Bio::Tools::Run::Phylo::Phylip Base
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Summary
Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules
Package variables
No package variables defined.
Included modules
Bio::Root::Root
Bio::Tools::Run::Phylo::Phylip::PhylipConf
Bio::Tools::Run::WrapperBase
Inherit
Bio::Root::Root Bio::Tools::Run::WrapperBase
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
Methods
BEGIN(1) Code
BEGIN(2) Code
outfileDescriptionCode
treefileDescriptionCode
fontfileDescriptionCode
plotfileDescriptionCode
versionDescriptionCode
Methods description
outfilecode    nextTop
 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)
treefilecodeprevnextTop
 Title   : treefile
 Usage   : $obj->treefile($newval)
 Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
 Returns : value of treefile
 Args    : newvalue (optional)
fontfilecodeprevnextTop
 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)
plotfilecodeprevnextTop
 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)
versioncodeprevnextTop
 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)
Methods code
BEGIN(1)Top
BEGIN {
    eval { require File::Spec };
    if( $@) { Bio::Root::RootI->throw("Must have installed File::Spec to run Bio::Tools::Run::Phylo::Phylip tools");
}
BEGIN(2)Top
BEGIN {
    %DEFAULT = ( 
		 'VERSION'   => $ENV{'PHYLIPVERSION'} || '3.6',
		 );
    %FILENAME = %Bio::Tools::Run::Phylo::Phylip::PhylipConf::FileName;
}
outfiledescriptionprevnextTop
sub outfile {
   my $self = shift;
   $self->{'_outfile'} = shift if @_;
   return $self->{'_outfile'} || $FILENAME{$self->version}{'OUTFILE'}
}
treefiledescriptionprevnextTop
sub treefile {
   my $self = shift;
   $self->{'_treefile'} = shift if @_;
   return $self->{'_treefile'} || $FILENAME{$self->version}{'TREEFILE'};
}
fontfiledescriptionprevnextTop
sub fontfile {
    my $self = shift;

    return $self->{'fontfile'} = shift if @_;
    return $self->{'fontfile'} ;
}
plotfiledescriptionprevnextTop
sub plotfile {
    my $self = shift;

    return $self->{'plotfile'} = shift if @_;
    return $self->{'plotfile'} || $FILENAME{$self->version}{'PLOTFILE'};
}
versiondescriptionprevnextTop
sub version {
    my $self = shift;

    return $self->{'version'} = shift if @_;
    return $self->{'version'} || $DEFAULT{'VERSION'};
}
1;
}
General documentation
FEEDBACKTop
Mailing ListsTop
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 Top
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 BugsTop
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 StajichTop
Email jason-at-bioperl.org
APPENDIXTop
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
newTop
 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    :