Bio::Tools::Run::Phylo::Phylip::Base.3pm

Langue: en

Version: 2009-11-04 (ubuntu - 24/10/10)

Section: 3 (Bibliothèques de fonctions)

NAME

Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules

SYNOPSIS

# Do not use directly # This module is for setting basic data sets for the Phylip wrapper # modules

DESCRIPTION

This module is just a base object for Bioperl Phylip wrappers.

IMPORTANT PHYLIP VERSION ISSUES By default we assume you have Phylip 3.5 installed, if you have installed Phylip 3.6 you need to set the environment variable PHYLIPVERSION

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 - Jason Stajich

Email jason-at-bioperl.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::Tools::Run::Phylo::Phylip::Base->new();
  Function: Builds a new Bio::Tools::Run::Phylo::Phylip::Base object 
  Returns : an instance of Bio::Tools::Run::Phylo::Phylip::Base
  Args    :
 
 

outfile

  Title   : outfile
  Usage   : $obj->outfile($newval)
  Function: Get/Set default PHYLIP outfile name ('outfile' usually)
            Changing this is only necessary when you have compiled
            PHYLIP to use a different filename for the default 'outfile'
            This will not change the default output filename by 
            PHYLIP
  Returns : value of outfile
  Args    : newvalue (optional)
 
 

treefile

  Title   : treefile
  Usage   : $obj->treefile($newval)
  Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
  Returns : value of treefile
  Args    : newvalue (optional)
 
 

fontfile

  Title   : fontfile
  Usage   : $obj->fontfile($newval)
  Function: Get/Set the fontfile
  Returns : value of fontfile (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

plotfile

  Title   : plotfile
  Usage   : $obj->plotfile($newval)
  Function: Get/Set the plotfile
  Returns : value of plotfile (a scalar)
  Args    : on set, new value (a scalar or undef, optional)
 
 

version

  Title   : version
  Usage   : $obj->version($newval)
  Function: Get/Set the version
  Returns : value of version (a scalar)
  Args    : on set, new value (a scalar or undef, optional)