[Bioperl-guts-l] bioperl commit

Shawn Hoon shawnh at pub.open-bio.org
Thu Feb 20 06:08:59 EST 2003


shawnh
Thu Feb 20 06:08:59 EST 2003
Update of /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter
In directory pub.open-bio.org:/tmp/cvs-serv22374/Converter

Modified Files:
	BaseEnsEMBLConverter.pm ExonToEnsEMBLConverter.pm 
	FeaturePairToEnsEMBLConverter.pm HSPToEnsEMBLConverter.pm 
	PredictionExonToEnsEMBLConverter.pm 
	PredictionGeneToEnsEMBLConverter.pm 
	SeqFeatureToEnsEMBLConverter.pm featurePair_bio2ens.pm 
	gene_bio2ens.pm 
Log Message:
Correct namespace
bioperl-pipeline/Bio/Pipeline/Utils/Converter BaseEnsEMBLConverter.pm,1.7,1.8 ExonToEnsEMBLConverter.pm,1.2,1.3 FeaturePairToEnsEMBLConverter.pm,1.2,1.3 HSPToEnsEMBLConverter.pm,1.6,1.7 PredictionExonToEnsEMBLConverter.pm,1.1,1.2 PredictionGeneToEnsEMBLConverter.pm,1.2,1.3 SeqFeatureToEnsEMBLConverter.pm,1.1,1.2 featurePair_bio2ens.pm,1.2,1.3 gene_bio2ens.pm,1.1,1.2
===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/BaseEnsEMBLConverter.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -u -r1.7 -r1.8
--- /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/BaseEnsEMBLConverter.pm	2003/02/19 11:21:12	1.7
+++ /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/BaseEnsEMBLConverter.pm	2003/02/20 11:08:59	1.8
@@ -1,14 +1,14 @@
 
-package Bio::Pipeline::Converter::BaseEnsEMBLConverter;
+package Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter;
 
 use vars qw(@ISA);
 
 use strict;
 # use Bio::SeqFeatureIO;
 use Bio::EnsEMBL::Analysis;
-use Bio::Pipeline::Converter;
+use Bio::Pipeline::Utils::Converter;
 
- at ISA = qw(Bio::Pipeline::Converter);
+ at ISA = qw(Bio::Pipeline::Utils::Converter);
 
 sub new {
     my ($class, @args) = @_;

===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/ExonToEnsEMBLConverter.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/ExonToEnsEMBLConverter.pm	2003/02/14 08:52:17	1.2
+++ /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/ExonToEnsEMBLConverter.pm	2003/02/20 11:08:59	1.3
@@ -1,13 +1,13 @@
-package Bio::Pipeline::Converter::ExonToEnsEMBLConverter;
+package Bio::Pipeline::Utils::Converter::ExonToEnsEMBLConverter;
 
 use Bio::EnsEMBL::Analysis;
 use Bio::EnsEMBL::RawContig;
 use Bio::EnsEMBL::Exon;
 use vars qw(@ISA);
 
-use Bio::Pipeline::Converter::BaseEnsEMBLConverter;
+use Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter;
 
- at ISA = qw(Bio::Pipeline::Converter::BaseEnsEMBLConverter);
+ at ISA = qw(Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter);
 
 =head2 new
 

===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/FeaturePairToEnsEMBLConverter.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/FeaturePairToEnsEMBLConverter.pm	2002/12/23 13:43:49	1.2
+++ /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/FeaturePairToEnsEMBLConverter.pm	2003/02/20 11:08:59	1.3
@@ -1,5 +1,5 @@
 
-package Bio::Pipeline::Converter::FeaturePairToEnsEMBLConverter;
+package Bio::Pipeline::Utils::Converter::FeaturePairToEnsEMBLConverter;
 
 use vars qw(@ISA);
 
@@ -7,9 +7,9 @@
 use Bio::EnsEMBL::RepeatFeature;
 use Bio::EnsEMBL::RepeatConsensus;
 use Bio::EnsEMBL::RawContig;
-use Bio::Pipeline::Converter::BaseEnsEMBLConverter;
+use Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter;
 
- at ISA = qw(Bio::Pipeline::Converter::BaseEnsEMBLConverter);
+ at ISA = qw(Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter);
 
 
 sub new{

===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/HSPToEnsEMBLConverter.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -u -r1.6 -r1.7
--- /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/HSPToEnsEMBLConverter.pm	2003/02/14 08:52:17	1.6
+++ /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/HSPToEnsEMBLConverter.pm	2003/02/20 11:08:59	1.7
@@ -1,10 +1,10 @@
 
-package Bio::Pipeline::Converter::HSPToEnsEMBLConverter;
+package Bio::Pipeline::Utils::Converter::HSPToEnsEMBLConverter;
 
 use vars qw(@ISA);
 
 use strict;
-use Bio::Pipeline::Converter::BaseEnsEMBLConverter;
+use Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter;
 use Bio::EnsEMBL::DnaPepAlignFeature;
 use Bio::EnsEMBL::DnaDnaAlignFeature;
 use Bio::EnsEMBL::Analysis;
@@ -12,7 +12,7 @@
 use Bio::EnsEMBL::SeqFeature;
 use Bio::EnsEMBL::FeaturePair;
 
- at ISA = qw(Bio::Pipeline::Converter::BaseEnsEMBLConverter);
+ at ISA = qw(Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter);
 
 sub new{
     my($class, @args) = @_;

===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/PredictionExonToEnsEMBLConverter.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/PredictionExonToEnsEMBLConverter.pm	2003/01/06 08:08:52	1.1
+++ /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/PredictionExonToEnsEMBLConverter.pm	2003/02/20 11:08:59	1.2
@@ -1,14 +1,14 @@
 
 
-package Bio::Pipeline::Converter::PredictionExonToEnsEMBLConverter;
+package Bio::Pipeline::Utils::Converter::PredictionExonToEnsEMBLConverter;
 
 use Bio::EnsEMBL::Analysis;
 use Bio::EnsEMBL::RawContig;
 use Bio::EnsEMBL::Exon;
 
-use Bio::Pipeline::Converter::BaseEnsEMBLConverter;
+use Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter;
 
- at ISA = qw(Bio::Pipeline::Converter::BaseEnsEMBLConverter);
+ at ISA = qw(Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter);
 
 =head2 new
 

===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/PredictionGeneToEnsEMBLConverter.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/PredictionGeneToEnsEMBLConverter.pm	2003/01/06 08:08:52	1.2
+++ /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/PredictionGeneToEnsEMBLConverter.pm	2003/02/20 11:08:59	1.3
@@ -8,11 +8,11 @@
 
 =head1 NAME
 
-Bio::Pipeline::Converter::PredictionGeneToEnsEMBLConverter
+Bio::Pipeline::Utils::Converter::PredictionGeneToEnsEMBLConverter
 
 =cut
 
-package Bio::Pipeline::Converter::PredictionGeneToEnsEMBLConverter;
+package Bio::Pipeline::Utils::Converter::PredictionGeneToEnsEMBLConverter;
 
 use strict;
 use vars qw(@ISA);
@@ -20,10 +20,10 @@
 use Bio::EnsEMBL::Analysis;
 use Bio::EnsEMBL::PredictionTranscript;
 
-use Bio::Pipeline::Converter::PredictionExonToEnsEMBLConverter;
-use Bio::Pipeline::Converter::BaseEnsEMBLConverter;
+use Bio::Pipeline::Utils::Converter::PredictionExonToEnsEMBLConverter;
+use Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter;
 
- at ISA = qw(Bio::Pipeline::Converter::BaseEnsEMBLConverter);
+ at ISA = qw(Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter);
 
 sub new{
     my ($class, @args) = @_;
@@ -48,7 +48,7 @@
 
     $output->analysis($self->analysis);
 
-    my $exonConverter = Bio::Pipeline::Converter::PredictionExonToEnsEMBLConverter->new();
+    my $exonConverter = Bio::Pipeline::Utils::Converter::PredictionExonToEnsEMBLConverter->new();
     $exonConverter->contig($self->contig);
 
     my @exons = $input->exons;

===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/SeqFeatureToEnsEMBLConverter.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/SeqFeatureToEnsEMBLConverter.pm	2003/02/14 08:52:17	1.1
+++ /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/SeqFeatureToEnsEMBLConverter.pm	2003/02/20 11:08:59	1.2
@@ -12,7 +12,7 @@
 
 =head1 NAME
 
-Bio::Pipeline::Converter::SeqFeatureToEnsEMBLConverter
+Bio::Pipeline::Utils::Converter::SeqFeatureToEnsEMBLConverter
 
 =head1 SYNOPSIS
 
@@ -27,15 +27,15 @@
 
 # Gentlemen, start your engine...
 
-package Bio::Pipeline::Converter::SeqFeatureToEnsEMBLConverter;
+package Bio::Pipeline::Utils::Converter::SeqFeatureToEnsEMBLConverter;
 
 use strict;
 use vars qw(@ISA);
 use Bio::EnsEMBL::Analysis;
 use Bio::EnsEMBL::SimpleFeature;
-use Bio::Pipeline::Converter::BaseEnsEMBLConverter;
+use Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter;
 
- at ISA = qw(Bio::Pipeline::Converter::BaseEnsEMBLConverter);
+ at ISA = qw(Bio::Pipeline::Utils::Converter::BaseEnsEMBLConverter);
 
 sub _convert_single{
      my ($self, $input) = @_;

===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/featurePair_bio2ens.pm,v
retrieving revision 1.2
retrieving revision 1.3
diff -u -r1.2 -r1.3
--- /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/featurePair_bio2ens.pm	2002/12/04 07:35:46	1.2
+++ /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/featurePair_bio2ens.pm	2003/02/20 11:08:59	1.3
@@ -1,14 +1,14 @@
 
-package Bio::Pipeline::Converter::featurePair_bio2ens;
+package Bio::Pipeline::Utils::Converter::featurePair_bio2ens;
 
 
 use vars qw(@ISA);
 
 use strict;
 use Bio::SeqFeatureIO;
-use Bio::Pipeline::Converter;
+use Bio::Pipeline::Utils::Converter;
 
- at ISA = qw(Bio::Pipeline::Converter);
+ at ISA = qw(Bio::Pipeline::Utils::Converter);
 
 sub ens_dbadaptor{
    my ($self, @args) = @_;

===================================================================
RCS file: /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/gene_bio2ens.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -u -r1.1 -r1.2
--- /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/gene_bio2ens.pm	2002/11/28 14:27:51	1.1
+++ /home/repository/bioperl/bioperl-pipeline/Bio/Pipeline/Utils/Converter/gene_bio2ens.pm	2003/02/20 11:08:59	1.2
@@ -1,13 +1,13 @@
 
-package Bio::Pipeline::Converter::gene_bio2ens;
+package Bio::Pipeline::Utils::Converter::gene_bio2ens;
 
 use vars qw(@ISA);
 
 use strict;
 use Bio::SeqFeatureIO;
-use Bio::Pipeline::Converter;
+use Bio::Pipeline::Utils::Converter;
 
- at ISA = qw(Bio::Pipeline::Converter);
+ at ISA = qw(Bio::Pipeline::Utils::Converter);
 
 sub converter{
 
@@ -20,4 +20,4 @@
 		
 	return $converter->convert(@args);
 }
-1;
\ No newline at end of file
+1;



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