Bio::Tools::Run::Phylo::PhyloBase(3pm) User Contributed Perl Documentation Bio::Tools::Run::Phylo::PhyloBase(3pm)
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 desribe 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 desribe 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
perl v5.12.3 2011-06-18 Bio::Tools::Run::Phylo::PhyloBase(3pm)