Bio::TreeIO::nexus.3pm

Langue: en

Autres versions - même langue

Version: 2008-01-11 (mandriva - 01/05/08)

Section: 3 (Bibliothèques de fonctions)

Sommaire

NAME

Bio::TreeIO::nexus - A TreeIO driver module for parsing Nexus tree output from PAUP

SYNOPSIS

   use Bio::TreeIO;
   my $in = new Bio::TreeIO(-file => 't/data/cat_tre.tre');
   while( my $tree = $in->next_tree ) {
   }

DESCRIPTION

This is a driver module for parsing PAUP Nexus tree format which basically is just a remapping of trees.

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-open-bio-dot-org

APPENDIX

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

new

  Title   : new
  Args    : -header    => boolean  default is true 
                          print/do not print #NEXUS header
            -translate => boolean default is true
                          print/do not print Node Id translation to a number

next_tree

  Title   : next_tree
  Usage   : my $tree = $treeio->next_tree
  Function: Gets the next tree in the stream
  Returns : Bio::Tree::TreeI
  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

header

  Title   : header
  Usage   : $obj->header($newval)
  Function: 
  Example : 
  Returns : value of header (a scalar)
  Args    : on set, new value (a scalar or undef, optional)

translate_node

  Title   : translate_node
  Usage   : $obj->translate_node($newval)
  Function: 
  Example : 
  Returns : value of translate_node (a scalar)
  Args    : on set, new value (a scalar or undef, optional)