Bio::TreeIO::cluster.3pm

Langue: en

Version: 2010-05-19 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::TreeIO::cluster - A TreeIO driver module for parsing Algorithm::Cluster::treecluster() output

SYNOPSIS

   # do not use this module directly
   use Bio::TreeIO;
   use Algorithm::Cluster;
   my ($result, $linkdist) = Algorithm::Cluster::treecluster(
     distances => $matrix
   );
   my $treeio = Bio::TreeIO->new(
     -format   => 'cluster',
     -result   =>  $result,
     -linkdist =>  $linkdist,
     -labels   =>  $labels
   );
   my $tree = $treeio->next_tree;
 
 

DESCRIPTION

This is a driver module for parsing Algorithm::Cluster::treecluster() output.

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 - Guillaume Rousse

Email Guillaume-dot-Rousse-at-inria-dot-fr

CONTRIBUTORS

Jason Stajich - jason-at-bioperl-dot-org

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::cluster->new();
  Function: Builds a new Bio::TreeIO::cluster object for reading Algorithm::Cluster::treecluster output
  Returns : Bio::TreeIO::cluster
  Args    :-result   => Algorithm::Cluster result
           -linkdist => distance between links
           -labels   => node labels
 
 

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   :
  Function: Sorry not possible with this format
  Returns : none
  Args    : none