bio::tools::run::phylo::phylip::phylipconf(3pm) [debian man page]
Bio::Tools::Run::Phylo::Phylip::PhylipConf(3pm) User Contributed Perl Documentation Bio::Tools::Run::Phylo::Phylip::PhylipConf(3pm)NAME
Bio::Tools::Run::Phylo::Phylip::PhylipConf
SYNOPSIS
use Bio::Tools::Run::Phylo::Phylip::PhylipConf;
my %menu = %{$Bio::Tools::Run::Phylo::Phylip::PhylipConf::Menu->{$version}->{'PROTDIST'}};
DESCRIPTION
A configuration for managing menu configuration differences between version 3.5 and 3.6
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 one
of the Bioperl mailing lists. 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 the bugs and their resolution. Bug reports can be submitted via the
web:
http://redmine.open-bio.org/projects/bioperl/
AUTHOR - Shawn Hoon
Email shawnh@fugu-sg.org
CONTRIBUTORS
Email:jason-at-bioperl.org
APPENDIX
The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _
perl v5.12.3 2011-06-18 Bio::Tools::Run::Phylo::Phylip::PhylipConf(3pm)
Check Out this Related Man Page
Bio::Tools::Run::Phylo::Phylip::Base(3pm) User Contributed Perl Documentation Bio::Tools::Run::Phylo::Phylip::Base(3pm)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)
perl v5.12.3 2011-06-18 Bio::Tools::Run::Phylo::Phylip::Base(3pm)