/usr/share/perl5/Bio/Tools/Run/Phylo/Phylip/Base.pm is in libbio-perl-run-perl 1.6.9-2.
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#
# BioPerl module for Bio::Tools::Run::Phylo::Phylip::Base
#
# Please direct questions and support issues to <bioperl-l@bioperl.org>
#
# Cared for by Jason Stajich <jason-AT-bioperl_DOT_org>
#
# Copyright Jason Stajich
#
# You may distribute this module under the same terms as perl itself
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules
=head1 SYNOPSIS
# Do not use directly
# This module is for setting basic data sets for the Phylip wrapper
# modules
=head1 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
=head1 FEEDBACK
=head2 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
=head2 Support
Please direct usage questions or support issues to the mailing list:
I<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.
=head2 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/
=head1 AUTHOR - Jason Stajich
Email jason-at-bioperl.org
=head1 APPENDIX
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
=cut
# Let the code begin...
package Bio::Tools::Run::Phylo::Phylip::Base;
use vars qw(@ISA %DEFAULT %FILENAME);
use strict;
BEGIN {
eval { require File::Spec };
if( $@) { Bio::Root::RootI->throw("Must have installed File::Spec to run Bio::Tools::Run::Phylo::Phylip tools");
}
}
use Bio::Root::Root;
use Bio::Tools::Run::WrapperBase;
use Bio::Tools::Run::Phylo::Phylip::PhylipConf;
@ISA = qw(Bio::Root::Root Bio::Tools::Run::WrapperBase);
BEGIN {
%DEFAULT = (
'VERSION' => $ENV{'PHYLIPVERSION'} || '3.6',
);
%FILENAME = %Bio::Tools::Run::Phylo::Phylip::PhylipConf::FileName;
}
=head2 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 :
=cut
=head2 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)
=cut
sub outfile{
my $self = shift;
$self->{'_outfile'} = shift if @_;
return $self->{'_outfile'} || $FILENAME{$self->version}{'OUTFILE'}
}
=head2 treefile
Title : treefile
Usage : $obj->treefile($newval)
Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
Returns : value of treefile
Args : newvalue (optional)
=cut
sub treefile{
my $self = shift;
$self->{'_treefile'} = shift if @_;
return $self->{'_treefile'} || $FILENAME{$self->version}{'TREEFILE'};
}
=head2 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)
=cut
sub fontfile{
my $self = shift;
return $self->{'fontfile'} = shift if @_;
return $self->{'fontfile'} ;
}
=head2 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)
=cut
sub plotfile {
my $self = shift;
return $self->{'plotfile'} = shift if @_;
return $self->{'plotfile'} || $FILENAME{$self->version}{'PLOTFILE'};
}
=head2 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)
=cut
sub version {
my $self = shift;
return $self->{'version'} = shift if @_;
return $self->{'version'} || $DEFAULT{'VERSION'};
}
1;
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