[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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