[Bioperl-guts-l] bioperl-live/Bio/Tree AlleleNode.pm, 1.16, 1.17 Compatible.pm, 1.7, 1.8 DistanceFactory.pm, 1.10, 1.11 Node.pm, 1.54, 1.55 NodeI.pm, 1.37, 1.38 NodeNHX.pm, 1.11, 1.12 RandomFactory.pm, 1.19, 1.20 Statistics.pm, 1.13, 1.14 Tree.pm, 1.23, 1.24 TreeFunctionsI.pm, 1.36, 1.37 TreeI.pm, 1.18, 1.19

Senduran Balasubramaniam sendu at dev.open-bio.org
Thu Jun 14 10:16:20 EDT 2007


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

Modified Files:
	AlleleNode.pm Compatible.pm DistanceFactory.pm Node.pm 
	NodeI.pm NodeNHX.pm RandomFactory.pm Statistics.pm Tree.pm 
	TreeFunctionsI.pm TreeI.pm 
Log Message:
removed bad "new Bio::Module" syntax, replaced with "Bio::Module->new"

Index: Compatible.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/Compatible.pm,v
retrieving revision 1.7
retrieving revision 1.8
diff -C2 -d -r1.7 -r1.8
*** Compatible.pm	26 Sep 2006 22:03:20 -0000	1.7
--- Compatible.pm	14 Jun 2007 14:16:18 -0000	1.8
***************
*** 20,24 ****
    use Bio::Tree::Compatible;
    use Bio::TreeIO;
!   my $input = new Bio::TreeIO('-format' => 'newick',
                                '-file'   => 'input.tre');
    my $t1 = $input->next_tree;
--- 20,24 ----
    use Bio::Tree::Compatible;
    use Bio::TreeIO;
!   my $input = Bio::TreeIO->new('-format' => 'newick',
                                '-file'   => 'input.tre');
    my $t1 = $input->next_tree;

Index: Node.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/Node.pm,v
retrieving revision 1.54
retrieving revision 1.55
diff -C2 -d -r1.54 -r1.55
*** Node.pm	12 Dec 2006 19:43:07 -0000	1.54
--- Node.pm	14 Jun 2007 14:16:18 -0000	1.55
***************
*** 18,26 ****
  
      use Bio::Tree::Node;
!     my $nodeA = new Bio::Tree::Node();
!     my $nodeL = new Bio::Tree::Node();
!     my $nodeR = new Bio::Tree::Node();
  
!     my $node = new Bio::Tree::Node();
      $node->add_Descendent($nodeL);
      $node->add_Descendent($nodeR);
--- 18,26 ----
  
      use Bio::Tree::Node;
!     my $nodeA = Bio::Tree::Node->new();
!     my $nodeL = Bio::Tree::Node->new();
!     my $nodeR = Bio::Tree::Node->new();
  
!     my $node = Bio::Tree::Node->new();
      $node->add_Descendent($nodeL);
      $node->add_Descendent($nodeR);
***************
*** 85,89 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tree::Node();
   Function: Builds a new Bio::Tree::Node object
   Returns : Bio::Tree::Node
--- 85,89 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tree::Node->new();
   Function: Builds a new Bio::Tree::Node object
   Returns : Bio::Tree::Node

Index: NodeI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/NodeI.pm,v
retrieving revision 1.37
retrieving revision 1.38
diff -C2 -d -r1.37 -r1.38
*** NodeI.pm	12 Dec 2006 19:43:07 -0000	1.37
--- NodeI.pm	14 Jun 2007 14:16:18 -0000	1.38
***************
*** 21,25 ****
      use Bio::TreeIO;
      # read in a clustalw NJ in phylip/newick format
!     my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'file.dnd');
  
      my $tree = $treeio->next_tree; # we'll assume it worked for demo purposes
--- 21,25 ----
      use Bio::TreeIO;
      # read in a clustalw NJ in phylip/newick format
!     my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'file.dnd');
  
      my $tree = $treeio->next_tree; # we'll assume it worked for demo purposes

Index: Statistics.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/Statistics.pm,v
retrieving revision 1.13
retrieving revision 1.14
diff -C2 -d -r1.13 -r1.14
*** Statistics.pm	26 Sep 2006 22:03:21 -0000	1.13
--- Statistics.pm	14 Jun 2007 14:16:18 -0000	1.14
***************
*** 75,79 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tree::Statistics();
   Function: Builds a new Bio::Tree::Statistics object 
   Returns : Bio::Tree::Statistics
--- 75,79 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tree::Statistics->new();
   Function: Builds a new Bio::Tree::Statistics object 
   Returns : Bio::Tree::Statistics

Index: DistanceFactory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/DistanceFactory.pm,v
retrieving revision 1.10
retrieving revision 1.11
diff -C2 -d -r1.10 -r1.11
*** DistanceFactory.pm	2 Oct 2006 04:06:17 -0000	1.10
--- DistanceFactory.pm	14 Jun 2007 14:16:18 -0000	1.11
***************
*** 98,102 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tree::DistanceFactory();
   Function: Builds a new Bio::Tree::DistanceFactory object 
   Returns : an instance of Bio::Tree::DistanceFactory
--- 98,102 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tree::DistanceFactory->new();
   Function: Builds a new Bio::Tree::DistanceFactory object 
   Returns : an instance of Bio::Tree::DistanceFactory

Index: NodeNHX.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/NodeNHX.pm,v
retrieving revision 1.11
retrieving revision 1.12
diff -C2 -d -r1.11 -r1.12
*** NodeNHX.pm	26 Sep 2006 22:03:21 -0000	1.11
--- NodeNHX.pm	14 Jun 2007 14:16:18 -0000	1.12
***************
*** 18,26 ****
  
      use Bio::Tree::NodeNHX;
!     my $nodeA = new Bio::Tree::NodeNHX();
!     my $nodeL = new Bio::Tree::NodeNHX();
!     my $nodeR = new Bio::Tree::NodeNHX();
  
!     my $node = new Bio::Tree::NodeNHX();
      $node->add_Descendents($nodeL);
      $node->add_Descendents($nodeR);
--- 18,26 ----
  
      use Bio::Tree::NodeNHX;
!     my $nodeA = Bio::Tree::NodeNHX->new();
!     my $nodeL = Bio::Tree::NodeNHX->new();
!     my $nodeR = Bio::Tree::NodeNHX->new();
  
!     my $node = Bio::Tree::NodeNHX->new();
      $node->add_Descendents($nodeL);
      $node->add_Descendents($nodeR);
***************
*** 82,86 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tree::NodeNHX();
   Function: Builds a new Bio::Tree::NodeNHX object
   Returns : Bio::Tree::NodeNHX
--- 82,86 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tree::NodeNHX->new();
   Function: Builds a new Bio::Tree::NodeNHX object
   Returns : Bio::Tree::NodeNHX

Index: TreeI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/TreeI.pm,v
retrieving revision 1.18
retrieving revision 1.19
diff -C2 -d -r1.18 -r1.19
*** TreeI.pm	26 Sep 2006 22:03:21 -0000	1.18
--- TreeI.pm	14 Jun 2007 14:16:18 -0000	1.19
***************
*** 20,24 ****
    # get a Bio::Tree::TreeI somehow
    # like from a TreeIO
!   my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'treefile.dnd');
    my $tree   = $treeio->next_tree;
    my @nodes  = $tree->get_nodes;
--- 20,24 ----
    # get a Bio::Tree::TreeI somehow
    # like from a TreeIO
!   my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd');
    my $tree   = $treeio->next_tree;
    my @nodes  = $tree->get_nodes;

Index: TreeFunctionsI.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/TreeFunctionsI.pm,v
retrieving revision 1.36
retrieving revision 1.37
diff -C2 -d -r1.36 -r1.37
*** TreeFunctionsI.pm	12 May 2007 22:58:07 -0000	1.36
--- TreeFunctionsI.pm	14 Jun 2007 14:16:18 -0000	1.37
***************
*** 18,22 ****
  
    use Bio::TreeIO;
!   my $in = new Bio::TreeIO(-format => 'newick', -file => 'tree.tre');
  
    my $tree = $in->next_tree;
--- 18,22 ----
  
    use Bio::TreeIO;
!   my $in = Bio::TreeIO->new(-format => 'newick', -file => 'tree.tre');
  
    my $tree = $in->next_tree;
***************
*** 883,887 ****
         $og_ancestor = $og_ancestor->ancestor;
     }
!    my $tree = new Bio::Tree::Tree(-root     => $clade_root,
  				  -nodelete => 1);
  
--- 883,887 ----
         $og_ancestor = $og_ancestor->ancestor;
     }
!    my $tree = Bio::Tree::Tree->new(-root     => $clade_root,
  				  -nodelete => 1);
  

Index: AlleleNode.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/AlleleNode.pm,v
retrieving revision 1.16
retrieving revision 1.17
diff -C2 -d -r1.16 -r1.17
*** AlleleNode.pm	12 Dec 2006 19:43:07 -0000	1.16
--- AlleleNode.pm	14 Jun 2007 14:16:18 -0000	1.17
***************
*** 84,88 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tree::AlleleNode();
   Function: Builds a new Bio::Tree::AlleleNode() object 
   Returns : an instance of Bio::Tree::AlleleNode
--- 84,88 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tree::AlleleNode->new();
   Function: Builds a new Bio::Tree::AlleleNode() object 
   Returns : an instance of Bio::Tree::AlleleNode

Index: RandomFactory.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/RandomFactory.pm,v
retrieving revision 1.19
retrieving revision 1.20
diff -C2 -d -r1.19 -r1.20
*** RandomFactory.pm	26 Sep 2006 22:03:21 -0000	1.19
--- RandomFactory.pm	14 Jun 2007 14:16:18 -0000	1.20
***************
*** 19,28 ****
    use Bio::Tree::RandomFactory
    my @taxonnames;
!   my $factory = new Bio::Tree::RandomFactory( -taxa => \@taxonnames,
    					      -maxcount => 10);
  
    # or for anonymous samples
  
!   my $factory = new Bio::Tree::RandomFactory( -num_taxa => 6,
  					      -maxcount => 50);
  
--- 19,28 ----
    use Bio::Tree::RandomFactory
    my @taxonnames;
!   my $factory = Bio::Tree::RandomFactory->new( -taxa => \@taxonnames,
    					      -maxcount => 10);
  
    # or for anonymous samples
  
!   my $factory = Bio::Tree::RandomFactory->new( -num_taxa => 6,
  					      -maxcount => 50);
  
***************
*** 110,114 ****
  
   Title   : new
!  Usage   : my $factory = new Bio::Tree::RandomFactory(-samples => \@samples,
  						      -maxcount=> $N);
   Function: Initializes a Bio::Tree::RandomFactory object
--- 110,114 ----
  
   Title   : new
!  Usage   : my $factory = Bio::Tree::RandomFactory->new(-samples => \@samples,
  						      -maxcount=> $N);
   Function: Initializes a Bio::Tree::RandomFactory object

Index: Tree.pm
===================================================================
RCS file: /home/repository/bioperl/bioperl-live/Bio/Tree/Tree.pm,v
retrieving revision 1.23
retrieving revision 1.24
diff -C2 -d -r1.23 -r1.24
*** Tree.pm	26 Sep 2006 22:03:21 -0000	1.23
--- Tree.pm	14 Jun 2007 14:16:18 -0000	1.24
***************
*** 18,22 ****
  
      # like from a TreeIO
!     my $treeio = new Bio::TreeIO(-format => 'newick', -file => 'treefile.dnd');
      my $tree = $treeio->next_tree;
      my @nodes = $tree->get_nodes;
--- 18,22 ----
  
      # like from a TreeIO
!     my $treeio = Bio::TreeIO->new(-format => 'newick', -file => 'treefile.dnd');
      my $tree = $treeio->next_tree;
      my @nodes = $tree->get_nodes;
***************
*** 78,82 ****
  
   Title   : new
!  Usage   : my $obj = new Bio::Tree::Tree();
   Function: Builds a new Bio::Tree::Tree object 
   Returns : Bio::Tree::Tree
--- 78,82 ----
  
   Title   : new
!  Usage   : my $obj = Bio::Tree::Tree->new();
   Function: Builds a new Bio::Tree::Tree object 
   Returns : Bio::Tree::Tree



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