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# $Id: drawgram.pm,v 1.6 2006/07/04 22:23:34 mauricio Exp $
# BioPerl module for Bio::Tools::Run::PiseApplication::drawgram
#
# Cared for by Catherine Letondal <letondal@pasteur.fr>
#
# For copyright and disclaimer see below.
#
# POD documentation - main docs before the code
=head1 NAME
Bio::Tools::Run::PiseApplication::drawgram
=head1 SYNOPSIS
#
=head1 DESCRIPTION
Bio::Tools::Run::PiseApplication::drawgram
Bioperl class for:
Phylip drawgram - Plots a cladogram- or phenogram-like rooted tree (Felsenstein)
References:
Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.
Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.
Parameters:
(see also:
for available values):
drawgram (String)
treefile (InFile)
Tree File
pipe: phylip_tree
screen_type (String)
plotter (Excl)
Which plotter or printer will the tree be drawn on
xres (Float)
X resolution
yres (Float)
Y resolution
laserjet_resolution (Excl)
Laserjet resolution
pcx_resolution (Excl)
Paintbrush PCX resolution
screen (String)
grows (Excl)
Tree grows...
tree_style (Excl)
Tree style
branch_lengths (Switch)
Use branch lengths
horizontal_margins (Float)
Horizontal margins
vertical_margins (Float)
Vertical margins
scale (Float)
Scale of branch length (default: Automatically rescaled)
depth (Float)
Depth/Breadth of tree
stem (Float)
Stem-length/tree-depth
character_height (Float)
Character ht / tip space
ancestral (Excl)
Ancestral nodes
font (String)
Font (PostScript only)
tops (String)
topict (String)
confirm (String)
=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 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:
=head1 AUTHOR
Catherine Letondal (letondal@pasteur.fr)
=head1 COPYRIGHT
Copyright (C) 2003 Institut Pasteur & Catherine Letondal.
All Rights Reserved.
This module is free software; you can redistribute it and/or modify
it under the same terms as Perl itself.
=head1 DISCLAIMER
This software is provided "as is" without warranty of any kind.
=head1 SEE ALSO
=over
=item *
=item *
Bio::Tools::Run::PiseApplication
=item *
Bio::Tools::Run::AnalysisFactory::Pise
=item *
Bio::Tools::Run::PiseJob
=back
=cut
#'
use vars qw(@ISA);
use strict;
@ISA = qw(Bio::Tools::Run::PiseApplication);
=head2 new
Title : new()
Usage : my $drawgram = Bio::Tools::Run::PiseApplication::drawgram->new($location, $email, @params);
Function: Creates a Bio::Tools::Run::PiseApplication::drawgram object.
This method should not be used directly, but rather by
a Bio::Tools::Run::AnalysisFactory::Pise instance.
my $factory = Bio::Tools::Run::AnalysisFactory::Pise->new();
my $drawgram = $factory->program('drawgram');
Example : -
Returns : An instance of Bio::Tools::Run::PiseApplication::drawgram.
=cut
sub new {
my ($class, $location, $email, @params) = @_;
my $self = $class->SUPER::new($location, $email);
# -- begin of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/drawgram.pm
$self->{COMMAND} = "drawgram";
$self->{VERSION} = "5.a";
$self->{TITLE} = "Phylip";
$self->{DESCRIPTION} = "drawgram - Plots a cladogram- or phenogram-like rooted tree";
$self->{OPT_EMAIL} = 0;
$self->{AUTHORS} = "Felsenstein";
$self->{REFERENCE} = [
"Felsenstein, J. 1993. PHYLIP (Phylogeny Inference Package) version 3.5c. Distributed by the author. Department of Genetics, University of Washington, Seattle.",
"Felsenstein, J. 1989. PHYLIP -- Phylogeny Inference Package (Version 3.2). Cladistics 5: 164-166.",
];
$self->{_INTERFACE_STANDOUT} = undef;
$self->{_STANDOUT_FILE} = undef;
$self->{TOP_PARAMETERS} = [
"drawgram",
"treefile",
"screen_type",
"options",
"screen",
"grows",
"tree_style",
"branch_lengths",
"horizontal_margins",
"vertical_margins",
"scale",
"depth",
"stem",
"character_height",
"ancestral",
"font",
"plotfile",
"psfile",
"pictfile",
"params",
"tops",
"topict",
"confirm",
];
$self->{PARAMETERS_ORDER} = [
"drawgram",
"treefile", # Tree File
"screen_type",
"options", # Drawgram options
"plotter", # Which plotter or printer will the tree be drawn on
"xbitmap_options", # Bitmap options
"xres", # X resolution
"yres", # Y resolution
"laserjet_options", # Laserjet options
"laserjet_resolution", # Laserjet resolution
"pcx_options", # Paintbrush options
"pcx_resolution", # Paintbrush PCX resolution
"screen",
"grows", # Tree grows...
"tree_style", # Tree style
"branch_lengths", # Use branch lengths
"horizontal_margins", # Horizontal margins
"vertical_margins", # Vertical margins
"scale", # Scale of branch length (default: Automatically rescaled)
"depth", # Depth/Breadth of tree
"stem", # Stem-length/tree-depth
"character_height", # Character ht / tip space
"ancestral", # Ancestral nodes
"font", # Font (PostScript only)
"plotfile",
"psfile",
"pictfile",
"params",
"tops",
"topict",
"confirm",
];
$self->{TYPE} = {
"drawgram" => 'String',
"treefile" => 'InFile',
"screen_type" => 'String',
"options" => 'Paragraph',
"plotter" => 'Excl',
"xbitmap_options" => 'Paragraph',
"xres" => 'Float',
"yres" => 'Float',
"laserjet_options" => 'Paragraph',
"laserjet_resolution" => 'Excl',
"pcx_options" => 'Paragraph',
"pcx_resolution" => 'Excl',
"screen" => 'String',
"grows" => 'Excl',
"tree_style" => 'Excl',
"branch_lengths" => 'Switch',
"horizontal_margins" => 'Float',
"vertical_margins" => 'Float',
"scale" => 'Float',
"depth" => 'Float',
"stem" => 'Float',
"character_height" => 'Float',
"ancestral" => 'Excl',
"font" => 'String',
"plotfile" => 'Results',
"psfile" => 'Results',
"pictfile" => 'Results',
"params" => 'Results',
"tops" => 'String',
"topict" => 'String',
"confirm" => 'String',
};
$self->{FORMAT} = {
"drawgram" => {
"perl" => ' "drawgram < params" ',
},
"treefile" => {
"perl" => '"ln -s $treefile intree; "',
},
"screen_type" => {
"perl" => '"0\\n"',
},
"options" => {
},
"plotter" => {
"perl" => '(defined $value and $value ne $vdef) ? "P\\n$value\\n" : ""',
},
"xbitmap_options" => {
},
"xres" => {
"perl" => '"$value\\n"',
},
"yres" => {
"perl" => '"$value\\n"',
},
"laserjet_options" => {
},
"laserjet_resolution" => {
"perl" => '"$value\\n"',
},
"pcx_options" => {
},
"pcx_resolution" => {
"perl" => '"$value\\n"',
},
"screen" => {
"perl" => '"V\\nN\\n"',
},
"grows" => {
"perl" => '($value ne $vdef) ? "H\\n" : "" ',
},
"tree_style" => {
},
"branch_lengths" => {
"perl" => '($value) ? "" : "B\\n"',
},
"horizontal_margins" => {
"perl" => '(defined $value and $value != $vdef)? "M\\n$value\\n$vertical_margins\\n" : ""',
},
"vertical_margins" => {
"perl" => '""',
},
"scale" => {
"perl" => '(defined $value) ? "R\\n$value\\n" : ""',
},
"depth" => {
"perl" => '(defined $value and $value != $vdef)? "D\\n$value\\n" : ""',
},
"stem" => {
"perl" => '(defined $value and $value != $vdef)? "T\\n$value\\n" : ""',
},
"character_height" => {
"perl" => '(defined $value and $value != $vdef)? "C\\n$value\\n" : ""',
},
"ancestral" => {
"perl" => '($value and $value ne $vdef)? "A\\n$value\\n" : ""',
},
"font" => {
"perl" => '($value and $value ne $vdef)? "F\\n$value\\n" : ""',
},
"plotfile" => {
},
"psfile" => {
},
"pictfile" => {
},
"params" => {
},
"tops" => {
"perl" => '($plotter eq "L") ? " ; ln -s plotfile plotfile.ps" : "" ',
},
"topict" => {
"perl" => '($plotter eq "M") ? " ; cp plotfile plotfile.pict" : "" ',
},
"confirm" => {
"perl" => '"Y\\n"',
},
};
$self->{FILENAMES} = {
"plotfile" => 'plotfile',
"psfile" => 'plotfile.ps',
"pictfile" => 'plotfile.pict',
"params" => 'params',
};
$self->{SEQFMT} = {
};
$self->{GROUP} = {
"drawgram" => 0,
"treefile" => -10,
"screen_type" => -1,
"plotter" => 2,
"xres" => 3,
"yres" => 4,
"laserjet_resolution" => 3,
"pcx_resolution" => 3,
"screen" => 1,
"grows" => 5,
"tree_style" => 5,
"branch_lengths" => 5,
"horizontal_margins" => 10,
"vertical_margins" => 9,
"scale" => 5,
"depth" => 5,
"stem" => 5,
"character_height" => 5,
"ancestral" => 5,
"font" => 5,
"tops" => 10,
"topict" => 10,
"confirm" => 1000,
};
$self->{BY_GROUP_PARAMETERS} = [
"treefile",
"screen_type",
"drawgram",
"options",
"params",
"xbitmap_options",
"laserjet_options",
"pcx_options",
"plotfile",
"psfile",
"pictfile",
"screen",
"plotter",
"pcx_resolution",
"laserjet_resolution",
"xres",
"yres",
"depth",
"stem",
"character_height",
"ancestral",
"font",
"grows",
"tree_style",
"branch_lengths",
"scale",
"vertical_margins",
"horizontal_margins",
"tops",
"topict",
"confirm",
];
$self->{SIZE} = {
"font" => 50,
};
$self->{ISHIDDEN} = {
"drawgram" => 1,
"treefile" => 0,
"screen_type" => 1,
"options" => 0,
"plotter" => 0,
"xbitmap_options" => 0,
"xres" => 0,
"yres" => 0,
"laserjet_options" => 0,
"laserjet_resolution" => 0,
"pcx_options" => 0,
"pcx_resolution" => 0,
"screen" => 1,
"grows" => 0,
"tree_style" => 0,
"branch_lengths" => 0,
"horizontal_margins" => 0,
"vertical_margins" => 0,
"scale" => 0,
"depth" => 0,
"stem" => 0,
"character_height" => 0,
"ancestral" => 0,
"font" => 0,
"plotfile" => 0,
"psfile" => 0,
"pictfile" => 0,
"params" => 0,
"tops" => 1,
"topict" => 1,
"confirm" => 1,
};
$self->{ISCOMMAND} = {
"drawgram" => 1,
"treefile" => 0,
"screen_type" => 0,
"options" => 0,
"plotter" => 0,
"xbitmap_options" => 0,
"xres" => 0,
"yres" => 0,
"laserjet_options" => 0,
"laserjet_resolution" => 0,
"pcx_options" => 0,
"pcx_resolution" => 0,
"screen" => 0,
"grows" => 0,
"tree_style" => 0,
"branch_lengths" => 0,
"horizontal_margins" => 0,
"vertical_margins" => 0,
"scale" => 0,
"depth" => 0,
"stem" => 0,
"character_height" => 0,
"ancestral" => 0,
"font" => 0,
"plotfile" => 0,
"psfile" => 0,
"pictfile" => 0,
"params" => 0,
"tops" => 0,
"topict" => 0,
"confirm" => 0,
};
$self->{ISMANDATORY} = {
"drawgram" => 0,
"treefile" => 1,
"screen_type" => 0,
"options" => 0,
"plotter" => 0,
"xbitmap_options" => 0,
"xres" => 1,
"yres" => 1,
"laserjet_options" => 0,
"laserjet_resolution" => 1,
"pcx_options" => 0,
"pcx_resolution" => 1,
"screen" => 0,
"grows" => 0,
"tree_style" => 0,
"branch_lengths" => 0,
"horizontal_margins" => 0,
"vertical_margins" => 0,
"scale" => 0,
"depth" => 0,
"stem" => 0,
"character_height" => 0,
"ancestral" => 0,
"font" => 0,
"plotfile" => 0,
"psfile" => 0,
"pictfile" => 0,
"params" => 0,
"tops" => 0,
"topict" => 0,
"confirm" => 0,
};
$self->{PROMPT} = {
"drawgram" => "",
"treefile" => "Tree File",
"screen_type" => "",
"options" => "Drawgram options",
"plotter" => "Which plotter or printer will the tree be drawn on",
"xbitmap_options" => "Bitmap options",
"xres" => "X resolution",
"yres" => "Y resolution",
"laserjet_options" => "Laserjet options",
"laserjet_resolution" => "Laserjet resolution",
"pcx_options" => "Paintbrush options",
"pcx_resolution" => "Paintbrush PCX resolution",
"screen" => "",
"grows" => "Tree grows...",
"tree_style" => "Tree style",
"branch_lengths" => "Use branch lengths",
"horizontal_margins" => "Horizontal margins",
"vertical_margins" => "Vertical margins",
"scale" => "Scale of branch length (default: Automatically rescaled)",
"depth" => "Depth/Breadth of tree",
"stem" => "Stem-length/tree-depth",
"character_height" => "Character ht / tip space",
"ancestral" => "Ancestral nodes",
"font" => "Font (PostScript only)",
"plotfile" => "",
"psfile" => "",
"pictfile" => "",
"params" => "",
"tops" => "",
"topict" => "",
"confirm" => "",
};
$self->{ISSTANDOUT} = {
"drawgram" => 0,
"treefile" => 0,
"screen_type" => 0,
"options" => 0,
"plotter" => 0,
"xbitmap_options" => 0,
"xres" => 0,
"yres" => 0,
"laserjet_options" => 0,
"laserjet_resolution" => 0,
"pcx_options" => 0,
"pcx_resolution" => 0,
"screen" => 0,
"grows" => 0,
"tree_style" => 0,
"branch_lengths" => 0,
"horizontal_margins" => 0,
"vertical_margins" => 0,
"scale" => 0,
"depth" => 0,
"stem" => 0,
"character_height" => 0,
"ancestral" => 0,
"font" => 0,
"plotfile" => 0,
"psfile" => 0,
"pictfile" => 0,
"params" => 0,
"tops" => 0,
"topict" => 0,
"confirm" => 0,
};
$self->{VLIST} = {
"options" => ['plotter','xbitmap_options','laserjet_options','pcx_options',],
"plotter" => ['L','L: Postscript printer file format','M','M: PICT format','J','J: HP Laserjet PCL file format','W','W: MS-Windows Bitmap','K','K: TeKtronix 4010 graphics terminal','H','H: Hewlett-Packard pen plotter (HPGL)','D','D: DEC ReGIS graphics (VT240 terminal)','B','B: Houston Instruments plotter','E','E: Epson MX-80 dot-matrix printer','C','C: Prowriter/Imagewriter dot-matrix printer','O','O: Okidata dot-matrix printer','T','T: Toshiba 24-pin dot-matrix printer','P','P: PCX file format','X','X: X Bitmap format','F','F: FIG 2.0 format','A','A: Idraw drawing program format','Z','Z: VRML Virtual Reality Markup Language file','V','V: POVRAY 3D rendering program file','R','R: Rayshade 3D rendering program file',],
"xbitmap_options" => ['xres','yres',],
"laserjet_options" => ['laserjet_resolution',],
"laserjet_resolution" => ['1','1: 75 DPI','2','2: 150 DPI','3','3: 300 DPI',],
"pcx_options" => ['pcx_resolution',],
"pcx_resolution" => ['1','1: EGA 640 X 350','2','2: VGA 800 X 600','3','3: VGA 1024 X 768',],
"grows" => ['Vertically','Vertically','Horizontally','Horizontally',],
"tree_style" => ['C','C: Cladogram','P','P: Phenogram','V','V: Curvogram','E','E: Eurogram','S','S: Swoopogram','O','O: Circular tree',],
"ancestral" => ['I','I: Intermediate','W','W: Weighted','C','C: Centered','N','N: Inner','V','V: So tree is V-shaped',],
};
$self->{FLIST} = {
"tree_style" => {
'V' => '"S\\nV\\n"',
'' => '',
'O' => '"S\\nO\\n"',
'P' => '"S\\nP\\n"',
'S' => '"S\\nS\\n"',
'C' => '',
'E' => '"S\\nE\\n"',
},
};
$self->{SEPARATOR} = {
};
$self->{VDEF} = {
"plotter" => 'L',
"xres" => '500',
"yres" => '500',
"laserjet_resolution" => '3',
"pcx_resolution" => '3',
"grows" => 'Horizontally',
"tree_style" => 'C',
"branch_lengths" => '1',
"horizontal_margins" => '1.65',
"vertical_margins" => '2.16',
"depth" => '1.00',
"stem" => '0.05',
"character_height" => '0.3333',
"ancestral" => 'I',
"font" => 'Hershey',
};
$self->{PRECOND} = {
"drawgram" => { "perl" => '1' },
"treefile" => { "perl" => '1' },
"screen_type" => { "perl" => '1' },
"options" => { "perl" => '1' },
"plotter" => { "perl" => '1' },
"xbitmap_options" => {
"perl" => '$plotter eq "X" or $plotter eq "W"',
},
"xres" => {
"perl" => '$plotter eq "X" or $plotter eq "W"',
},
"yres" => {
"perl" => '$plotter eq "X" or $plotter eq "W"',
},
"laserjet_options" => {
"perl" => '$plotter eq "J"',
},
"laserjet_resolution" => {
"perl" => '$plotter eq "J"',
},
"pcx_options" => {
"perl" => '$plotter eq "P"',
},
"pcx_resolution" => {
"perl" => '$plotter eq "P"',
},
"screen" => { "perl" => '1' },
"grows" => { "perl" => '1' },
"tree_style" => { "perl" => '1' },
"branch_lengths" => { "perl" => '1' },
"horizontal_margins" => { "perl" => '1' },
"vertical_margins" => { "perl" => '1' },
"scale" => { "perl" => '1' },
"depth" => { "perl" => '1' },
"stem" => { "perl" => '1' },
"character_height" => { "perl" => '1' },
"ancestral" => { "perl" => '1' },
"font" => {
"perl" => '$plotter eq "L"',
},
"plotfile" => {
"perl" => '$plotter ne "L"',
},
"psfile" => {
"perl" => '$plotter eq "L"',
},
"pictfile" => {
"perl" => '$plotter eq "M"',
},
"params" => { "perl" => '1' },
"tops" => { "perl" => '1' },
"topict" => { "perl" => '1' },
"confirm" => { "perl" => '1' },
};
$self->{CTRL} = {
"stem" => {
"perl" => {
'$value < 0 || $value >= 1' => "You should enter a value between 0 and 1.",
},
},
};
$self->{PIPEOUT} = {
};
$self->{WITHPIPEOUT} = {
};
$self->{PIPEIN} = {
"treefile" => {
"phylip_tree" => '1',
},
};
$self->{WITHPIPEIN} = {
};
$self->{ISCLEAN} = {
"drawgram" => 0,
"treefile" => 0,
"screen_type" => 0,
"options" => 0,
"plotter" => 0,
"xbitmap_options" => 0,
"xres" => 0,
"yres" => 0,
"laserjet_options" => 0,
"laserjet_resolution" => 0,
"pcx_options" => 0,
"pcx_resolution" => 0,
"screen" => 0,
"grows" => 0,
"tree_style" => 0,
"branch_lengths" => 0,
"horizontal_margins" => 0,
"vertical_margins" => 0,
"scale" => 0,
"depth" => 0,
"stem" => 0,
"character_height" => 0,
"ancestral" => 0,
"font" => 0,
"plotfile" => 0,
"psfile" => 0,
"pictfile" => 0,
"params" => 0,
"tops" => 0,
"topict" => 0,
"confirm" => 0,
};
$self->{ISSIMPLE} = {
"drawgram" => 0,
"treefile" => 1,
"screen_type" => 0,
"options" => 0,
"plotter" => 0,
"xbitmap_options" => 0,
"xres" => 0,
"yres" => 0,
"laserjet_options" => 0,
"laserjet_resolution" => 0,
"pcx_options" => 0,
"pcx_resolution" => 0,
"screen" => 0,
"grows" => 0,
"tree_style" => 0,
"branch_lengths" => 0,
"horizontal_margins" => 0,
"vertical_margins" => 0,
"scale" => 0,
"depth" => 0,
"stem" => 0,
"character_height" => 0,
"ancestral" => 0,
"font" => 0,
"plotfile" => 0,
"psfile" => 0,
"pictfile" => 0,
"params" => 0,
"tops" => 0,
"topict" => 0,
"confirm" => 0,
};
$self->{PARAMFILE} = {
"screen_type" => "params",
"plotter" => "params",
"xres" => "params",
"yres" => "params",
"laserjet_resolution" => "params",
"pcx_resolution" => "params",
"screen" => "params",
"grows" => "params",
"tree_style" => "params",
"branch_lengths" => "params",
"horizontal_margins" => "params",
"vertical_margins" => "params",
"scale" => "params",
"depth" => "params",
"stem" => "params",
"character_height" => "params",
"ancestral" => "params",
"font" => "params",
"confirm" => "params",
};
$self->{COMMENT} = {
"stem" => [
"Enter the stem length as fraction of tree depth (a value between 0 and 1).",
],
"character_height" => [
"Enter character height as fraction of tip spacing.",
],
"font" => [
"Possible values: courier, helvetica, avantgarde_demi, souvenir_demi, ... (depends on local web server configuration)",
],
};
$self->{SCALEMIN} = {
};
$self->{SCALEMAX} = {
};
$self->{SCALEINC} = {
};
$self->{INFO} = {
};
# -- end of definitions extracted from /local/gensoft/lib/Pise/5.a/PerlDef/drawgram.pm
$self->_init_params(@params);
return $self;
}
1; # Needed to keep compiler happy