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.IX Title "Bio::Tools::Run::Phylo::Phylip::DrawTree 3pm"
.TH Bio::Tools::Run::Phylo::Phylip::DrawTree 3pm "2023-01-22" "perl v5.36.0" "User Contributed Perl Documentation"
.\" For nroff, turn off justification.  Always turn off hyphenation; it makes
.\" way too many mistakes in technical documents.
.if n .ad l
.nh
.SH "NAME"
Bio::Tools::Run::Phylo::Phylip::DrawTree \- use Phylip DrawTree 
program to draw trees
.SH "SYNOPSIS"
.IX Header "SYNOPSIS"
.Vb 1
\&  use Bio::Tools::Run::Phylo::Phylip::DrawTree;
\&
\&  my $treedraw = Bio::Tools::Run::Phylo::Phylip::DrawTree\->new();
\&  my $treeimagefile = $drawfact\->run($tree);
.Ve
.SH "DESCRIPTION"
.IX Header "DESCRIPTION"
This is a module for automating drawing of trees through Joe
Felsenstein's Phylip suite.
.PP
To set parameters with option you need to pass in an array reference or
a string, depending on the parameter. For example:
.PP
.Vb 4
\&  $treedraw\->HORIZMARGINS([\*(Aq2.00\*(Aq,\*(Aq2.5\*(Aq]);
\&  $treedraw\->ANCESTRALNODES(\*(AqC\*(Aq);
\&  $treedraw\->TREESTYLE(\*(AqPHEN\*(Aq);
\&  $treedraw\->USEBRANCHLENS(\*(AqN\*(Aq);
.Ve
.PP
This can be a brittle module as the menus change in \s-1PHYLIP.\s0  It should
support phylip 3.6 but no guarantees.
.SH "FEEDBACK"
.IX Header "FEEDBACK"
.SS "Mailing Lists"
.IX Subsection "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.
.PP
.Vb 2
\&  bioperl\-l@bioperl.org                  \- General discussion
\&  http://bioperl.org/wiki/Mailing_lists  \- About the mailing lists
.Ve
.SS "Support"
.IX Subsection "Support"
Please direct usage questions or support issues to the mailing list:
.PP
\&\fIbioperl\-l@bioperl.org\fR
.PP
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.
.SS "Reporting Bugs"
.IX Subsection "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:
.PP
.Vb 1
\&  http://redmine.open\-bio.org/projects/bioperl/
.Ve
.SH "AUTHOR \- Jason Stajich"
.IX Header "AUTHOR - Jason Stajich"
Email jason\-at\-bioperl.org
.SH "APPENDIX"
.IX Header "APPENDIX"
The rest of the documentation details each of the object methods.
Internal methods are usually preceded with a _
.SS "program_name"
.IX Subsection "program_name"
.Vb 5
\& Title   : program_name
\& Usage   : $obj\->program_name()
\& Function: holds the program name
\& Returns:  string
\& Args    : None
.Ve
.SS "program_dir"
.IX Subsection "program_dir"
.Vb 5
\& Title   : program_dir
\& Usage   : $drawfact\->program_dir()
\& Function: returns the program directory, obtained from ENV variable.
\& Returns :  string
\& Args    :
.Ve
.SS "new"
.IX Subsection "new"
.Vb 5
\& 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
.Ve
.SS "run"
.IX Subsection "run"
.Vb 7
\& 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
.Ve
.SS "draw_tree"
.IX Subsection "draw_tree"
.Vb 7
\& 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
.Ve
.SS "_run"
.IX Subsection "_run"
.Vb 7
\& 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
.Ve
.SS "\fB_setinput()\fP"
.IX Subsection "_setinput()"
.Vb 6
\& 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
.Ve
.SS "\fB_setparams()\fP"
.IX Subsection "_setparams()"
.Vb 6
\& 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
.Ve
.SH "Bio::Tools::Run::Wrapper methods"
.IX Header "Bio::Tools::Run::Wrapper methods"
.SS "no_param_checks"
.IX Subsection "no_param_checks"
.Vb 6
\& 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)
.Ve
.SS "save_tempfiles"
.IX Subsection "save_tempfiles"
.Vb 5
\& Title   : save_tempfiles
\& Usage   : $obj\->save_tempfiles($newval)
\& Function: 
\& Returns : value of save_tempfiles
\& Args    : newvalue (optional)
.Ve
.SS "outfile_name"
.IX Subsection "outfile_name"
.Vb 6
\& 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
.Ve
.SS "tempdir"
.IX Subsection "tempdir"
.Vb 5
\& 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
.Ve
.SS "cleanup"
.IX Subsection "cleanup"
.Vb 5
\& Title   : cleanup
\& Usage   : $codeml\->cleanup();
\& Function: Will cleanup the tempdir directory after a DrawTree run
\& Returns : none
\& Args    : none
.Ve
.SS "io"
.IX Subsection "io"
.Vb 5
\& Title   : io
\& Usage   : $obj\->io($newval)
\& Function: Gets a Bio::Root::IO object
\& Returns : Bio::Root::IO object
\& Args    : none
.Ve
.PP
See Bio::Root::IO