move lib/Bio/JBrowse/Cmd/FlatFileToJson/FeatureStream* to lib/Bio/JBr…

…owse/FeatureStream*
GMOD · May 29, 2012 · a95e58b · a95e58b
1 parent 26fbef7
commit a95e58b
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Showing 4 changed files with 10 additions and 10 deletions.
diff --git a/lib/Bio/JBrowse/Cmd/FlatFileToJson.pm b/lib/Bio/JBrowse/Cmd/FlatFileToJson.pm
@@ -188,11 +188,11 @@ sub make_gff_stream {
     my $self = shift;
 
     require Bio::GFF3::LowLevel::Parser;
-    require Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::GFF3_LowLevel;
+    require Bio::JBrowse::FeatureStream::GFF3_LowLevel;
 
     my $p = Bio::GFF3::LowLevel::Parser->new( $self->opt('gff') );
 
-    return Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::GFF3_LowLevel->new(
+    return Bio::JBrowse::FeatureStream::GFF3_LowLevel->new(
         parser => $p,
         track_label => $self->opt('trackLabel')
      );
@@ -202,7 +202,7 @@ sub make_bed_stream {
     my ( $self, $config_hash ) = @_;
 
     require Bio::FeatureIO;
-    require Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::BioPerl;
+    require Bio::JBrowse::FeatureStream::BioPerl;
 
     my $io = Bio::FeatureIO->new(
         -format => 'bed',
@@ -211,7 +211,7 @@ sub make_bed_stream {
         ($self->opt('thickType') ? ("-thick_type" => $self->opt('thickType')) : ()),
         );
 
-    return Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::BioPerl->new(
+    return Bio::JBrowse::FeatureStream::BioPerl->new(
         stream => sub { $io->next_feature },
         track_label => $self->opt('trackLabel'),
     );

diff --git a/...rowse/Cmd/FlatFileToJson/FeatureStream.pm → lib/Bio/JBrowse/FeatureStream.pm b/...rowse/Cmd/FlatFileToJson/FeatureStream.pm → lib/Bio/JBrowse/FeatureStream.pm
@@ -1,11 +1,11 @@
 =head1 NAME
 
-Script::FlatFileToJson::FeatureStream - base class for feature streams
+FeatureStream - base class for feature streams
 used for handling features inside FlatFileToJson.pm
 
 =cut
 
-package Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream;
+package Bio::JBrowse::FeatureStream;
 use strict;
 use warnings;
 

diff --git a/...d/FlatFileToJson/FeatureStream/BioPerl.pm → lib/Bio/JBrowse/FeatureStream/BioPerl.pm b/...d/FlatFileToJson/FeatureStream/BioPerl.pm → lib/Bio/JBrowse/FeatureStream/BioPerl.pm
@@ -5,10 +5,10 @@ for working with BioPerl seqfeature objects
 
 =cut
 
-package Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream::BioPerl;
+package Bio::JBrowse::FeatureStream::BioPerl;
 use strict;
 use warnings;
-use base 'Bio::JBrowse::Cmd::FlatFileToJson::FeatureStream';
+use base 'Bio::JBrowse::FeatureStream';
 
 sub next_items {
     my ( $self ) = @_;

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