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lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm  view on Meta::CPAN

This can be a brittle module as the menus change in PHYLIP.  It should
support phylip 3.6 but no guarantees.

=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::DrawTree;
use vars qw($AUTOLOAD @ISA $PROGRAM $PROGRAMDIR $PROGRAMNAME
				$FONTFILE @DRAW_PARAMS @OTHER_SWITCHES
				%OK_FIELD %DEFAULT);
use strict;
# inherit from Phylip::Base which has some methods for dealing with
# Phylip specifics
use Bio::Tools::Run::Phylo::Phylip::Base;
use Cwd;

@ISA = qw( Bio::Tools::Run::Phylo::Phylip::Base );

use Bio::Tools::Run::Phylo::Phylip::PhylipConf qw(%Menu);

# You will need to enable the neighbor program. This
# can be done in (at least) 3 ways:
#
# 1. define an environmental variable PHYLIPDIR:
# export PHYLIPDIR=/home/shawnh/PHYLIP/bin
#
# 2. include a definition of an environmental variable PHYLIPDIR in
# every script that will use DrawTree.pm.
# $ENV{PHYLIPDIR} = '/home/shawnh/PHYLIP/bin';
#
# 3. You can set the path to the program through doing:
# my @params('program'=>'/usr/local/bin/drawgram');
# my $neighbor_factory = Bio::Tools::Run::Phylo::Phylip::DrawTree->new(@params)

BEGIN {
	%DEFAULT = ('PLOTTER' => 'P',
					'SCREEN'  => 'N');
	$DEFAULT{'FONTFILE'} = Bio::Root::IO->catfile($ENV{'PHYLIPDIR'},"font1") if $ENV{'PHYLIPDIR'};

	$PROGRAMNAME="drawtree";
	if (defined $ENV{'PHYLIPDIR'}) {
		$PROGRAMDIR = $ENV{'PHYLIPDIR'} || '';
		$PROGRAM = Bio::Root::IO->catfile($PROGRAMDIR,
													 $PROGRAMNAME.($^O =~ /mswin/i ?'.exe':''));	
		$DEFAULT{'FONTFILE'} = Bio::Root::IO->catfile($ENV{'PHYLIPDIR'},"font1");
	}
	else {
		$PROGRAM = $PROGRAMNAME;
	}

	@DRAW_PARAMS = qw(PLOTTER SCREEN LABEL_ANGLE ROTATION TREEARC
							ITERATE SCALE HORIZMARGINS VERTICALMARGINS FONT
						  );
	@OTHER_SWITCHES = qw(QUIET);
	foreach my $attr(@DRAW_PARAMS,@OTHER_SWITCHES) {
		$OK_FIELD{$attr}++;
	}
}

=head2 program_name

 Title   : program_name
 Usage   : $obj->program_name()
 Function: holds the program name
 Returns:  string
 Args    : None

=cut

sub program_name {
  return $PROGRAMNAME;
}

=head2 program_dir

 Title   : program_dir
 Usage   : $drawfact->program_dir()
 Function: returns the program directory, obtained from ENV variable.
 Returns :  string

lib/Bio/Tools/Run/Phylo/Phylip/DrawTree.pm  view on Meta::CPAN

    $self->throw("drawgram did not create plotfile correctly ($plotfile)")
	unless (-e $plotfile);    		
    return $plotfile;
}

=head2  _setinput()

 Title   :  _setinput
 Usage   :  Internal function, not to be called directly	
 Function:  Create input file for drawing program
 Example :
 Returns : filename containing tree in newick format
 Args    : Bio::Tree::TreeI object

=cut

sub _setinput {
    my ($self, $input) = @_;
    my $treefile;
    unless (ref $input) {
        # check that file exists or throw
        $treefile = $input;
        unless (-e $input) {return 0;}
	
    } elsif ($input->isa("Bio::Tree::TreeI")) {
        #  Open temporary file for both reading & writing of BioSeq array
	my $tfh;
	($tfh,$treefile) = $self->io->tempfile(-dir=>$self->tempdir);
	my $treeIO = Bio::TreeIO->new(-fh => $tfh, 
				      -format=>'newick');
	$treeIO->write_tree($input);
	$treeIO->close();
	close($tfh);
	undef $tfh;
    }
    return $treefile;
}

=head2  _setparams()

 Title   :  _setparams
 Usage   :  Internal function, not to be called directly	
 Function:   Create parameter inputs for drawgram program
 Example :
 Returns : parameter string to be passed to drawgram
 Args    : name of calling object

=cut



sub _setparams {
	my ($attr, $value, $self);

	#do nothing for now
	$self = shift;
	my $param_string = "";
	my $cat = 0;
	my ($hmargin,$vmargin);
	my %menu = %{$Menu{$self->version}->{'DRAWTREE'}};
	foreach  my $attr ( @DRAW_PARAMS) {	
		$value = $self->$attr();
		next unless defined $value;
		my @vals;
		if( ref($value) ) {
			($value,@vals) = @$value;
		}
		$attr = uc($attr);
		if( ! exists $menu{$attr} ) {
			$self->warn("unknown parameter $attr, known params are ". 
							join(",",keys %menu). "\n");
		}	
		if( ref ($menu{$attr}) !~ /HASH/i ) {
			unless( @vals ) {
				$param_string .= $menu{$attr};
			} else { 
				$param_string .= sprintf($menu{$attr},$value,@vals);
			}
			next;
		}
		my $seen = 0;
		for my $stype ( keys %{$menu{$attr}} ) {	    
			if( $value =~ /$stype/i ) {		
				$param_string .= sprintf($menu{$attr}->{$stype},@vals);	    
				$seen = 1;
				last;
			}		
		}
		unless( $seen ) {
			$self->warn("Unknown requested attribute $attr, $value is not known\n");
		}
	}
	$param_string .="Y\n";	
	return $param_string;
}


=head1 Bio::Tools::Run::Wrapper methods

=cut

=head2 no_param_checks

 Title   : no_param_checks
 Usage   : $obj->no_param_checks($newval)
 Function: Boolean flag as to whether or not we should
           trust the sanity checks for parameter values  
 Returns : value of no_param_checks
 Args    : newvalue (optional)


=cut

=head2 save_tempfiles

 Title   : save_tempfiles
 Usage   : $obj->save_tempfiles($newval)
 Function: 
 Returns : value of save_tempfiles
 Args    : newvalue (optional)