[Bioperl-guts-l] bioperl-live/Bio/Assembly Contig.pm, 1.16, 1.17 ContigAnalysis.pm, 1.7, 1.8 Scaffold.pm, 1.14, 1.15 Singlet.pm, 1.11, 1.12

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


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

Modified Files:
	Contig.pm ContigAnalysis.pm Scaffold.pm Singlet.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: Singlet.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Assembly/Singlet.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** Singlet.pm	26 Sep 2006 22:03:05 -0000	1.11
--- Singlet.pm	14 Jun 2007 14:16:10 -0000	1.12
***************
*** 22,26 ****
  
      # Assembly loading methods
!     $aio = new Bio::Assembly::IO(-file=>"test.ace.1",
                                 -format=>'phrap');
  
--- 22,26 ----
  
      # Assembly loading methods
!     $aio = Bio::Assembly::IO->new(-file=>"test.ace.1",
                                 -format=>'phrap');
  
***************
*** 102,106 ****
      $self->seqref($seq);
      $self->strand(1);
!      my $lseq = new Bio::LocatableSeq(
                 -seq =>   $seq->seq(),
                 -start    =>   1,
--- 102,106 ----
      $self->seqref($seq);
      $self->strand(1);
!      my $lseq = Bio::LocatableSeq->new(
                 -seq =>   $seq->seq(),
                 -start    =>   1,

Index: ContigAnalysis.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Assembly/ContigAnalysis.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** ContigAnalysis.pm	26 Sep 2006 22:03:05 -0000	1.7
--- ContigAnalysis.pm	14 Jun 2007 14:16:10 -0000	1.8
***************
*** 22,26 ****
  
      # Assembly loading methods
!     my $ca = new Bio::Assembly::ContigAnalysis( -contig=>$contigOBJ );
  
      my @lcq = $ca->low_consensus_quality;
--- 22,26 ----
  
      # Assembly loading methods
!     my $ca = Bio::Assembly::ContigAnalysis->new( -contig=>$contigOBJ );
  
      my @lcq = $ca->low_consensus_quality;

Index: Contig.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Assembly/Contig.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** Contig.pm	8 Mar 2007 15:53:27 -0000	1.16
--- Contig.pm	14 Jun 2007 14:16:10 -0000	1.17
***************
*** 23,27 ****
  
      # Assembly loading methods
!     $aio = new Bio::Assembly::IO(-file=>"test.ace.1",
                                 -format=>'phrap');
  
--- 23,27 ----
  
      # Assembly loading methods
!     $aio = Bio::Assembly::IO->new(-file=>"test.ace.1",
                                 -format=>'phrap');
  
***************
*** 218,222 ****
  
   Title     : new
!  Usage     : my $contig = new Bio::Assembly::Contig();
   Function  : Creates a new contig object
   Returns   : Bio::Assembly::Contig
--- 218,222 ----
  
   Title     : new
!  Usage     : my $contig = Bio::Assembly::Contig->new();
   Function  : Creates a new contig object
   Returns   : Bio::Assembly::Contig

Index: Scaffold.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Assembly/Scaffold.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** Scaffold.pm	26 Sep 2006 22:03:05 -0000	1.14
--- Scaffold.pm	14 Jun 2007 14:16:10 -0000	1.15
***************
*** 19,23 ****
  
      # Assembly loading methods
!     my $aio = new Bio::Assembly::IO(-file=>"test.ace.1", -format=>'phrap');
      my $assembly = $aio->next_assembly;
  
--- 19,23 ----
  
      # Assembly loading methods
!     my $aio = Bio::Assembly::IO->new(-file=>"test.ace.1", -format=>'phrap');
      my $assembly = $aio->next_assembly;
  



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