| Bio::Tools::Run::Phylo::Phylip::Base(3pm) | User Contributed Perl Documentation | Bio::Tools::Run::Phylo::Phylip::Base(3pm) |
Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules
# Do not use directly # This module is for setting basic data sets for the Phylip wrapper # modules
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
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
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.
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/
Email jason-at-bioperl.org
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
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 :
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)
Title : treefile
Usage : $obj->treefile($newval)
Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
Returns : value of treefile
Args : newvalue (optional)
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)
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)
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)
| 2023-01-22 | perl v5.36.0 |