/ 
BioPerl-1.7.8
River stage two • 61 direct dependents • 66 total dependents
/ Bio::Tools::Run::Phylo::PhyloBase

NAME

Bio::Tools::Run::Phylo::PhyloBase- base module for phylo wrappers

SYNOPSIS

use base qw(Bio::Tools::Run::Phylo::PhyloBase);

DESCRIPTION

For use by Bio::Tools::Run::Phylo modules as a base in place of Bio::Tools::Run::WrapperBase.

This is based on WrapperBase but provides additional phylo-related private helper subs.

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://redmine.open-bio.org/projects/bioperl/

AUTHOR - Sendu Bala

Email bix@sendu.me.uk

APPENDIX

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

_alignment

Title   : _alignment
Usage   : $aln = $obj->_alignment()
Function: Get/set an alignment object, generating one from a file if desired.
Returns : Bio::Align::AlignI (probably a Bio::SimpleAlign)
Args    : none to get
          OR filename & input format of the alignment file (latter defaults to
          guess) to set from file
          OR Bio::Align::AlignI to set

_write_alignment

Title   : _write_alignment
Usage   : $obj->_write_alignment()
Function: Writes the alignment object returned by _alignment() out in the
          desired format to a temp file.
Returns : filename
Args    : string to describe format (default 'fasta'), any other options to pass
          to AlignIO

_tree

Title   : _tree
Usage   : $tree = $obj->_tree()
Function: Get/set a tree object, generating one from a file/database if desired
Returns : Bio::Tree::TreeI
Args    : none to get, OR to set:
          OR filename & input format of the tree file (latter defaults to
          guess) to set from file
          OR Bio::Tree::TreeI
          OR Bio::DB::Taxonomy when _alignment() has been set and where
          sequences in the alignment have ids matching species in the taxonomy
          database

_write_tree

Title   : _write_tree
Usage   : $obj->_write_tree()
Function: Writes the tree object returned by _tree() out in the desired format
          to a temp file.
Returns : filename
Args    : string to describe format (default 'newick')

_get_seq_names

Title   : _get_seq_names
Usage   : @names = $obj->_get_seq_names()
Function: Get all the sequence names (from id()) of the sequenes in the
          alignment.  _alignment() must be set prior to calling this.
Returns : list of strings (seq ids)
Args    : none

_get_node_names

Title   : _get_node_names
Usage   : @names = $obj->_get_node_names()
Function: Get all the node names (from id()) of the nodes in the tree.
          _tree must be set prior to calling this.
Returns : list of strings (node ids)
Args    : none

_check_names

Title   : _check_names
Usage   : if ($obj->_check_names) { ... }
Function: Determine if all sequences in the alignment file have a corresponding
          node in the tree file. _alignment() and _tree() must be set
          prior to calling this.
Returns : boolean (will also warn about the specific problems when returning
          false)
Args    : none