[Bioperl-guts-l] bioperl-live/Bio/Cluster ClusterFactory.pm, 1.7, 1.8 SequenceFamily.pm, 1.14, 1.15 UniGene.pm, 1.39, 1.40

Senduran Balasubramaniam sendu at dev.open-bio.org
Thu Jun 14 10:16:12 EDT 2007


Update of /home/repository/bioperl/bioperl-live/Bio/Cluster
In directory dev.open-bio.org:/tmp/cvs-serv22328/Bio/Cluster

Modified Files:
	ClusterFactory.pm SequenceFamily.pm UniGene.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: UniGene.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Cluster/UniGene.pm,v
retrieving revision 1.39
retrieving revision 1.40
diff -C2 -d -r1.39 -r1.40
*** UniGene.pm	26 Sep 2006 22:03:05 -0000	1.39
--- UniGene.pm	14 Jun 2007 14:16:10 -0000	1.40
***************
*** 275,279 ****
      $self->version($v) if defined($v);
      if( ! defined $seqfact ) {
! 	$seqfact = new Bio::Seq::SeqFactory
  	    (-verbose => $self->verbose(), 
  	     -type => 'Bio::Seq::RichSeq');
--- 275,279 ----
      $self->version($v) if defined($v);
      if( ! defined $seqfact ) {
! 	$seqfact = Bio::Seq::SeqFactory->new
  	    (-verbose => $self->verbose(), 
  	     -type => 'Bio::Seq::RichSeq');

Index: SequenceFamily.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Cluster/SequenceFamily.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** SequenceFamily.pm	8 Mar 2007 17:34:00 -0000	1.14
--- SequenceFamily.pm	14 Jun 2007 14:16:10 -0000	1.15
***************
*** 24,28 ****
  
    my $file =  File::Spec->catfile('t','data','swiss.dat');
!   my $seqio= new Bio::SeqIO(-format => 'swiss',
                              -file => $file);
    my @mem;
--- 24,28 ----
  
    my $file =  File::Spec->catfile('t','data','swiss.dat');
!   my $seqio= Bio::SeqIO->new(-format => 'swiss',
                              -file => $file);
    my @mem;

Index: ClusterFactory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Cluster/ClusterFactory.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** ClusterFactory.pm	26 Sep 2006 22:03:05 -0000	1.7
--- ClusterFactory.pm	14 Jun 2007 14:16:10 -0000	1.8
***************
*** 34,38 ****
      # if you don't provide a default type, the factory will try
      # some guesswork based on display_id and namespace
!     my $factory = new Bio::Cluster::ClusterFactory(-type => 'Bio::Cluster::UniGene');
      my $clu = $factory->create_object(-description => 'NAT',
                                        -display_id  => 'Hs.2');
--- 34,38 ----
      # if you don't provide a default type, the factory will try
      # some guesswork based on display_id and namespace
!     my $factory = Bio::Cluster::ClusterFactory->new(-type => 'Bio::Cluster::UniGene');
      my $clu = $factory->create_object(-description => 'NAT',
                                        -display_id  => 'Hs.2');
***************
*** 88,92 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Cluster::ClusterFactory();
   Function: Builds a new Bio::Cluster::ClusterFactory object 
   Returns : Bio::Cluster::ClusterFactory
--- 88,92 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Cluster::ClusterFactory->new();
   Function: Builds a new Bio::Cluster::ClusterFactory object 
   Returns : Bio::Cluster::ClusterFactory



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