Bio::Tools::Run::Phylo::Phylip::DrawGram - use Phylip DrawTree program to draw phylograms or phenograms use Bio::Tools::Run::Phylo::Phylip::DrawGram; my $drawfact = new Bio::Tools::Run::Phylo::Phylip::DrawGram(); my $treeimage = $drawfact->run($tree); This is a module for automating drawing of trees through Joe Felsenstein's Phylip suite.

Mailing Lists
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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://bugzilla.bioperl.org/ Email jason-at-bioperl.org The rest of the documentation details each of the object methods. Internal methods are usually preceded with a _

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

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

new
Title : new Usage : my $obj = new Bio::Tools::Run::Phylo::Phylip::DrawGram(); Function: Builds a new Bio::Tools::Run::Phylo::Phylip::DrawGram object Returns : an instance of Bio::Tools::Run::Phylo::Phylip::DrawGram Args : The available DrawGram parameters

run
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_tree
Title : draw_tree Usage : my $file = $app->draw_tree($treefile); Function: This method is deprecated. Please use run instead. Returns : File containing the rendered tree Args : either a Bio::Tree::TreeI OR filename of a tree in newick format

_run
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()
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()
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

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)

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

outfile_name
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

tempdir
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

cleanup
Title : cleanup Usage : $codeml->cleanup(); Function: Will cleanup the tempdir directory after a DrawGram run Returns : none Args : none

io
Title : io Usage : $obj->io($newval) Function: Gets a L<Bio::Root::IO> object Returns : L<Bio::Root::IO> Args : none