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 3.6
installed, if you have installed Phylip 3.5 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://redmine.open-bio.org/projects/bioperl/
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)