/ 
bioperl-1.5.2_004-RCf
/ Bio::TreeIO

NAME

Bio::TreeIO - Parser for Tree files

SYNOPSIS

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

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 = new Bio::TreeIO();
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

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)

_guess_format

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