forester/java/src/org/forester/clade_analysis/CladeAnalysisTest.java

   1
   2 package org.forester.clade_analysis;
   3
   4 import java.io.File;
   5
   6 import org.forester.io.parsers.PhylogenyParser;
   7 import org.forester.io.parsers.util.ParserUtils;
   8 import org.forester.phylogeny.Phylogeny;
   9 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  10 import org.forester.phylogeny.factories.PhylogenyFactory;
  11 import org.forester.util.ForesterUtil;
  12
  13 public class CladeAnalysisTest {
  14
  15     private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
  16             + "test_data" + ForesterUtil.getFileSeparator();
  17
  18     public static void main( final String[] args ) {
  19         boolean failed = false;
  20         if ( !testCladeAnalysis1() ) {
  21             System.out.println( "Clade analysis 1 failed" );
  22             failed = true;
  23         }
  24         if ( !testCladeAnalysis2() ) {
  25             System.out.println( "Clade analysis 2 failed" );
  26             failed = true;
  27         }
  28         if ( !testCladeAnalysis3() ) {
  29             System.out.println( "Clade analysis 3 failed" );
  30             failed = true;
  31         }
  32         if ( !testCladeAnalysis4() ) {
  33             System.out.println( "Clade analysis 4 failed" );
  34             failed = true;
  35         }
  36         if ( !testCladeAnalysis5() ) {
  37             System.out.println( "Clade analysis 5 failed" );
  38             failed = true;
  39         }
  40         if ( !testCladeAnalysis6() ) {
  41             System.out.println( "Clade analysis 6 failed" );
  42             failed = true;
  43         }
  44         if ( !failed ) {
  45             System.out.println( "OK" );
  46         }
  47         else {
  48             System.out.println( "NOT OK" );
  49         }
  50     }
  51
  52     public static boolean test() {
  53         if ( !testCladeAnalysis1() ) {
  54             return false;
  55         }
  56         if ( !testCladeAnalysis2() ) {
  57             return false;
  58         }
  59         if ( !testCladeAnalysis3() ) {
  60             return false;
  61         }
  62         if ( !testCladeAnalysis4() ) {
  63             return false;
  64         }
  65         if ( !testCladeAnalysis5() ) {
  66             return false;
  67         }
  68         if ( !testCladeAnalysis6() ) {
  69             return false;
  70         }
  71         return true;
  72     }
  73
  74     private static boolean testCladeAnalysis1() {
  75         try {
  76             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_1.xml" );
  77             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  78             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
  79             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
  80             ResultSingle res = AnalysisSingle.execute( p1, "A.1.1.1", "." );
  81             if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
  82                 return false;
  83             }
  84             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
  85                 return false;
  86             }
  87             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
  88                 return false;
  89             }
  90             if ( res.getLeastEncompassingCladeSize() != 4 ) {
  91                 return false;
  92             }
  93             if ( res.getTreeSize() != 25 ) {
  94                 return false;
  95             }
  96             if ( res.getWarnings().size() != 0 ) {
  97                 return false;
  98             }
  99             res = AnalysisSingle.execute( p1, "A.1.1.2", "." );
 100             if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
 101                 return false;
 102             }
 103             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 104                 return false;
 105             }
 106             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
 107                 return false;
 108             }
 109             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 110                 return false;
 111             }
 112             if ( res.getTreeSize() != 25 ) {
 113                 return false;
 114             }
 115             if ( res.getWarnings().size() != 0 ) {
 116                 return false;
 117             }
 118             res = AnalysisSingle.execute( p1, "A.1.1.3", "." );
 119             if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
 120                 return false;
 121             }
 122             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 123                 return false;
 124             }
 125             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
 126                 return false;
 127             }
 128             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 129                 return false;
 130             }
 131             if ( res.getTreeSize() != 25 ) {
 132                 return false;
 133             }
 134             if ( res.getWarnings().size() != 0 ) {
 135                 return false;
 136             }
 137             res = AnalysisSingle.execute( p1, "A.1.1.4", "." );
 138             if ( !res.getGreatestCommonPrefix().equals( "A.1.1" ) ) {
 139                 return false;
 140             }
 141             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 142                 return false;
 143             }
 144             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.1" ) ) {
 145                 return false;
 146             }
 147             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 148                 return false;
 149             }
 150             if ( res.getTreeSize() != 25 ) {
 151                 return false;
 152             }
 153             if ( res.getWarnings().size() != 0 ) {
 154                 return false;
 155             }
 156             res = AnalysisSingle.execute( p1, "A.1.2.1", "." );
 157             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 158                 return false;
 159             }
 160             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 161                 return false;
 162             }
 163             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 164                 return false;
 165             }
 166             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 167                 return false;
 168             }
 169             if ( res.getTreeSize() != 25 ) {
 170                 return false;
 171             }
 172             if ( res.getWarnings().size() != 0 ) {
 173                 return false;
 174             }
 175             res = AnalysisSingle.execute( p1, "A.2.1.1", "." );
 176             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 177                 return false;
 178             }
 179             if ( !res.getGreatestCommonPrefixDown().equals( "A.2.1.2" ) ) {
 180                 return false;
 181             }
 182             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 183                 return false;
 184             }
 185             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 186                 return false;
 187             }
 188             if ( res.getTreeSize() != 25 ) {
 189                 return false;
 190             }
 191             if ( res.getWarnings().size() != 0 ) {
 192                 return false;
 193             }
 194             res = AnalysisSingle.execute( p1, "A.2.1.2", "." );
 195             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 196                 return false;
 197             }
 198             if ( !res.getGreatestCommonPrefixDown().equals( "A.2.1.1" ) ) {
 199                 return false;
 200             }
 201             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 202                 return false;
 203             }
 204             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 205                 return false;
 206             }
 207             if ( res.getTreeSize() != 25 ) {
 208                 return false;
 209             }
 210             if ( res.getWarnings().size() != 0 ) {
 211                 return false;
 212             }
 213             res = AnalysisSingle.execute( p1, "A.3.1.1", "." );
 214             if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
 215                 return false;
 216             }
 217             if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1.2" ) ) {
 218                 return false;
 219             }
 220             if ( !res.getGreatestCommonPrefixUp().equals( "A.3.2.1" ) ) {
 221                 return false;
 222             }
 223             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 224                 return false;
 225             }
 226             if ( res.getTreeSize() != 25 ) {
 227                 return false;
 228             }
 229             if ( res.getWarnings().size() != 0 ) {
 230                 return false;
 231             }
 232             res = AnalysisSingle.execute( p1, "A.3.1.2", "." );
 233             if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
 234                 return false;
 235             }
 236             if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1.1" ) ) {
 237                 return false;
 238             }
 239             if ( !res.getGreatestCommonPrefixUp().equals( "A.3.2.1" ) ) {
 240                 return false;
 241             }
 242             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 243                 return false;
 244             }
 245             if ( res.getTreeSize() != 25 ) {
 246                 return false;
 247             }
 248             if ( res.getWarnings().size() != 0 ) {
 249                 return false;
 250             }
 251             res = AnalysisSingle.execute( p1, "A.3.2.1", "." );
 252             if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
 253                 return false;
 254             }
 255             if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1" ) ) {
 256                 return false;
 257             }
 258             if ( !res.getGreatestCommonPrefixUp().equals( "A.3.3.1" ) ) {
 259                 return false;
 260             }
 261             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 262                 return false;
 263             }
 264             if ( res.getTreeSize() != 25 ) {
 265                 return false;
 266             }
 267             if ( res.getWarnings().size() != 0 ) {
 268                 return false;
 269             }
 270             res = AnalysisSingle.execute( p1, "A.3.3.1", "." );
 271             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 272                 return false;
 273             }
 274             if ( !res.getGreatestCommonPrefixDown().equals( "A.3" ) ) {
 275                 return false;
 276             }
 277             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 278                 return false;
 279             }
 280             if ( res.getLeastEncompassingCladeSize() != 10 ) {
 281                 return false;
 282             }
 283             if ( res.getTreeSize() != 25 ) {
 284                 return false;
 285             }
 286             if ( res.getWarnings().size() != 0 ) {
 287                 return false;
 288             }
 289             res = AnalysisSingle.execute( p1, "A.4.1.1", "." );
 290             if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
 291                 return false;
 292             }
 293             if ( !res.getGreatestCommonPrefixDown().equals( "A.4.1.1.a" ) ) {
 294                 return false;
 295             }
 296             if ( !res.getGreatestCommonPrefixUp().equals( "A.4.1.2" ) ) {
 297                 return false;
 298             }
 299             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 300                 return false;
 301             }
 302             if ( res.getTreeSize() != 25 ) {
 303                 return false;
 304             }
 305             if ( res.getWarnings().size() != 0 ) {
 306                 return false;
 307             }
 308             res = AnalysisSingle.execute( p1, "A.4.1.1.a", "." );
 309             if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
 310                 return false;
 311             }
 312             if ( !res.getGreatestCommonPrefixDown().equals( "A.4.1.1" ) ) {
 313                 return false;
 314             }
 315             if ( !res.getGreatestCommonPrefixUp().equals( "A.4.1.2" ) ) {
 316                 return false;
 317             }
 318             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 319                 return false;
 320             }
 321             if ( res.getTreeSize() != 25 ) {
 322                 return false;
 323             }
 324             if ( res.getWarnings().size() != 0 ) {
 325                 return false;
 326             }
 327             res = AnalysisSingle.execute( p1, "A.4.1.2", "." );
 328             res = AnalysisSingle.execute( p1, "A.4.1.2.a", "." );
 329             res = AnalysisSingle.execute( p1, "A.5.1.1", "." );
 330             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 331                 return false;
 332             }
 333             if ( !res.getGreatestCommonPrefixDown().equals( "A.5.1.2" ) ) {
 334                 return false;
 335             }
 336             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 337                 return false;
 338             }
 339             if ( res.getLeastEncompassingCladeSize() != 10 ) {
 340                 return false;
 341             }
 342             if ( res.getTreeSize() != 25 ) {
 343                 return false;
 344             }
 345             if ( res.getWarnings().size() != 0 ) {
 346                 return false;
 347             }
 348             res = AnalysisSingle.execute( p1, "A.5.1.2", "." );
 349             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 350                 return false;
 351             }
 352             if ( !res.getGreatestCommonPrefixDown().equals( "A.5.1.1" ) ) {
 353                 return false;
 354             }
 355             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 356                 return false;
 357             }
 358             if ( res.getLeastEncompassingCladeSize() != 10 ) {
 359                 return false;
 360             }
 361             if ( res.getTreeSize() != 25 ) {
 362                 return false;
 363             }
 364             if ( res.getWarnings().size() != 0 ) {
 365                 return false;
 366             }
 367             res = AnalysisSingle.execute( p1, "A.6.3.12", "." );
 368             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 369                 return false;
 370             }
 371             if ( !res.getGreatestCommonPrefixDown().equals( "A" ) ) {
 372                 return false;
 373             }
 374             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 375                 return false;
 376             }
 377             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 378                 return false;
 379             }
 380             if ( res.getTreeSize() != 25 ) {
 381                 return false;
 382             }
 383             if ( res.getWarnings().size() != 0 ) {
 384                 return false;
 385             }
 386             res = AnalysisSingle.execute( p1, "B.1.1.1", "." );
 387             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 388                 return false;
 389             }
 390             if ( !res.getGreatestCommonPrefixDown().equals( "B.1.234.3" ) ) {
 391                 return false;
 392             }
 393             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 394                 return false;
 395             }
 396             if ( res.getLeastEncompassingCladeSize() != 25 ) {
 397                 return false;
 398             }
 399             if ( res.getTreeSize() != 25 ) {
 400                 return false;
 401             }
 402             if ( res.getWarnings().size() != 2 ) {
 403                 return false;
 404             }
 405             res = AnalysisSingle.execute( p1, "B.1.234.3", "." );
 406             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 407                 return false;
 408             }
 409             if ( !res.getGreatestCommonPrefixDown().equals( "B.1.1.1" ) ) {
 410                 return false;
 411             }
 412             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 413                 return false;
 414             }
 415             if ( res.getLeastEncompassingCladeSize() != 25 ) {
 416                 return false;
 417             }
 418             if ( res.getTreeSize() != 25 ) {
 419                 return false;
 420             }
 421             if ( res.getWarnings().size() != 2 ) {
 422                 return false;
 423             }
 424             res = AnalysisSingle.execute( p1, "C.1.1.1", "." );
 425             if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
 426                 return false;
 427             }
 428             if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1.2" ) ) {
 429                 return false;
 430             }
 431             if ( !res.getGreatestCommonPrefixUp().equals( "C.1.2.1" ) ) {
 432                 return false;
 433             }
 434             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 435                 return false;
 436             }
 437             if ( res.getTreeSize() != 25 ) {
 438                 return false;
 439             }
 440             if ( res.getWarnings().size() != 0 ) {
 441                 return false;
 442             }
 443             res = AnalysisSingle.execute( p1, "C.1.1.2", "." );
 444             if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
 445                 return false;
 446             }
 447             if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1.1" ) ) {
 448                 return false;
 449             }
 450             if ( !res.getGreatestCommonPrefixUp().equals( "C.1.2.1" ) ) {
 451                 return false;
 452             }
 453             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 454                 return false;
 455             }
 456             if ( res.getTreeSize() != 25 ) {
 457                 return false;
 458             }
 459             if ( res.getWarnings().size() != 0 ) {
 460                 return false;
 461             }
 462             res = AnalysisSingle.execute( p1, "C.1.2.1", "." );
 463             if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
 464                 return false;
 465             }
 466             if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1" ) ) {
 467                 return false;
 468             }
 469             if ( !res.getGreatestCommonPrefixUp().equals( "C.2.1" ) ) {
 470                 return false;
 471             }
 472             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 473                 return false;
 474             }
 475             if ( res.getTreeSize() != 25 ) {
 476                 return false;
 477             }
 478             if ( res.getWarnings().size() != 0 ) {
 479                 return false;
 480             }
 481             res = AnalysisSingle.execute( p1, "C.2.1", "." );
 482             if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
 483                 return false;
 484             }
 485             if ( !res.getGreatestCommonPrefixDown().equals( "C.1" ) ) {
 486                 return false;
 487             }
 488             if ( !res.getGreatestCommonPrefixUp().equals( "C.3" ) ) {
 489                 return false;
 490             }
 491             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 492                 return false;
 493             }
 494             if ( res.getTreeSize() != 25 ) {
 495                 return false;
 496             }
 497             if ( res.getWarnings().size() != 0 ) {
 498                 return false;
 499             }
 500             res = AnalysisSingle.execute( p1, "C.3", "." );
 501             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 502                 return false;
 503             }
 504             if ( !res.getGreatestCommonPrefixDown().equals( "C" ) ) {
 505                 return false;
 506             }
 507             if ( !res.getGreatestCommonPrefixUp().equals( "QE.1.1.1.2.1" ) ) {
 508                 return false;
 509             }
 510             if ( res.getLeastEncompassingCladeSize() != 5 ) {
 511                 return false;
 512             }
 513             if ( res.getTreeSize() != 25 ) {
 514                 return false;
 515             }
 516             if ( res.getWarnings().size() != 1 ) {
 517                 return false;
 518             }
 519             res = AnalysisSingle.execute( p1, "QE.1.1.1.2.1", "." );
 520             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 521                 return false;
 522             }
 523             if ( !res.getGreatestCommonPrefixDown().equals( "C" ) ) {
 524                 return false;
 525             }
 526             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 527                 return false;
 528             }
 529             if ( res.getLeastEncompassingCladeSize() != 25 ) {
 530                 return false;
 531             }
 532             if ( res.getTreeSize() != 25 ) {
 533                 return false;
 534             }
 535             if ( res.getWarnings().size() != 2 ) {
 536                 return false;
 537             }
 538         }
 539         catch ( final Exception e ) {
 540             e.printStackTrace( System.out );
 541             return false;
 542         }
 543         return true;
 544     }
 545
 546     private static boolean testCladeAnalysis2() {
 547         try {
 548             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_2.xml" );
 549             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 550             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 551             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 552             ResultSingle res = AnalysisSingle.execute( p1, "6_DQ278891", null );
 553             if ( !res.getGreatestCommonPrefix().equals( "6_" ) ) {
 554                 return false;
 555             }
 556             if ( !res.getGreatestCommonPrefixDown().equals( "6_DQ278893" ) ) {
 557                 return false;
 558             }
 559             if ( !res.getGreatestCommonPrefixUp().equals( "6_JX183550" ) ) {
 560                 return false;
 561             }
 562             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 563                 return false;
 564             }
 565             if ( res.getTreeSize() != 219 ) {
 566                 return false;
 567             }
 568             if ( res.getWarnings().size() != 0 ) {
 569                 return false;
 570             }
 571             res = AnalysisSingle.execute( p1, "6xa_EU408330", null );
 572             if ( !res.getGreatestCommonPrefix().equals( "6xa_EU40833" ) ) {
 573                 return false;
 574             }
 575             if ( !res.getGreatestCommonPrefixDown().equals( "6xa_EU408331" ) ) {
 576                 return false;
 577             }
 578             if ( !res.getGreatestCommonPrefixUp().equals( "6xa_EU408332" ) ) {
 579                 return false;
 580             }
 581             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 582                 return false;
 583             }
 584             if ( res.getTreeSize() != 219 ) {
 585                 return false;
 586             }
 587             if ( res.getWarnings().size() != 0 ) {
 588                 return false;
 589             }
 590             res = AnalysisSingle.execute( p1, "7a_EF108306", null );
 591             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 592                 return false;
 593             }
 594             if ( !res.getGreatestCommonPrefixDown().equals( "2" ) ) {
 595                 return false;
 596             }
 597             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 598                 return false;
 599             }
 600             if ( res.getLeastEncompassingCladeSize() != 219 ) {
 601                 return false;
 602             }
 603             if ( res.getTreeSize() != 219 ) {
 604                 return false;
 605             }
 606             if ( res.getWarnings().size() != 2 ) {
 607                 return false;
 608             }
 609         }
 610         catch ( final Exception e ) {
 611             e.printStackTrace( System.out );
 612             return false;
 613         }
 614         return true;
 615     }
 616
 617     private static boolean testCladeAnalysis3() {
 618         try {
 619             final ResultMulti res1 = new ResultMulti();
 620             res1.addGreatestCommonPrefix( "A.1.1", 0.3 );
 621             res1.addGreatestCommonPrefix( "A.1.2", 0.3 );
 622             res1.addGreatestCommonPrefix( "A.1.3", 0.3 );
 623             res1.addGreatestCommonPrefix( "B.1", 0.1 );
 624             res1.analyze( 0.5 );
 625             System.out.print( res1.toString() );
 626             System.out.println( "------------------------- " );
 627             System.out.println();
 628             final ResultMulti res2 = new ResultMulti( "." );
 629             res2.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
 630             res2.addGreatestCommonPrefix( "A.1", 0.7 );
 631             res2.addGreatestCommonPrefix( "A.1.2", 0.1 );
 632             res2.addGreatestCommonPrefix( "B.1", 0.1 );
 633             res2.analyze( 0.3 );
 634             System.out.print( res2.toString() );
 635             System.out.println( "------------------------- " );
 636             System.out.println();
 637             final ResultMulti res3 = new ResultMulti( "." );
 638             res3.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
 639             res3.addGreatestCommonPrefix( "A.1.1.1.1", 0.6 );
 640             res3.addGreatestCommonPrefix( "A.1", 0.1 );
 641             res3.addGreatestCommonPrefix( "A.1.2", 0.1 );
 642             res3.addGreatestCommonPrefix( "B.1", 0.1 );
 643             res3.analyze( 0.3 );
 644             System.out.print( res3.toString() );
 645             System.out.println( "------------------------- " );
 646             System.out.println();
 647             final ResultMulti res33 = new ResultMulti( "." );
 648             res33.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
 649             res33.addGreatestCommonPrefix( "A.1.1.1.1", 0.3 );
 650             res33.addGreatestCommonPrefix( "A.1", 0.1 );
 651             res33.addGreatestCommonPrefix( "A.1.2", 0.1 );
 652             res33.addGreatestCommonPrefix( "B.1", 0.1 );
 653             res33.addGreatestCommonPrefix( "B.1.1.1", 0.3 );
 654             res33.analyze( 0.3 );
 655             System.out.print( res33.toString() );
 656             System.out.println( "------------------------- " );
 657             System.out.println();
 658             final ResultMulti res4 = new ResultMulti();
 659             res4.addGreatestCommonPrefix( "A.1.1.1.1", 0.35 );
 660             res4.addGreatestCommonPrefix( "A.1.1.1.2", 0.35 );
 661             res4.addGreatestCommonPrefix( "A.1", 0.1 );
 662             res4.addGreatestCommonPrefix( "A.1.2", 0.1 );
 663             res4.addGreatestCommonPrefix( "B.1", 0.1 );
 664             res4.analyze( 0.3 );
 665             System.out.print( res4.toString() );
 666             System.out.println( "------------------------- " );
 667             System.out.println();
 668             final ResultMulti res5 = new ResultMulti();
 669             res5.addGreatestCommonPrefix( "A.1.1.1.1", 0.2 );
 670             res5.addGreatestCommonPrefix( "C.2.3", 0.2 );
 671             res5.addGreatestCommonPrefix( "A.1.5", 0.1 );
 672             res5.addGreatestCommonPrefix( "A.3.1.4", 0.2 );
 673             res5.addGreatestCommonPrefix( "B.1.1", 0.2 );
 674             res5.addGreatestCommonPrefix( "B.1.2", 0.09 );
 675             res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 );
 676             res5.analyze( 0.3 );
 677             System.out.print( res5.toString() );
 678             System.out.println( "------------------------- " );
 679             System.out.println();
 680             final ResultMulti res6 = new ResultMulti();
 681             res6.addGreatestCommonPrefix( "A.1.1.1", 0.05 );
 682             res6.addGreatestCommonPrefix( "A.1.1.1.1", 0.65 );
 683             res6.addGreatestCommonPrefix( "A.1", 0.1 );
 684             res6.addGreatestCommonPrefix( "A.1.2", 0.1 );
 685             res6.addGreatestCommonPrefix( "B.1", 0.1 );
 686             res6.analyze( 0.3 );
 687             System.out.print( res6.toString() );
 688             System.out.println( "------------------------- " );
 689             System.out.println();
 690             final ResultMulti res7 = new ResultMulti();
 691             res7.addGreatestCommonPrefix( "A.1.1.1", 0.07 );
 692             res7.addGreatestCommonPrefix( "A.1.1.1.1", 0.9 );
 693             res7.addGreatestCommonPrefix( "A.1", 0.01 );
 694             res7.addGreatestCommonPrefix( "A.1.2", 0.01 );
 695             res7.addGreatestCommonPrefix( "B.1", 0.01 );
 696             res7.analyze( 0.3 );
 697             System.out.print( res7.toString() );
 698             System.out.println( "------------------------- " );
 699             System.out.println();
 700             final ResultMulti res8 = new ResultMulti( "_/_" );
 701             res8.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
 702             res8.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.9 );
 703             res8.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
 704             res8.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
 705             res8.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
 706             res8.analyze( 0.3 );
 707             System.out.print( res8.toString() );
 708             System.out.println( "------------------------- " );
 709             System.out.println();
 710             final ResultMulti res9 = new ResultMulti( "_/_" );
 711             res9.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
 712             res9.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.6 );
 713             res9.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
 714             res9.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
 715             res9.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
 716             res9.addGreatestCommonPrefix( "BB_/_fke_/_dme_/_nx2", 0.3 );
 717             res9.analyze( 0.3 );
 718             System.out.print( res9.toString() );
 719             System.out.println( "------------------------- " );
 720             System.out.println();
 721         }
 722         catch ( final Exception e ) {
 723             e.printStackTrace( System.out );
 724             return false;
 725         }
 726         return true;
 727     }
 728
 729     private static boolean testCladeAnalysis4() {
 730         try {
 731             final File intreefile1 = new File( PATH_TO_TEST_DATA + "pplacer_2.tre" );
 732             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 733             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 734             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 735             final ResultMulti res2 = AnalysisMulti.execute( p1 );
 736             res2.analyze( 0.3 );
 737             System.out.print( res2.toString() );
 738             System.out.println( "------------------------- " );
 739             System.out.println();
 740         }
 741         catch ( final Exception e ) {
 742             e.printStackTrace( System.out );
 743             return false;
 744         }
 745         return true;
 746     }
 747
 748     private static boolean testCladeAnalysis5() {
 749         try {
 750             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_3.xml" );
 751             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 752             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 753             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 754             final ResultMulti res = AnalysisMulti.execute( p1 );
 755             res.analyze( 0.3 );
 756             System.out.print( res.toString() );
 757             System.out.println( "------------------------- " );
 758             System.out.println();
 759         }
 760         catch ( final Exception e ) {
 761             e.printStackTrace( System.out );
 762             return false;
 763         }
 764         return true;
 765     }
 766
 767     private static boolean testCladeAnalysis6() {
 768         try {
 769             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_4.xml" );
 770             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 771             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 772             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 773             final ResultMulti res = AnalysisMulti.execute( p1, 0.45 );
 774             System.out.print( res.toString() );
 775             System.out.println( "------------------------- " );
 776             System.out.println();
 777         }
 778         catch ( final Exception e ) {
 779             e.printStackTrace( System.out );
 780             return false;
 781         }
 782         return true;
 783     }
 784 }