bio::JBrowse::Cmd::FlatFileToJson->new( @args )->run;
     } [], 'ran without warnings';
 }
 

diff --git a/tests/perl_tests/remove-track.pl.t b/tests/perl_tests/remove-track.pl.t
@@ -12,10 +12,10 @@ use File::Copy::Recursive 'dircopy';
 
 use FileSlurping 'slurp';
 
-use Bio::JBrowse::Script::RemoveTrack;
+use Bio::JBrowse::Cmd::RemoveTrack;
 
 sub remove_track {
-    Bio::JBrowse::Script::RemoveTrack->new( '--quiet',  @_ )->run
+    Bio::JBrowse::Cmd::RemoveTrack->new( '--quiet',  @_ )->run
 }
 
 {