[Bioperl-guts-l] bioperl-run/Bio/Tools/Run/Alignment Amap.pm, 1.6, 1.7 Clustalw.pm, 1.52, 1.53 Kalign.pm, 1.1, 1.2 Lagan.pm, 1.21, 1.22 Muscle.pm, 1.13, 1.14 Probalign.pm, 1.3, 1.4 Probcons.pm, 1.10, 1.11 Proda.pm, 1.3, 1.4 StandAloneFasta.pm, 1.14, 1.15 TCoffee.pm, 1.44, 1.45

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/Alignment
In directory dev.open-bio.org:/tmp/cvs-serv24084/Bio/Tools/Run/Alignment

Modified Files:
	Amap.pm Clustalw.pm Kalign.pm Lagan.pm Muscle.pm Probalign.pm 
	Probcons.pm Proda.pm StandAloneFasta.pm TCoffee.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: Clustalw.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/Clustalw.pm,v
retrieving revision 1.52
retrieving revision 1.53
diff -C2 -d -r1.52 -r1.53
*** Clustalw.pm	1 Jun 2007 08:03:51 -0000	1.52
--- Clustalw.pm	14 Jun 2007 15:23:08 -0000	1.53
***************
*** 759,763 ****
      }
      
!     my $in = new Bio::TreeIO('-file'  => $treefile,
                               '-format'=> 'newick');
      
--- 759,763 ----
      }
      
!     my $in = Bio::TreeIO->new('-file'  => $treefile,
                               '-format'=> 'newick');
      

Index: Probcons.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/Probcons.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** Probcons.pm	6 Nov 2006 18:04:23 -0000	1.10
--- Probcons.pm	14 Jun 2007 15:23:08 -0000	1.11
***************
*** 18,22 ****
  
    # Build a muscle alignment factory
!   $factory = new Bio::Tools::Run::Alignment::Probcons (@params);
  
    # Pass the factory a list of sequences to be aligned.
--- 18,22 ----
  
    # Build a muscle alignment factory
!   $factory = Bio::Tools::Run::Alignment::Probcons->new(@params);
  
    # Pass the factory a list of sequences to be aligned.
***************
*** 38,42 ****
  
    #First round to generate train.params
!   $factory = new Bio::Tools::Run::Alignment::Probcons
        (
         'iterative-refinement'  => '1000',
--- 38,42 ----
  
    #First round to generate train.params
!   $factory = Bio::Tools::Run::Alignment::Probcons->new
        (
         'iterative-refinement'  => '1000',
***************
*** 56,60 ****
    $factory = '';
  
!   $factory = new Bio::Tools::Run::Alignment::Probcons
        (
         'iterative-refinement'  => '1000',
--- 56,60 ----
    $factory = '';
  
!   $factory = Bio::Tools::Run::Alignment::Probcons->new
        (
         'iterative-refinement'  => '1000',

Index: Probalign.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/Probalign.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Probalign.pm	7 Dec 2006 12:27:47 -0000	1.3
--- Probalign.pm	14 Jun 2007 15:23:08 -0000	1.4
***************
*** 18,22 ****
  
    # Build a muscle alignment factory
!   $factory = new Bio::Tools::Run::Alignment::Probalign(@params);
  
    # Pass the factory a list of sequences to be aligned.
--- 18,22 ----
  
    # Build a muscle alignment factory
!   $factory = Bio::Tools::Run::Alignment::Probalign->new(@params);
  
    # Pass the factory a list of sequences to be aligned.
***************
*** 35,39 ****
    #See the DESCRIPTION section that follows for additional details.
  
!   $factory = new Bio::Tools::Run::Alignment::Probalign();
    $factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
    $aln = $factory->align($seq_array_ref);
--- 35,39 ----
    #See the DESCRIPTION section that follows for additional details.
  
!   $factory = Bio::Tools::Run::Alignment::Probalign->new();
    $factory->outfile_name("$dir/$subdir/$outdir/outfile.afa");
    $aln = $factory->align($seq_array_ref);

Index: Kalign.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/Kalign.pm,v
retrieving revision 1.1
retrieving revision 1.2
diff -C2 -d -r1.1 -r1.2
*** Kalign.pm	2 Sep 2006 12:24:01 -0000	1.1
--- Kalign.pm	14 Jun 2007 15:23:08 -0000	1.2
***************
*** 20,24 ****
  
    # Build a kalign alignment factory
!   $factory = new Bio::Tools::Run::Alignment::Kalign (@params);
  
    # Pass the factory a list of sequences to be aligned.
--- 20,24 ----
  
    # Build a kalign alignment factory
!   $factory = Bio::Tools::Run::Alignment::Kalign->new(@params);
  
    # Pass the factory a list of sequences to be aligned.

Index: StandAloneFasta.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/StandAloneFasta.pm,v
retrieving revision 1.14
retrieving revision 1.15
diff -C2 -d -r1.14 -r1.15
*** StandAloneFasta.pm	4 Jul 2006 22:23:32 -0000	1.14
--- StandAloneFasta.pm	14 Jun 2007 15:23:08 -0000	1.15
***************
*** 464,468 ****
      if( ! ref $input ) {
  	if( -e $input ) {
! 	    my $seqio = new Bio::SeqIO(-format => 'fasta', -file => $input);
  	    while( my $seq = $seqio->next_seq ) {
  		push @seqs, $seq;
--- 464,468 ----
      if( ! ref $input ) {
  	if( -e $input ) {
! 	    my $seqio = Bio::SeqIO->new(-format => 'fasta', -file => $input);
  	    while( my $seq = $seqio->next_seq ) {
  		push @seqs, $seq;

Index: Muscle.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/Muscle.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** Muscle.pm	9 Nov 2006 17:38:44 -0000	1.13
--- Muscle.pm	14 Jun 2007 15:23:08 -0000	1.14
***************
*** 20,24 ****
  
    # Build a muscle alignment factory
!   $factory = new Bio::Tools::Run::Alignment::Muscle (@params);
  
    # Pass the factory a list of sequences to be aligned.
--- 20,24 ----
  
    # Build a muscle alignment factory
!   $factory = Bio::Tools::Run::Alignment::Muscle->new(@params);
  
    # Pass the factory a list of sequences to be aligned.

Index: TCoffee.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/TCoffee.pm,v
retrieving revision 1.44
retrieving revision 1.45
diff -C2 -d -r1.44 -r1.45
*** TCoffee.pm	16 Nov 2006 09:03:18 -0000	1.44
--- TCoffee.pm	14 Jun 2007 15:23:08 -0000	1.45
***************
*** 21,25 ****
    # Build a tcoffee alignment factory
    @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
!   $factory = new Bio::Tools::Run::Alignment::TCoffee (@params);
  
    # Pass the factory a list of sequences to be aligned.
--- 21,25 ----
    # Build a tcoffee alignment factory
    @params = ('ktuple' => 2, 'matrix' => 'BLOSUM');
!   $factory = Bio::Tools::Run::Alignment::TCoffee->new(@params);
  
    # Pass the factory a list of sequences to be aligned.

Index: Amap.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/Amap.pm,v
retrieving revision 1.6
retrieving revision 1.7
diff -C2 -d -r1.6 -r1.7
*** Amap.pm	26 Oct 2006 12:50:41 -0000	1.6
--- Amap.pm	14 Jun 2007 15:23:08 -0000	1.7
***************
*** 18,22 ****
  
    # Build a muscle alignment factory
!   $factory = new Bio::Tools::Run::Alignment::Amap (@params);
  
    # Pass the factory a list of sequences to be aligned.
--- 18,22 ----
  
    # Build a muscle alignment factory
!   $factory = Bio::Tools::Run::Alignment::Amap->new(@params);
  
    # Pass the factory a list of sequences to be aligned.
***************
*** 38,42 ****
  
    #First round to generate train.params
!   $factory = new Bio::Tools::Run::Alignment::Amap
        (
         'iterative-refinement'  => '1000',
--- 38,42 ----
  
    #First round to generate train.params
!   $factory = Bio::Tools::Run::Alignment::Amap->new
        (
         'iterative-refinement'  => '1000',
***************
*** 56,60 ****
    $factory = '';
  
!   $factory = new Bio::Tools::Run::Alignment::Amap
        (
         'iterative-refinement'  => '1000',
--- 56,60 ----
    $factory = '';
  
!   $factory = Bio::Tools::Run::Alignment::Amap->new
        (
         'iterative-refinement'  => '1000',

Index: Lagan.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/Lagan.pm,v
retrieving revision 1.21
retrieving revision 1.22
diff -C2 -d -r1.21 -r1.22
*** Lagan.pm	23 Feb 2007 17:08:19 -0000	1.21
--- Lagan.pm	14 Jun 2007 15:23:08 -0000	1.22
***************
*** 60,64 ****
  TO USE LAGAN:
  
!   my $lagan = new Bio::Tools::Run::Alignment::Lagan(@params);
    my $report_out = $lagan->lagan($seq1, $seq2);
  
--- 60,64 ----
  TO USE LAGAN:
  
!   my $lagan = Bio::Tools::Run::Alignment::Lagan->new(@params);
    my $report_out = $lagan->lagan($seq1, $seq2);
  
***************
*** 67,71 ****
  TO USE MLAGAN:
  
!   my $lagan = new Bio::Tools::Run::Alignment::Lagan();
    my $tree = "(($seqname1 $seqname2) $seqname3)";
    my @sequence_objs; 	#an array of bioperl Seq objects
--- 67,71 ----
  TO USE MLAGAN:
  
!   my $lagan = Bio::Tools::Run::Alignment::Lagan->new();
    my $tree = "(($seqname1 $seqname2) $seqname3)";
    my @sequence_objs; 	#an array of bioperl Seq objects

Index: Proda.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-run/Bio/Tools/Run/Alignment/Proda.pm,v
retrieving revision 1.3
retrieving revision 1.4
diff -C2 -d -r1.3 -r1.4
*** Proda.pm	15 Dec 2006 19:11:29 -0000	1.3
--- Proda.pm	14 Jun 2007 15:23:08 -0000	1.4
***************
*** 18,22 ****
  
    # Build a Proda alignment factory
!   $factory = new Bio::Tools::Run::Alignment::Proda(@params);
  
    # Pass the factory a list of sequences to be aligned.
--- 18,22 ----
  
    # Build a Proda alignment factory
!   $factory = Bio::Tools::Run::Alignment::Proda->new(@params);
  
    # Pass the factory a list of sequences to be aligned.
***************
*** 35,39 ****
    #See the DESCRIPTION section that follows for additional details.
  
!   $factory = new Bio::Tools::Run::Alignment::Proda();
    @alns = $factory->align($seq_array_ref);
  
--- 35,39 ----
    #See the DESCRIPTION section that follows for additional details.
  
!   $factory = Bio::Tools::Run::Alignment::Proda->new();
    @alns = $factory->align($seq_array_ref);
  



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