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Bio::TreeIO.3pm

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.

   bioperl-l@bioperl.org                  - General discussion
   http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
 
 

Support

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

bioperl-l@bioperl.org

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:

   http://bugzilla.open-bio.org/
 
 

AUTHOR - Jason Stajich

Email jason-at-bioperl-dot-org

CONTRIBUTORS

Allen Day <allenday@ucla.edu>

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
    -internal_node_id : what is stored in the internal node ids, 
                        bootstrap values or ids, coded as 
                        'bootstrap' or 'id'
 
 

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    :
 
 

newline_each_node

  Title   : newline_each_node
  Usage   : $obj->newline_each_node($newval)
  Function: Get/set newline each node flag which is only applicable
            for writing tree formats for nhx and newick, will
            print a newline after each node or paren
  Returns : value of newline_each_node (boolean)
  Args    : on set, new value (a boolean or undef, optional)
 
 

internal_node_id

  Title   : internal_node_id
  Usage   : $obj->internal_node_id($newval)
  Function: Internal Node Id type, coded as 'bootstrap' or 'id'
            Default is 'id'
  Returns : value of internal_node_id (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

_guess_format

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