[Bioperl-guts-l] bioperl-live/Bio/Matrix/IO mlagan.pm, 1.1, 1.2 phylip.pm, 1.5, 1.6 scoring.pm, 1.6, 1.7

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


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

Modified Files:
	mlagan.pm phylip.pm scoring.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: mlagan.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/IO/mlagan.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** mlagan.pm	23 Feb 2007 09:56:28 -0000	1.1
--- mlagan.pm	14 Jun 2007 14:16:12 -0000	1.2
***************
*** 18,22 ****
  
    use Bio::Matrix::IO;
!   my $parser = new Bio::Matrix::IO(-format => 'mlagan',
                                     -file   => 'nucmatrix.txt');
    my $matrix = $parser->next_matrix;
--- 18,22 ----
  
    use Bio::Matrix::IO;
!   my $parser = Bio::Matrix::IO->new(-format => 'mlagan',
                                     -file   => 'nucmatrix.txt');
    my $matrix = $parser->next_matrix;

Index: scoring.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/IO/scoring.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** scoring.pm	26 Sep 2006 22:03:09 -0000	1.6
--- scoring.pm	14 Jun 2007 14:16:12 -0000	1.7
***************
*** 18,22 ****
  
    use Bio::Matrix::IO;
!   my $parser = new Bio::Matrix::IO(-format => 'scoring',
                                     -file   => 'BLOSUM50');
    my $matrix = $parser->next_matrix;
--- 18,22 ----
  
    use Bio::Matrix::IO;
!   my $parser = Bio::Matrix::IO->new(-format => 'scoring',
                                     -file   => 'BLOSUM50');
    my $matrix = $parser->next_matrix;
***************
*** 69,73 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Matrix::IO::scoring();
   Function: Builds a new Bio::Matrix::IO::scoring object 
   Returns : an instance of Bio::Matrix::IO::scoring
--- 69,73 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Matrix::IO::scoring->new();
   Function: Builds a new Bio::Matrix::IO::scoring object 
   Returns : an instance of Bio::Matrix::IO::scoring
***************
*** 141,145 ****
         }
     }
!    my $matrix = new Bio::Matrix::Scoring(-values     => \@matrix,
  					 -rownames   => \@rows,
  					 -colnames   => \@cols,
--- 141,145 ----
         }
     }
!    my $matrix = Bio::Matrix::Scoring->new(-values     => \@matrix,
  					 -rownames   => \@rows,
  					 -colnames   => \@cols,

Index: phylip.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Matrix/IO/phylip.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** phylip.pm	26 Sep 2006 22:03:09 -0000	1.5
--- phylip.pm	14 Jun 2007 14:16:12 -0000	1.6
***************
*** 18,22 ****
  
    use Bio::Matrix::IO;
!   my $parser = new Bio::Matrix::IO(-format   => 'phylip'
                                     -file     => 't/data/phylipdist.out');
    my $matrix = $parser->next_matrix;
--- 18,22 ----
  
    use Bio::Matrix::IO;
!   my $parser = Bio::Matrix::IO->new(-format   => 'phylip'
                                     -file     => 't/data/phylipdist.out');
    my $matrix = $parser->next_matrix;
***************
*** 73,77 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Matrix::IO::phylip();
   Function: Builds a new Bio::Matrix::IO::phylip object 
   Returns : an instance of Bio::Matrix::IO::phylip
--- 73,77 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Matrix::IO::phylip->new();
   Function: Builds a new Bio::Matrix::IO::phylip object 
   Returns : an instance of Bio::Matrix::IO::phylip



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