Linux Certif

Toute la documentation sur la certification Linux LPI

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://bugzilla.open-bio.org/
 
 

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