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