Bio::Tools::Run::Phylo::Phylip DrawTree
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Summary
Bio::Tools::Run::Phylo::Phylip::DrawTree - use Phylip DrawTree
program to draw trees
Package variables
No package variables defined.
Included modules
Bio::Tools::Run::Phylo::Phylip::Base
Bio::Tools::Run::Phylo::Phylip::PhylipConf qw ( %Menu )
Cwd
Inherit
Bio::Tools::Run::Phylo::Phylip::Base
Synopsis
  use Bio::Tools::Run::Phylo::Phylip::DrawTree;
my $treedraw = Bio::Tools::Run::Phylo::Phylip::DrawTree->new(); my $treeimagefile = $drawfact->run($tree);
Description
This is a module for automating drawing of trees through Joe
Felsenstein's Phylip suite.
To set parameters with option you need to pass in an array reference or
a string, depending on the parameter. For example:
  $treedraw->HORIZMARGINS(['2.00','2.5']);
$treedraw->ANCESTRALNODES('C');
$treedraw->TREESTYLE('PHEN');
$treedraw->USEBRANCHLENS('N');
This can be a brittle module as the menus change in PHYLIP. It should
support phylip 3.6 but no guarantees.
Methods
BEGIN Code
program_nameDescriptionCode
program_dirDescriptionCode
newDescriptionCode
AUTOLOAD
No description
Code
runDescriptionCode
draw_treeDescriptionCode
_runDescriptionCode
_setinputDescriptionCode
_setparamsDescriptionCode
Methods description
program_namecode    nextTop
 Title   : program_name
Usage : $obj->program_name()
Function: holds the program name
Returns: string
Args : None
program_dircodeprevnextTop
 Title   : program_dir
Usage : $drawfact->program_dir()
Function: returns the program directory, obtained from ENV variable.
Returns : string
Args :
newcodeprevnextTop
 Title   : new
Usage : my $obj = Bio::Tools::Run::Phylo::Phylip::DrawTree->new();
Function: Builds a new Bio::Tools::Run::Phylo::Phylip::DrawTree object
Returns : an instance of Bio::Tools::Run::Phylo::Phylip::DrawTree
Args : The available DrawGram parameters
runcodeprevnextTop
 Title   : run
Usage : my $file = $app->run($treefile);
Function: Draw a tree
Returns : File containing the rendered tree
Args : either a Bio::Tree::TreeI
OR
filename of a tree in newick format
draw_treecodeprevnextTop
 Title   : draw_tree
Usage : my $file = $app->draw_tree($treefile);
Function: This method is deprecated. Please use run method.
Returns : File containing the rendered tree
Args : either a Bio::Tree::TreeI
OR
filename of a tree in newick format
_runcodeprevnextTop
 Title   :  _run
Usage : Internal function, not to be called directly
Function: makes actual system call to drawgram program
Example :
Returns : Bio::Tree object
Args : Name of a file the tree to draw in newick format
and a parameter string to be passed to drawgram
_setinput()codeprevnextTop
 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
_setparams()codeprevnextTop
 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
Methods code
BEGINTop
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}++;
}
program_namedescriptionprevnextTop
sub program_name {
  return $PROGRAMNAME;
}
program_dirdescriptionprevnextTop
sub program_dir {
  return Bio::Root::IO->catfile($ENV{PHYLIPDIR}) if $ENV{PHYLIPDIR};
}
newdescriptionprevnextTop
sub new {
  my($class,@args) = @_;

  my $self = $class->SUPER::new(@args);
  
  my ($attr, $value);
  
  while (@args)  {
	  $attr =   shift @args;
	  $value =  shift @args;
	  next if( $attr =~ /^-/ ); # don't want named parameters
if ($attr =~/PROGRAM/i) { $self->executable($value); next; } $self->$attr($value); } $self->plotter($DEFAULT{'PLOTTER'}) unless $self->plotter; $self->screen($DEFAULT{'SCREEN'}) unless $self->screen; $self->fontfile($DEFAULT{'FONTFILE'}) unless $self->fontfile; return $self;
}
AUTOLOADdescriptionprevnextTop
sub AUTOLOAD {
    my $self = shift;
    my $attr = $AUTOLOAD;
    $attr =~ s/.*:://;
    $attr = uc $attr;
    $self->throw("Unallowed parameter: $attr !") unless $OK_FIELD{$attr};
    $self->{$attr} = shift if @_;
    return $self->{$attr};
}
rundescriptionprevnextTop
sub run {
   my ($self,$input) = @_;
   
   # Create input file pointer
my ($infilename) = $self->_setinput($input); if (!$infilename) { $self->throw("Problems setting up for drawgram. Probably bad input data in $input !"); } # Create parameter string to pass to neighbor program
my $param_string = $self->_setparams(); # run drawgram
my $plotfile = $self->_run($infilename,$param_string); return $plotfile;
}
draw_treedescriptionprevnextTop
sub draw_tree {
	return shift->run(@_);
}
_rundescriptionprevnextTop
sub _run {
    my ($self,$infile,$param_string) = @_;
    my $instring;
    my $curpath = cwd;
    
    unless( File::Spec->file_name_is_absolute($infile) ) {
	$infile = $self->io->catfile($curpath,$infile);
    }
    $instring = $infile . "\n";
    if( ! defined $self->fontfile ) { 
	$self->throw("You must have defined a fontfile");
    }

    if( -e $self->io->catfile($curpath,'fontfile') ) {
	$instring .= $self->io->catfile($curpath,'fontfile')."\n";
    } elsif( File::Spec->file_name_is_absolute($self->fontfile) ) {	 
	#$instring .= $self->io->catfile($self->tempdir,$self->fontfile)."\n";
$instring .= $self->io->catfile($self->fontfile)."\n"; } else { $instring .= $self->io->catfile($curpath,$self->fontfile)."\n"; } chdir($self->tempdir); $instring .= $param_string; $self->debug( "Program ".$self->executable." $param_string\n"); # open a pipe to run drawgram to bypass interactive menus
if ($self->quiet() || $self->verbose() < 0) { open(DRAW,"|".$self->executable.">/dev/null"); } else { open(DRAW,"|".$self->executable); } print DRAW $instring; close(DRAW); chdir($curpath); #get the results
my $plotfile = $self->io->catfile($self->tempdir,$self->plotfile); $self->throw("drawgram did not create plotfile correctly ($plotfile)") unless (-e $plotfile); return $plotfile;
}
_setinputdescriptionprevnextTop
sub _setinput {
    my ($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 $treefile;
}
_setparamsdescriptionprevnextTop
sub _setparams {
	my ($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;
}
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://bugzilla.open-bio.org/
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 _
Bio::Tools::Run::Wrapper methodsTop
no_param_checksTop
 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)
save_tempfilesTop
 Title   : save_tempfiles
Usage : $obj->save_tempfiles($newval)
Function:
Returns : value of save_tempfiles
Args : newvalue (optional)
outfile_nameTop
 Title   : outfile_name
Usage : my $outfile = $dragram->outfile_name();
Function: Get/Set the name of the output file for this run
(if you wanted to do something special)
Returns : string
Args : [optional] string to set value to
tempdirTop
 Title   : tempdir
Usage : my $tmpdir = $self->tempdir();
Function: Retrieve a temporary directory name (which is created)
Returns : string which is the name of the temporary directory
Args : none
cleanupTop
 Title   : cleanup
Usage : $codeml->cleanup();
Function: Will cleanup the tempdir directory after a DrawTree run
Returns : none
Args : none
ioTop
 Title   : io
Usage : $obj->io($newval)
Function: Gets a Bio::Root::IO object
Returns : Bio::Root::IO object
Args : none
See Bio::Root::IO