Reference

Bio::TreeIO(3pm)

Parser for Tree files

NAME

Bio::TreeIO - Parser for Tree files

SYNOPSIS

  {
      use Bio::TreeIO;
      my $treeio = Bio::TreeIO->new(-format => 'newick',
                                    -file   => 'globin.dnd');
      while( my $tree = $treeio->next_tree ) {
                print "Tree is ", $tree->number_nodes, "\n";
      }
  }

DESCRIPTION

This is the driver module for Tree reading from data streams and flatfiles. This is intended to be able to create Bio::Tree::TreeI objects.

FEEDBACK

Mailing Lists

User feedback is an integral part of the evolution of this and other Bioperl modules. Send your comments and suggestions preferably to the Bioperl mailing list. Your participation is much appreciated.

  [email protected]                  - General discussion
  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists

Support

Please direct usage questions or support issues to the mailing list:

[email protected]

rather than to the module maintainer directly. Many experienced and reponsive experts will be able look at the problem and quickly address it. Please include a thorough description of the problem with code and data examples if at all possible.

Reporting Bugs

Report bugs to the Bioperl bug tracking system to help us keep track of the bugs and their resolution. Bug reports can be submitted via the web:

  https://github.com/bioperl/bioperl-live/issues

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

CONTRIBUTORS

Allen Day <[email protected]>

APPENDIX

The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

new

 Title   : new
 Usage   : my $obj = Bio::TreeIO->new();
 Function: Builds a new Bio::TreeIO object 
 Returns : Bio::TreeIO
 Args    : a hash.  useful keys:
   -format : Specify the format of the file.  Supported formats:
     newick             Newick tree format
     nexus              Nexus tree format
     nhx                NHX tree format
     svggraph           SVG graphical representation of tree
     tabtree            ASCII text representation of tree
     lintree            lintree output format

format

 Title   : format
 Usage   : $format = $obj->format()
 Function: Get the tree format
 Returns : tree format
 Args    : none

next_tree

 Title   : next_tree
 Usage   : my $tree = $treeio->next_tree;
 Function: Gets the next tree off the stream
 Returns : Bio::Tree::TreeI or undef if no more trees
 Args    : none

write_tree

 Title   : write_tree
 Usage   : $treeio->write_tree($tree);
 Function: Writes a tree onto the stream
 Returns : none
 Args    : Bio::Tree::TreeI

attach_EventHandler

 Title   : attach_EventHandler
 Usage   : $parser->attatch_EventHandler($handler)
 Function: Adds an event handler to listen for events
 Returns : none
 Args    : Bio::Event::EventHandlerI

_eventHandler

 Title   : _eventHandler
 Usage   : private
 Function: Get the EventHandler
 Returns : Bio::Event::EventHandlerI
 Args    : none

_load_format_module

 Title   : _load_format_module
 Usage   : *INTERNAL TreeIO stuff*
 Function: Loads up (like use) a module at run time on demand
 Example :
 Returns :
 Args    :

_guess_format

 Title   : _guess_format
 Usage   : $obj->_guess_format($filename)
 Function:
 Example :
 Returns : guessed format of filename (lower case)
 Args    :

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