[Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Phylo/Hyphy Base.pm, 1.1, 1.2 FEL.pm, 1.3, 1.4 Modeltest.pm, 1.3, 1.4 REL.pm, 1.3, 1.4 SLAC.pm, 1.5, 1.6

Senduran Balasubramaniam sendu at dev.open-bio.org
Thu Jun 14 11:23:11 EDT 2007


Update of /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Hyphy
In directory dev.open-bio.org:/tmp/cvs-serv24084/Bio/Tools/Run/Phylo/Hyphy

Modified Files:
	Base.pm FEL.pm Modeltest.pm REL.pm SLAC.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: Base.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Hyphy/Base.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Base.pm	17 Dec 2006 12:58:55 -0000	1.1
--- Base.pm	14 Jun 2007 15:23:09 -0000	1.2
***************
*** 122,126 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tools::Run::Phylo::Hyphy();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy object 
   Returns : Bio::Tools::Run::Phylo::Hyphy
--- 122,126 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy->new();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy object 
   Returns : Bio::Tools::Run::Phylo::Hyphy
***************
*** 177,181 ****
  	   ('-dir' => $tempdir, 
  	    UNLINK => ($self->save_tempfiles ? 0 : 1));
!        my $alnout = new Bio::AlignIO('-format'      => 'phylip',
  				     '-fh'          => $tempseqFH,
                                       '-interleaved' => 0);
--- 177,181 ----
  	   ('-dir' => $tempdir, 
  	    UNLINK => ($self->save_tempfiles ? 0 : 1));
!        my $alnout = Bio::AlignIO->new('-format'      => 'phylip',
  				     '-fh'          => $tempseqFH,
                                       '-interleaved' => 0);
***************
*** 198,202 ****
  	    UNLINK => ($self->save_tempfiles ? 0 : 1));
  
!        my $treeout = new Bio::TreeIO('-format' => 'newick',
  				     '-fh'     => $temptreeFH);
         $treeout->write_tree($tree);
--- 198,202 ----
  	    UNLINK => ($self->save_tempfiles ? 0 : 1));
  
!        my $treeout = Bio::TreeIO->new('-format' => 'newick',
  				     '-fh'     => $temptreeFH);
         $treeout->write_tree($tree);

Index: REL.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Hyphy/REL.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** REL.pm	29 Jan 2007 17:17:19 -0000	1.3
--- REL.pm	14 Jun 2007 15:23:09 -0000	1.4
***************
*** 20,24 ****
    use Bio::AlignIO;
  
!   my $alignio = new Bio::AlignIO(-format => 'fasta',
    			         -file   => 't/data/hyphy1.fasta');
  
--- 20,24 ----
    use Bio::AlignIO;
  
!   my $alignio = Bio::AlignIO->new(-format => 'fasta',
    			         -file   => 't/data/hyphy1.fasta');
  
***************
*** 28,32 ****
        -format => 'newick', -file => 't/data/hyphy1.tree');
  
!   my $rel = new Bio::Tools::Run::Phylo::Hyphy::REL();
    $rel->alignment($aln);
    $rel->tree($tree);
--- 28,32 ----
        -format => 'newick', -file => 't/data/hyphy1.tree');
  
!   my $rel = Bio::Tools::Run::Phylo::Hyphy::REL->new();
    $rel->alignment($aln);
    $rel->tree($tree);
***************
*** 117,121 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tools::Run::Phylo::Hyphy::REL();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::REL object 
   Returns : Bio::Tools::Run::Phylo::Hyphy::REL
--- 117,121 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::REL->new();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::REL object 
   Returns : Bio::Tools::Run::Phylo::Hyphy::REL

Index: Modeltest.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Hyphy/Modeltest.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Modeltest.pm	29 Jan 2007 17:14:50 -0000	1.3
--- Modeltest.pm	14 Jun 2007 15:23:09 -0000	1.4
***************
*** 20,24 ****
    use Bio::AlignIO;
  
!   my $alignio = new Bio::AlignIO(-format => 'fasta',
    			         -file   => 't/data/hyphy1.fasta');
  
--- 20,24 ----
    use Bio::AlignIO;
  
!   my $alignio = Bio::AlignIO->new(-format => 'fasta',
    			         -file   => 't/data/hyphy1.fasta');
  
***************
*** 28,32 ****
        -format => 'newick', -file => 't/data/hyphy1.tree');
  
!   my $modeltest = new Bio::Tools::Run::Phylo::Hyphy::Modeltest();
    $modeltest->alignment($aln);
    $modeltest->tree($tree);
--- 28,32 ----
        -format => 'newick', -file => 't/data/hyphy1.tree');
  
!   my $modeltest = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
    $modeltest->alignment($aln);
    $modeltest->tree($tree);
***************
*** 124,128 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tools::Run::Phylo::Hyphy::Modeltest();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::Modeltest object 
   Returns : Bio::Tools::Run::Phylo::Hyphy::Modeltest
--- 124,128 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::Modeltest->new();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::Modeltest object 
   Returns : Bio::Tools::Run::Phylo::Hyphy::Modeltest

Index: FEL.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Hyphy/FEL.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** FEL.pm	29 Jan 2007 17:16:48 -0000	1.3
--- FEL.pm	14 Jun 2007 15:23:09 -0000	1.4
***************
*** 20,24 ****
    use Bio::AlignIO;
  
!   my $alignio = new Bio::AlignIO(-format => 'fasta',
    			         -file   => 't/data/hyphy1.fasta');
  
--- 20,24 ----
    use Bio::AlignIO;
  
!   my $alignio = Bio::AlignIO->new(-format => 'fasta',
    			         -file   => 't/data/hyphy1.fasta');
  
***************
*** 28,32 ****
        -format => 'newick', -file => 't/data/hyphy1.tree');
  
!   my $fel = new Bio::Tools::Run::Phylo::Hyphy::FEL();
    $fel->alignment($aln);
    $fel->tree($tree);
--- 28,32 ----
        -format => 'newick', -file => 't/data/hyphy1.tree');
  
!   my $fel = Bio::Tools::Run::Phylo::Hyphy::FEL->new();
    $fel->alignment($aln);
    $fel->tree($tree);
***************
*** 153,157 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tools::Run::Phylo::Hyphy::FEL();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::FEL object 
   Returns : Bio::Tools::Run::Phylo::Hyphy::FEL
--- 153,157 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::FEL->new();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::FEL object 
   Returns : Bio::Tools::Run::Phylo::Hyphy::FEL

Index: SLAC.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Phylo/Hyphy/SLAC.pm,v
retrieving revision 1.5
retrieving revision 1.6
diff -C2 -d -r1.5 -r1.6
*** SLAC.pm	29 Jan 2007 17:17:51 -0000	1.5
--- SLAC.pm	14 Jun 2007 15:23:09 -0000	1.6
***************
*** 20,24 ****
    use Bio::AlignIO;
  
!   my $alignio = new Bio::AlignIO(-format => 'fasta',
    			         -file   => 't/data/hyphy1.fasta');
  
--- 20,24 ----
    use Bio::AlignIO;
  
!   my $alignio = Bio::AlignIO->new(-format => 'fasta',
    			         -file   => 't/data/hyphy1.fasta');
  
***************
*** 28,32 ****
        -format => 'newick', -file => 't/data/hyphy1.tree');
  
!   my $slac = new Bio::Tools::Run::Phylo::Hyphy::SLAC();
    $slac->alignment($aln);
    $slac->tree($tree);
--- 28,32 ----
        -format => 'newick', -file => 't/data/hyphy1.tree');
  
!   my $slac = Bio::Tools::Run::Phylo::Hyphy::SLAC->new();
    $slac->alignment($aln);
    $slac->tree($tree);
***************
*** 135,139 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tools::Run::Phylo::Hyphy::SLAC();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::SLAC object 
   Returns : Bio::Tools::Run::Phylo::Hyphy::SLAC
--- 135,139 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tools::Run::Phylo::Hyphy::SLAC->new();
   Function: Builds a new Bio::Tools::Run::Phylo::Hyphy::SLAC object 
   Returns : Bio::Tools::Run::Phylo::Hyphy::SLAC



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