1# BioPerl module for Bio::Tools::Run::Phylo::Phylip::PhylipConf
2#
3# Created by
4#
5# Shawn Hoon
6#
7# You may distribute this module under the same terms as perl itself
8
9# POD documentation - main docs before the code
10
11=head1 NAME
12
13Bio::Tools::Run::Phylo::Phylip::PhylipConf
14
15=head1 SYNOPSIS
16
17  use Bio::Tools::Run::Phylo::Phylip::PhylipConf;
18  my %menu = %{$Bio::Tools::Run::Phylo::Phylip::PhylipConf::Menu->{$version}->{'PROTDIST'}};
19
20=head1 DESCRIPTION
21
22A configuration for managing menu configuration differences
23between version 3.5 and 3.6
24
25=head1 FEEDBACK
26
27=head2 Mailing Lists
28
29User feedback is an integral part of the evolution of this and other
30Bioperl modules. Send your comments and suggestions preferably to one
31of the Bioperl mailing lists.  Your participation is much appreciated.
32
33  bioperl-l@bioperl.org                  - General discussion
34  http://bioperl.org/wiki/Mailing_lists  - About the mailing lists
35
36=head2 Support
37
38Please direct usage questions or support issues to the mailing list:
39
40I<bioperl-l@bioperl.org>
41
42rather than to the module maintainer directly. Many experienced and
43reponsive experts will be able look at the problem and quickly
44address it. Please include a thorough description of the problem
45with code and data examples if at all possible.
46
47=head2 Reporting Bugs
48
49Report bugs to the Bioperl bug tracking system to help us keep track
50the bugs and their resolution.  Bug reports can be submitted via the
51web:
52
53  http://redmine.open-bio.org/projects/bioperl/
54
55=head1 AUTHOR - Shawn Hoon
56
57Email shawnh@fugu-sg.org
58
59=head1 CONTRIBUTORS
60
61Email:jason-at-bioperl.org
62
63=head1 APPENDIX
64
65The rest of the documentation details each of the object
66methods. Internal methods are usually preceded with a _
67
68=cut
69
70#'
71
72package Bio::Tools::Run::Phylo::Phylip::PhylipConf;
73
74use strict;
75use Exporter;
76use vars qw(@ISA %Menu %FileName $RESOLUTIONX $RESOLUTIONY @EXPORT_OK);
77use base 'Exporter';
78
79$RESOLUTIONX = 300;
80$RESOLUTIONY = 300;
81
82@EXPORT_OK = qw(%FileName %Menu);
83
84%FileName = (
85              "3.5"=>{'OUTFILE'=>'outfile',
86                      'TREEFILE'=>'treefile',
87                      'PLOTFILE'=>'plotfile',
88                     },
89              "3.6"=>{'OUTFILE'=>'outfile',
90                      'TREEFILE'=>'outtree',
91                      'PLOTFILE'=>'plotfile',
92                     },
93);
94
95%Menu =
96    (
97     "3.5" => {
98	 'PROTDIST' => {
99	     'MODEL'  => {
100		 'CAT'   =>"P\nP\n",
101		 'KIMURA'=>"P\n",
102	     },
103	     'GENCODE'=>  {
104		 'ALLOWED'=>"UMVFY",
105		 'OPTION' =>"C\n",
106	     },
107	     'CATEGORY'=>{
108		 'ALLOWED'=>"CHG",
109		 'OPTION' =>"A\n",
110	     },
111	     'PROBCHANGE'=>"E\n",
112	     'TRANS'     =>"T\n",
113	     'FREQ'      =>"F\n",
114	     'SUBMIT'    =>"Y\n",
115	     'MULTIPLE'  =>"M\n",
116	 },
117	 'NEIGHBOR'=>{
118	     'TYPE'    => {
119		 'UPGMA'=>"N\n",
120	     },
121	     'OUTGROUP'=>"O\n",
122	     'LOWTRI'  =>"L\n",
123	     'UPPTRI'  =>"R\n",
124	     'SUBREP'  =>"S\n",
125	     'JUMBLE'  =>"J\n",
126	     'SUBMIT'    =>"Y\n",
127	     'MULTIPLE'  =>"M\n",
128	 },
129	 'PROTPARS'=>{
130	     'THRESHOLD'=>"T\n",
131	     'JUMBLE'   =>"J\n",
132	     'OUTGROUP' =>"O\n",
133	     'SUBMIT'   =>"Y\n",
134	 },
135
136	 'SEQBOOT'=>{
137	     'DATATYPE' =>{
138		 'SEQUENCE'=>"",
139		 'MORPH'   =>"D\n",
140		 'REST'    =>"D\nD\n",
141		 'GENEFREQ'=>"D\nD\nD\n",
142	     },
143	     'ALLELES'  => "A\n",
144	     'PERMUTE'  => {
145		 'BOOTSTRAP'=>"",
146		 'JACKKNIFE'=>"J\n",
147		 'PERMUTE'  =>"J\nJ\n",
148	     },
149	     'REPLICATES'=>"R\n",
150	     'SUBMIT'    =>"Y\n",
151	 },
152	 'CONSENSE'=>{
153	     'ROOTED'   => "R\n",
154	     'OUTGROUP' => "O\n",
155	     'SUBMIT'    =>"Y\n",
156	 },
157     },
158     "3.6"=>{
159	 'PROTDIST'=>{
160	     'MODEL'  => {
161		 'PMB'        =>"P\n",
162		 'PAM'        =>"P\nP\n",
163		 'KIMURA'     =>"P\nP\nP\n",
164		 'CAT'        =>"P\nP\nP\nP\n",
165		 'JTT'        =>"Y\n",
166	     },
167	     'GENCODE'=>  {
168		 'ALLOWED'=>"UMVFY",
169		 'OPTION' =>"U\n",
170	     },
171	     'CATEGORY'=> {
172		 'ALLOWED'=>"CHG",
173		 'OPTION' =>"A\n",
174	     },
175	     'PROBCHANGE'=>"E\n",
176	     'TRANS'     =>"T\n",
177	     'FREQ'      =>"F\n",
178	     'WEIGHTS'   =>"W\n",
179	     'SUBMIT'    => "Y\n",
180	     'MULTIPLE'  =>"M\nD\n",
181	 },
182	 'NEIGHBOR' => {
183	     'TYPE'    => {
184		 'UPGMA'=>"N\n",
185	     },
186	     'OUTGROUP'=>"O\n",
187	     'LOWTRI'  =>"L\n",
188	     'UPPTRI'  =>"R\n",
189	     'SUBREP'  =>"S\n",
190	     'JUMBLE'  =>"J\n",
191	     'SUBMIT'    =>"Y\n",
192	     'MULTIPLE'  =>"M\n",
193	 },
194	 'PROTPARS' => {
195	     'THRESHOLD'=>"T\n",
196	     'JUMBLE'   =>"J\n",
197	     'OUTGROUP' =>"O\n",
198	     'SUBMIT'   =>"Y\n",
199	 },
200	 'DRAWGRAM' => {
201	     'SCALE'             => "R\n",
202	     'HORIZMARGINS'      => "M\n%.2f\n%.2f\n",
203	     'VERTICALMARGINS'   => "M\n%.2f\n%.2f",
204	     'SCREEN' => {
205		 'Y|YES|1' => "V\nX\n",
206		 'N|NO|0'  => "V\nN\n",
207	     },
208	     'FONT'         => "F\n%s\n",
209	     'PAGES'        => {
210		 'L|PAGES|SIZE'       => "#\nL\n%d\n%d\nM\n",
211		 'P|PHYSICAL'         => "#\nP\n%.4f\n%.4f\nM\n",
212		 'O|OVERLAP'          => "#\nO\n%.4f\n%.4f\nM\n",
213	     },
214	     'PLOTTER' => {
215		 'P|POSTSCRIPT'     => "P\nL\n",
216		 'PICT'             => "P\nM\n",
217		 "HP|PCL|LaserJect" => "P\nJ\n",
218		 "BMP"              => "P\nW\n$RESOLUTIONX\n$RESOLUTIONY",
219		 "FIG"              => "P\nF\n",
220		 "IDRAW"            => "P\nA\n",
221		 "VRML"             => "P\nZ\n",
222		 "PCX"              => "P\nP\n3\n",
223	     },
224	     'ANCESTRALNODES'  => {
225		 'I|INTER|INTERMEDIETE' => "A\nI\n",
226		 'W|WEIGHTED'           => "A\nW\n",
227		 'C|CENT|CENTERED'      => "A\nC\n",
228		 'N|INNER|INNERMOST'    => "A\nN\n",
229		 'V'                    => "A\nV\n",
230	     },
231	     'TREESTYLE' => {
232		 'C|CLAD|CLADOGRAM'      => "S\nC\n",
233		 'P|PHEN|PHENOGRAM'      => "S\nP\n",
234		 'V|CURV|CURVOGRAM'    => "S\nV\n",
235		 'E|EURO|EUROGRAM'     => "S\nE\n",
236		 'S|SWOOP|SWOOPOGRAM'  => "S\nS\n",
237		 'O|CIRC|CIRCULAR'   => "S\nO\n",
238	     },
239	     'TIPSPACE'      => "C\n%.4f\n",
240	     'STEMLEN'       => "T\n%.4f\n",
241	     'TREEDEPTH'     => "D\n%.4f\n",
242	     'LABEL_ANGLE'   => "L\n%.4f\n",
243	     'USEBRANCHLENS' => {
244		 '1|Y|YES'   => "",
245		 '0|N|NO'    => "B\n",
246	     },
247	 },
248	 'DRAWTREE' => {
249	     'SCREEN' => {
250		 'Y|YES|1' => "V\nX\n",
251		 'N|NO|0'  => "V\nN\n",
252	     },
253	     'PLOTTER'           => {
254		 'L|P|POSTSCRIPT'     => "P\nL\n",
255		 'PICT'             => "P\nM\n",
256		 "HP|PCL|LaserJect" => "P\nJ\n",
257		 "BMP"              => "P\nW\n$RESOLUTIONX\n$RESOLUTIONY",
258		 "FIG"              => "P\nF\n",
259		 "IDRAW"            => "P\nA\n",
260		 "VRML"             => "P\nZ\n",
261		 "PCX"              => "P\nP\n3\n",
262	     },
263	     'LABEL_ANGLE'       => {
264		 'F|FIXED'         => "L\nF\n%d\n",
265		 'R|RADIAL'        => "L\nR\n",
266		 'A|ALONG'         => "L\nA\n",
267		 'M|MIDDLE'        => "L\nM\n",
268	     },
269	     'ROTATION'            => "R\n%d\n",
270	     'ITERATE'             => {
271		 'E|EQUAL|DAYLIGHT' => "",
272		 'N|NBODY|N-BODY'   => "I\n",
273		 'NO|FALSE'         => "I\nI\n",
274	     },
275	     'TREEARC'             => "I\nI\nA\n%d\n",
276	     'SCALE'               => "S\n%.2f\n",
277	     'PAGES'        => {
278		 'L|PAGES|SIZE'       => "#\nL\n%d\n%d\nM\n",
279		 'P|PHYSICAL'         => "#\nP\n%.4f\n%.4f\nM\n",
280		 'O|OVERLAP'          => "#\nO\n%.4f\n%.4f\nM\n",
281	     },
282	     'HORIZMARGINS'      => "M\n%.2f\n%.2f\n",
283	     'VERTICALMARGINS'   => "M\n%.2f\n%.2f",
284	 },
285	 'SEQBOOT'=>{
286	     'DATATYPE' => {
287		 'SEQUENCE'=> "",
288		 'MORPH'   =>"D\n",
289		 'REST'    =>"D\nD\n",
290		 'GENEFREQ'=>"D\nD\nD\n",
291	     },
292	     'ALLELES'  => "A\n",
293	     'PERMUTE'  => {
294		 'BOOTSTRAP'=>"",
295		 'JACKKNIFE'=>"J\n",
296		 'PERMUTE'  =>"J\nJ\n",
297	     },
298	     'REPLICATES'=>"R\n",
299	     'SUBMIT'   =>"Y\n",
300	 },
301	 'CONSENSE'=>{
302	     'TYPE'     => {
303		 'MRE'     =>"",
304		 'STRICT'  =>"C\n",
305		 'MR'      =>"C\nC\n",
306		 'ML'      =>"C\nC\nC\n",
307	     },
308	     'ROOTED'   => "R\n",
309	     'OUTGROUP' => "O\n",
310	     'SUBMIT'    =>"Y\n",
311	 },
312     },
313     );
314
3151;
316