Bio/Tools/Run/Phylo/Phylip/Base.pm

   1 # $Id $
   2 #
   3 # BioPerl module for Bio::Tools::Run::Phylo::Phylip::Base
   4 #
   5 # Cared for by Jason Stajich <jason@bioperl.org>
   6 #
   7 # Copyright Jason Stajich
   8 #
   9 # You may distribute this module under the same terms as perl itself
  10
  11 # POD documentation - main docs before the code
  12
  13 =head1 NAME
  14
  15 Bio::Tools::Run::Phylo::Phylip::Base - Base object for Phylip modules
  16
  17 =head1 SYNOPSIS
  18
  19 # Do not use directly
  20 # This module is for setting basic data sets for the Phylip wrapper
  21 # modules
  22
  23 =head1 DESCRIPTION
  24
  25 This module is just a base object for Bioperl Phylip wrappers.
  26
  27 IMPORTANT PHYLIP VERSION ISSUES
  28 By default we assume you have Phylip 3.5 installed, if you
  29 have installed Phylip 3.6 you need to set the environment variable
  30 PHYLIPVERSION
  31
  32
  33 =head1 FEEDBACK
  34
  35 =head2 Mailing Lists
  36
  37 User feedback is an integral part of the evolution of this and other
  38 Bioperl modules. Send your comments and suggestions preferably to
  39 the Bioperl mailing list.  Your participation is much appreciated.
  40
  41   bioperl-l@bioperl.org              - General discussion
  42   http://bioperl.org/MailList.shtml  - About the mailing lists
  43
  44 =head2 Reporting Bugs
  45
  46 Report bugs to the Bioperl bug tracking system to help us keep track
  47 of the bugs and their resolution. Bug reports can be submitted via
  48 email or the web:
  49
  50   bioperl-bugs@bioperl.org
  51   http://bugzilla.bioperl.org/bioperl-bugs/
  52
  53 =head1 AUTHOR - Jason Stajich
  54
  55 Email jason@bioperl.org
  56
  57 Describe contact details here
  58
  59 =head1 CONTRIBUTORS
  60
  61 Additional contributors names and emails here
  62
  63 =head1 APPENDIX
  64
  65 The rest of the documentation details each of the object methods.
  66 Internal methods are usually preceded with a _
  67
  68 =cut
  69
  70
  71 # Let the code begin...
  72
  73
  74 package Bio::Tools::Run::Phylo::Phylip::Base;
  75 use vars qw(@ISA %DEFAULT %FILENAME);
  76 use strict;
  77
  78 BEGIN {
  79     eval { require File::Spec };
  80     if( $@) { Bio::Root::RootI->throw("Must have installed File::Spec to run Bio::Tools::Run::Phylo::Phylip tools");
  81   }
  82
  83 }
  84
  85 use Bio::Root::Root;
  86 use Bio::Tools::Run::WrapperBase;
  87 use Bio::Tools::Run::Phylo::Phylip::PhylipConf;
  88 @ISA = qw(Bio::Root::Root  Bio::Tools::Run::WrapperBase);
  89
  90 BEGIN {
  91     %DEFAULT = (
  92      'VERSION'   => $ENV{'PHYLIPVERSION'} || '3.5',
  93                  );
  94     %FILENAME = %Bio::Tools::Run::Phylo::Phylip::PhylipConf::FileName;
  95 }
  96
  97 =head2 new
  98
  99  Title   : new
 100  Usage   : my $obj = new Bio::Tools::Run::Phylo::Phylip::Base();
 101  Function: Builds a new Bio::Tools::Run::Phylo::Phylip::Base object
 102  Returns : an instance of Bio::Tools::Run::Phylo::Phylip::Base
 103  Args    :
 104
 105 =cut
 106
 107 =head2 outfile
 108
 109  Title   : outfile
 110  Usage   : $obj->outfile($newval)
 111  Function: Get/Set default PHYLIP outfile name ('outfile' usually)
 112            Changing this is only necessary when you have compiled
 113            PHYLIP to use a different filename for the default 'outfile'
 114            This will not change the default output filename by
 115            PHYLIP
 116  Returns : value of outfile
 117  Args    : newvalue (optional)
 118
 119
 120 =cut
 121
 122 sub outfile{
 123    my $self = shift;
 124    $self->{'_outfile'} = shift if @_;
 125    return $self->{'_outfile'} || $FILENAME{$self->version}{'OUTFILE'}
 126 }
 127
 128
 129 =head2 treefile
 130
 131  Title   : treefile
 132  Usage   : $obj->treefile($newval)
 133  Function: Get/Set the default PHYLIP treefile name ('treefile' usually)
 134  Returns : value of treefile
 135  Args    : newvalue (optional)
 136
 137
 138 =cut
 139
 140 sub treefile{
 141    my $self = shift;
 142    $self->{'_treefile'} = shift if @_;
 143    return $self->{'_treefile'} || $FILENAME{$self->version}{'TREEFILE'};
 144 }
 145
 146
 147 =head2 fontfile
 148
 149  Title   : fontfile
 150  Usage   : $obj->fontfile($newval)
 151  Function: Get/Set the fontfile
 152  Returns : value of fontfile (a scalar)
 153  Args    : on set, new value (a scalar or undef, optional)
 154
 155
 156 =cut
 157
 158 sub fontfile{
 159     my $self = shift;
 160
 161     return $self->{'fontfile'} = shift if @_;
 162     return $self->{'fontfile'} ;
 163 }
 164
 165 =head2 plotfile
 166
 167  Title   : plotfile
 168  Usage   : $obj->plotfile($newval)
 169  Function: Get/Set the plotfile
 170  Returns : value of plotfile (a scalar)
 171  Args    : on set, new value (a scalar or undef, optional)
 172
 173
 174 =cut
 175
 176 sub plotfile {
 177     my $self = shift;
 178
 179     return $self->{'plotfile'} = shift if @_;
 180     return $self->{'plotfile'} || $FILENAME{$self->version}{'PLOTFILE'};
 181 }
 182
 183 =head2 version
 184
 185  Title   : version
 186  Usage   : $obj->version($newval)
 187  Function: Get/Set the version
 188  Returns : value of version (a scalar)
 189  Args    : on set, new value (a scalar or undef, optional)
 190
 191
 192 =cut
 193
 194 sub version {
 195     my $self = shift;
 196
 197     return $self->{'version'} = shift if @_;
 198     return $self->{'version'} || $DEFAULT{'VERSION'};
 199 }
 200 1;