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

   1
   2 package org.forester.clade_analysis;
   3
   4 import java.io.File;
   5 import java.util.List;
   6 import java.util.regex.Pattern;
   7
   8 import org.forester.io.parsers.PhylogenyParser;
   9 import org.forester.io.parsers.util.ParserUtils;
  10 import org.forester.phylogeny.Phylogeny;
  11 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  12 import org.forester.phylogeny.factories.PhylogenyFactory;
  13 import org.forester.util.ForesterUtil;
  14
  15 public class CladeAnalysisTest {
  16
  17     private final static String PATH_TO_TEST_DATA = System.getProperty( "user.dir" ) + ForesterUtil.getFileSeparator()
  18             + "test_data" + ForesterUtil.getFileSeparator();
  19
  20     public static void main( final String[] args ) {
  21         boolean failed = false;
  22         if ( !testCladeAnalysis1() ) {
  23             System.out.println( "Clade analysis 1 failed" );
  24             failed = true;
  25         }
  26         if ( !testCladeAnalysis2() ) {
  27             System.out.println( "Clade analysis 2 failed" );
  28             failed = true;
  29         }
  30         if ( !testCladeAnalysis3() ) {
  31             System.out.println( "Clade analysis 3 failed" );
  32             failed = true;
  33         }
  34         if ( !testCladeAnalysis4() ) {
  35             System.out.println( "Clade analysis 3 failed" );
  36             failed = true;
  37         }
  38         if ( !failed ) {
  39             System.out.println( "OK" );
  40         }
  41     }
  42
  43     public static boolean test() {
  44         if ( !testCladeAnalysis1() ) {
  45             return false;
  46         }
  47         if ( !testCladeAnalysis2() ) {
  48             return false;
  49         }
  50         if ( !testCladeAnalysis3() ) {
  51             return false;
  52         }
  53         if ( !testCladeAnalysis4() ) {
  54             return false;
  55         }
  56         return true;
  57     }
  58
  59     private static boolean testCladeAnalysis1() {
  60         try {
  61             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_1.xml" );
  62             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  63             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
  64             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
  65             Result res = Analysis.execute( p1, "A.1.1.1", "." );
  66             if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
  67                 return false;
  68             }
  69             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
  70                 return false;
  71             }
  72             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
  73                 return false;
  74             }
  75             if ( res.getLeastEncompassingCladeSize() != 4 ) {
  76                 return false;
  77             }
  78             if ( res.getTreeSize() != 25 ) {
  79                 return false;
  80             }
  81             if ( res.getWarnings().size() != 0 ) {
  82                 return false;
  83             }
  84             res = Analysis.execute( p1, "A.1.1.2", "." );
  85             if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
  86                 return false;
  87             }
  88             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
  89                 return false;
  90             }
  91             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
  92                 return false;
  93             }
  94             if ( res.getLeastEncompassingCladeSize() != 4 ) {
  95                 return false;
  96             }
  97             if ( res.getTreeSize() != 25 ) {
  98                 return false;
  99             }
 100             if ( res.getWarnings().size() != 0 ) {
 101                 return false;
 102             }
 103             res = Analysis.execute( p1, "A.1.1.3", "." );
 104             if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
 105                 return false;
 106             }
 107             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 108                 return false;
 109             }
 110             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
 111                 return false;
 112             }
 113             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 114                 return false;
 115             }
 116             if ( res.getTreeSize() != 25 ) {
 117                 return false;
 118             }
 119             if ( res.getWarnings().size() != 0 ) {
 120                 return false;
 121             }
 122             res = Analysis.execute( p1, "A.1.1.4", "." );
 123             if ( !res.getGreatestCommonPrefix().equals( "A.1.1" ) ) {
 124                 return false;
 125             }
 126             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 127                 return false;
 128             }
 129             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.1" ) ) {
 130                 return false;
 131             }
 132             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 133                 return false;
 134             }
 135             if ( res.getTreeSize() != 25 ) {
 136                 return false;
 137             }
 138             if ( res.getWarnings().size() != 0 ) {
 139                 return false;
 140             }
 141             res = Analysis.execute( p1, "A.1.2.1", "." );
 142             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 143                 return false;
 144             }
 145             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 146                 return false;
 147             }
 148             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 149                 return false;
 150             }
 151             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 152                 return false;
 153             }
 154             if ( res.getTreeSize() != 25 ) {
 155                 return false;
 156             }
 157             if ( res.getWarnings().size() != 0 ) {
 158                 return false;
 159             }
 160             res = Analysis.execute( p1, "A.2.1.1", "." );
 161             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 162                 return false;
 163             }
 164             if ( !res.getGreatestCommonPrefixDown().equals( "A.2.1.2" ) ) {
 165                 return false;
 166             }
 167             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 168                 return false;
 169             }
 170             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 171                 return false;
 172             }
 173             if ( res.getTreeSize() != 25 ) {
 174                 return false;
 175             }
 176             if ( res.getWarnings().size() != 0 ) {
 177                 return false;
 178             }
 179             res = Analysis.execute( p1, "A.2.1.2", "." );
 180             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 181                 return false;
 182             }
 183             if ( !res.getGreatestCommonPrefixDown().equals( "A.2.1.1" ) ) {
 184                 return false;
 185             }
 186             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 187                 return false;
 188             }
 189             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 190                 return false;
 191             }
 192             if ( res.getTreeSize() != 25 ) {
 193                 return false;
 194             }
 195             if ( res.getWarnings().size() != 0 ) {
 196                 return false;
 197             }
 198             res = Analysis.execute( p1, "A.3.1.1", "." );
 199             if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
 200                 return false;
 201             }
 202             if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1.2" ) ) {
 203                 return false;
 204             }
 205             if ( !res.getGreatestCommonPrefixUp().equals( "A.3.2.1" ) ) {
 206                 return false;
 207             }
 208             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 209                 return false;
 210             }
 211             if ( res.getTreeSize() != 25 ) {
 212                 return false;
 213             }
 214             if ( res.getWarnings().size() != 0 ) {
 215                 return false;
 216             }
 217             res = Analysis.execute( p1, "A.3.1.2", "." );
 218             if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
 219                 return false;
 220             }
 221             if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1.1" ) ) {
 222                 return false;
 223             }
 224             if ( !res.getGreatestCommonPrefixUp().equals( "A.3.2.1" ) ) {
 225                 return false;
 226             }
 227             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 228                 return false;
 229             }
 230             if ( res.getTreeSize() != 25 ) {
 231                 return false;
 232             }
 233             if ( res.getWarnings().size() != 0 ) {
 234                 return false;
 235             }
 236             res = Analysis.execute( p1, "A.3.2.1", "." );
 237             if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
 238                 return false;
 239             }
 240             if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1" ) ) {
 241                 return false;
 242             }
 243             if ( !res.getGreatestCommonPrefixUp().equals( "A.3.3.1" ) ) {
 244                 return false;
 245             }
 246             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 247                 return false;
 248             }
 249             if ( res.getTreeSize() != 25 ) {
 250                 return false;
 251             }
 252             if ( res.getWarnings().size() != 0 ) {
 253                 return false;
 254             }
 255             res = Analysis.execute( p1, "A.3.3.1", "." );
 256             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 257                 return false;
 258             }
 259             if ( !res.getGreatestCommonPrefixDown().equals( "A.3" ) ) {
 260                 return false;
 261             }
 262             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 263                 return false;
 264             }
 265             if ( res.getLeastEncompassingCladeSize() != 10 ) {
 266                 return false;
 267             }
 268             if ( res.getTreeSize() != 25 ) {
 269                 return false;
 270             }
 271             if ( res.getWarnings().size() != 0 ) {
 272                 return false;
 273             }
 274             res = Analysis.execute( p1, "A.4.1.1", "." );
 275             if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
 276                 return false;
 277             }
 278             if ( !res.getGreatestCommonPrefixDown().equals( "A.4.1.1.a" ) ) {
 279                 return false;
 280             }
 281             if ( !res.getGreatestCommonPrefixUp().equals( "A.4.1.2" ) ) {
 282                 return false;
 283             }
 284             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 285                 return false;
 286             }
 287             if ( res.getTreeSize() != 25 ) {
 288                 return false;
 289             }
 290             if ( res.getWarnings().size() != 0 ) {
 291                 return false;
 292             }
 293             res = Analysis.execute( p1, "A.4.1.1.a", "." );
 294             if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
 295                 return false;
 296             }
 297             if ( !res.getGreatestCommonPrefixDown().equals( "A.4.1.1" ) ) {
 298                 return false;
 299             }
 300             if ( !res.getGreatestCommonPrefixUp().equals( "A.4.1.2" ) ) {
 301                 return false;
 302             }
 303             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 304                 return false;
 305             }
 306             if ( res.getTreeSize() != 25 ) {
 307                 return false;
 308             }
 309             if ( res.getWarnings().size() != 0 ) {
 310                 return false;
 311             }
 312             res = Analysis.execute( p1, "A.4.1.2", "." );
 313             res = Analysis.execute( p1, "A.4.1.2.a", "." );
 314             res = Analysis.execute( p1, "A.5.1.1", "." );
 315             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 316                 return false;
 317             }
 318             if ( !res.getGreatestCommonPrefixDown().equals( "A.5.1.2" ) ) {
 319                 return false;
 320             }
 321             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 322                 return false;
 323             }
 324             if ( res.getLeastEncompassingCladeSize() != 10 ) {
 325                 return false;
 326             }
 327             if ( res.getTreeSize() != 25 ) {
 328                 return false;
 329             }
 330             if ( res.getWarnings().size() != 0 ) {
 331                 return false;
 332             }
 333             res = Analysis.execute( p1, "A.5.1.2", "." );
 334             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 335                 return false;
 336             }
 337             if ( !res.getGreatestCommonPrefixDown().equals( "A.5.1.1" ) ) {
 338                 return false;
 339             }
 340             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 341                 return false;
 342             }
 343             if ( res.getLeastEncompassingCladeSize() != 10 ) {
 344                 return false;
 345             }
 346             if ( res.getTreeSize() != 25 ) {
 347                 return false;
 348             }
 349             if ( res.getWarnings().size() != 0 ) {
 350                 return false;
 351             }
 352             res = Analysis.execute( p1, "A.6.3.12", "." );
 353             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 354                 return false;
 355             }
 356             if ( !res.getGreatestCommonPrefixDown().equals( "A" ) ) {
 357                 return false;
 358             }
 359             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 360                 return false;
 361             }
 362             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 363                 return false;
 364             }
 365             if ( res.getTreeSize() != 25 ) {
 366                 return false;
 367             }
 368             if ( res.getWarnings().size() != 0 ) {
 369                 return false;
 370             }
 371             res = Analysis.execute( p1, "B.1.1.1", "." );
 372             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 373                 return false;
 374             }
 375             if ( !res.getGreatestCommonPrefixDown().equals( "B.1.234.3" ) ) {
 376                 return false;
 377             }
 378             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 379                 return false;
 380             }
 381             if ( res.getLeastEncompassingCladeSize() != 25 ) {
 382                 return false;
 383             }
 384             if ( res.getTreeSize() != 25 ) {
 385                 return false;
 386             }
 387             if ( res.getWarnings().size() != 2 ) {
 388                 return false;
 389             }
 390             res = Analysis.execute( p1, "B.1.234.3", "." );
 391             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 392                 return false;
 393             }
 394             if ( !res.getGreatestCommonPrefixDown().equals( "B.1.1.1" ) ) {
 395                 return false;
 396             }
 397             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 398                 return false;
 399             }
 400             if ( res.getLeastEncompassingCladeSize() != 25 ) {
 401                 return false;
 402             }
 403             if ( res.getTreeSize() != 25 ) {
 404                 return false;
 405             }
 406             if ( res.getWarnings().size() != 2 ) {
 407                 return false;
 408             }
 409             res = Analysis.execute( p1, "C.1.1.1", "." );
 410             if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
 411                 return false;
 412             }
 413             if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1.2" ) ) {
 414                 return false;
 415             }
 416             if ( !res.getGreatestCommonPrefixUp().equals( "C.1.2.1" ) ) {
 417                 return false;
 418             }
 419             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 420                 return false;
 421             }
 422             if ( res.getTreeSize() != 25 ) {
 423                 return false;
 424             }
 425             if ( res.getWarnings().size() != 0 ) {
 426                 return false;
 427             }
 428             res = Analysis.execute( p1, "C.1.1.2", "." );
 429             if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
 430                 return false;
 431             }
 432             if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1.1" ) ) {
 433                 return false;
 434             }
 435             if ( !res.getGreatestCommonPrefixUp().equals( "C.1.2.1" ) ) {
 436                 return false;
 437             }
 438             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 439                 return false;
 440             }
 441             if ( res.getTreeSize() != 25 ) {
 442                 return false;
 443             }
 444             if ( res.getWarnings().size() != 0 ) {
 445                 return false;
 446             }
 447             res = Analysis.execute( p1, "C.1.2.1", "." );
 448             if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
 449                 return false;
 450             }
 451             if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1" ) ) {
 452                 return false;
 453             }
 454             if ( !res.getGreatestCommonPrefixUp().equals( "C.2.1" ) ) {
 455                 return false;
 456             }
 457             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 458                 return false;
 459             }
 460             if ( res.getTreeSize() != 25 ) {
 461                 return false;
 462             }
 463             if ( res.getWarnings().size() != 0 ) {
 464                 return false;
 465             }
 466             res = Analysis.execute( p1, "C.2.1", "." );
 467             if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
 468                 return false;
 469             }
 470             if ( !res.getGreatestCommonPrefixDown().equals( "C.1" ) ) {
 471                 return false;
 472             }
 473             if ( !res.getGreatestCommonPrefixUp().equals( "C.3" ) ) {
 474                 return false;
 475             }
 476             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 477                 return false;
 478             }
 479             if ( res.getTreeSize() != 25 ) {
 480                 return false;
 481             }
 482             if ( res.getWarnings().size() != 0 ) {
 483                 return false;
 484             }
 485             res = Analysis.execute( p1, "C.3", "." );
 486             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 487                 return false;
 488             }
 489             if ( !res.getGreatestCommonPrefixDown().equals( "C" ) ) {
 490                 return false;
 491             }
 492             if ( !res.getGreatestCommonPrefixUp().equals( "QE.1.1.1.2.1" ) ) {
 493                 return false;
 494             }
 495             if ( res.getLeastEncompassingCladeSize() != 5 ) {
 496                 return false;
 497             }
 498             if ( res.getTreeSize() != 25 ) {
 499                 return false;
 500             }
 501             if ( res.getWarnings().size() != 1 ) {
 502                 return false;
 503             }
 504             res = Analysis.execute( p1, "QE.1.1.1.2.1", "." );
 505             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 506                 return false;
 507             }
 508             if ( !res.getGreatestCommonPrefixDown().equals( "C" ) ) {
 509                 return false;
 510             }
 511             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 512                 return false;
 513             }
 514             if ( res.getLeastEncompassingCladeSize() != 25 ) {
 515                 return false;
 516             }
 517             if ( res.getTreeSize() != 25 ) {
 518                 return false;
 519             }
 520             if ( res.getWarnings().size() != 2 ) {
 521                 return false;
 522             }
 523         }
 524         catch ( final Exception e ) {
 525             e.printStackTrace( System.out );
 526             return false;
 527         }
 528         return true;
 529     }
 530
 531     private static boolean testCladeAnalysis2() {
 532         try {
 533             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_2.xml" );
 534             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 535             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 536             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 537             Result res = Analysis.execute( p1, "6_DQ278891", null );
 538             if ( !res.getGreatestCommonPrefix().equals( "6_" ) ) {
 539                 return false;
 540             }
 541             if ( !res.getGreatestCommonPrefixDown().equals( "6_DQ278893" ) ) {
 542                 return false;
 543             }
 544             if ( !res.getGreatestCommonPrefixUp().equals( "6_JX183550" ) ) {
 545                 return false;
 546             }
 547             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 548                 return false;
 549             }
 550             if ( res.getTreeSize() != 219 ) {
 551                 return false;
 552             }
 553             if ( res.getWarnings().size() != 0 ) {
 554                 return false;
 555             }
 556             res = Analysis.execute( p1, "6xa_EU408330", null );
 557             if ( !res.getGreatestCommonPrefix().equals( "6xa_EU40833" ) ) {
 558                 return false;
 559             }
 560             if ( !res.getGreatestCommonPrefixDown().equals( "6xa_EU408331" ) ) {
 561                 return false;
 562             }
 563             if ( !res.getGreatestCommonPrefixUp().equals( "6xa_EU408332" ) ) {
 564                 return false;
 565             }
 566             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 567                 return false;
 568             }
 569             if ( res.getTreeSize() != 219 ) {
 570                 return false;
 571             }
 572             if ( res.getWarnings().size() != 0 ) {
 573                 return false;
 574             }
 575             res = Analysis.execute( p1, "7a_EF108306", null );
 576             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 577                 return false;
 578             }
 579             if ( !res.getGreatestCommonPrefixDown().equals( "2" ) ) {
 580                 return false;
 581             }
 582             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 583                 return false;
 584             }
 585             if ( res.getLeastEncompassingCladeSize() != 219 ) {
 586                 return false;
 587             }
 588             if ( res.getTreeSize() != 219 ) {
 589                 return false;
 590             }
 591             if ( res.getWarnings().size() != 2 ) {
 592                 return false;
 593             }
 594         }
 595         catch ( final Exception e ) {
 596             e.printStackTrace( System.out );
 597             return false;
 598         }
 599         return true;
 600     }
 601
 602     private static boolean testCladeAnalysis3() {
 603         try {
 604             final Result2 res1 = new Result2();
 605             res1.addGreatestCommonPrefix( "A.1.1", 0.3 );
 606             res1.addGreatestCommonPrefix( "A.1.2", 0.3 );
 607             res1.addGreatestCommonPrefix( "A.1.3", 0.3 );
 608             res1.addGreatestCommonPrefix( "B.1", 0.1 );
 609             res1.analyzeGreatestCommonPrefixes( 0.3 );
 610             System.out.print( res1.toString());
 611             System.out.println( "------------------------- ");
 612             System.out.println();
 613
 614             final Result2 res2 = new Result2( "." );
 615             res2.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
 616             res2.addGreatestCommonPrefix( "A.1", 0.7 );
 617             res2.addGreatestCommonPrefix( "A.1.2", 0.1 );
 618             res2.addGreatestCommonPrefix( "B.1", 0.1 );
 619             res2.analyzeGreatestCommonPrefixes( 0.3 );
 620             System.out.print( res2.toString());
 621             System.out.println( "------------------------- ");
 622             System.out.println();
 623
 624             final Result2 res3 = new Result2( "." );
 625             res3.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
 626             res3.addGreatestCommonPrefix( "A.1.1.1.1", 0.6 );
 627             res3.addGreatestCommonPrefix( "A.1", 0.1 );
 628             res3.addGreatestCommonPrefix( "A.1.2", 0.1 );
 629             res3.addGreatestCommonPrefix( "B.1", 0.1 );
 630             res3.analyzeGreatestCommonPrefixes( 0.3 );
 631             System.out.print( res3.toString());
 632             System.out.println( "------------------------- ");
 633             System.out.println();
 634
 635             final Result2 res33 = new Result2( "." );
 636             res33.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
 637             res33.addGreatestCommonPrefix( "A.1.1.1.1", 0.3 );
 638             res33.addGreatestCommonPrefix( "A.1", 0.1 );
 639             res33.addGreatestCommonPrefix( "A.1.2", 0.1 );
 640             res33.addGreatestCommonPrefix( "B.1", 0.1 );
 641             res33.addGreatestCommonPrefix( "B.1.1.1", 0.3 );
 642             res33.analyzeGreatestCommonPrefixes( 0.3 );
 643             System.out.print( res33.toString());
 644             System.out.println( "------------------------- ");
 645             System.out.println();
 646
 647             final Result2 res4 = new Result2();
 648             res4.addGreatestCommonPrefix( "A.1.1.1.1", 0.35 );
 649             res4.addGreatestCommonPrefix( "A.1.1.1.2", 0.35 );
 650             res4.addGreatestCommonPrefix( "A.1", 0.1 );
 651             res4.addGreatestCommonPrefix( "A.1.2", 0.1 );
 652             res4.addGreatestCommonPrefix( "B.1", 0.1 );
 653             res4.analyzeGreatestCommonPrefixes( 0.3 );
 654             System.out.print( res4.toString());
 655             System.out.println( "------------------------- ");
 656             System.out.println();
 657
 658             final Result2 res5 = new Result2();
 659             res5.addGreatestCommonPrefix( "A.1.1.1.1", 0.2 );
 660             res5.addGreatestCommonPrefix( "C.2.3", 0.2 );
 661             res5.addGreatestCommonPrefix( "A.1.5", 0.1 );
 662             res5.addGreatestCommonPrefix( "A.3.1.4", 0.2 );
 663             res5.addGreatestCommonPrefix( "B.1.1", 0.2 );
 664             res5.addGreatestCommonPrefix( "B.1.2", 0.09 );
 665             res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 );
 666             res5.analyzeGreatestCommonPrefixes( 0.3 );
 667             System.out.print( res5.toString());
 668             System.out.println( "------------------------- ");
 669             System.out.println();
 670
 671             final Result2 res6 = new Result2();
 672             res6.addGreatestCommonPrefix( "A.1.1.1", 0.05 );
 673             res6.addGreatestCommonPrefix( "A.1.1.1.1", 0.65 );
 674             res6.addGreatestCommonPrefix( "A.1", 0.1 );
 675             res6.addGreatestCommonPrefix( "A.1.2", 0.1 );
 676             res6.addGreatestCommonPrefix( "B.1", 0.1 );
 677             res6.analyzeGreatestCommonPrefixes( 0.3 );
 678             System.out.print( res6.toString());
 679             System.out.println( "------------------------- ");
 680             System.out.println();
 681
 682             final Result2 res7 = new Result2();
 683             res7.addGreatestCommonPrefix( "A.1.1.1", 0.07 );
 684             res7.addGreatestCommonPrefix( "A.1.1.1.1", 0.9 );
 685             res7.addGreatestCommonPrefix( "A.1", 0.01 );
 686             res7.addGreatestCommonPrefix( "A.1.2", 0.01 );
 687             res7.addGreatestCommonPrefix( "B.1", 0.01 );
 688             res7.analyzeGreatestCommonPrefixes( 0.3 );
 689             System.out.print( res7.toString());
 690             System.out.println( "------------------------- ");
 691             System.out.println();
 692
 693             final Result2 res8 = new Result2( "_/_" );
 694             res8.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
 695             res8.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.9 );
 696             res8.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
 697             res8.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
 698             res8.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
 699             res8.analyzeGreatestCommonPrefixes( 0.3 );
 700             System.out.print( res8.toString());
 701             System.out.println( "------------------------- ");
 702             System.out.println();
 703
 704             final Result2 res9 = new Result2( "_/_" );
 705             res9.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
 706             res9.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.6 );
 707             res9.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
 708             res9.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
 709             res9.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
 710             res9.addGreatestCommonPrefix( "BB_/_fke_/_dme_/_nx2", 0.3 );
 711             res9.analyzeGreatestCommonPrefixes( 0.3 );
 712             System.out.print( res9.toString());
 713             System.out.println( "------------------------- ");
 714             System.out.println();
 715         }
 716         catch ( final Exception e ) {
 717             e.printStackTrace( System.out );
 718             return false;
 719         }
 720         return true;
 721     }
 722
 723     private static boolean testCladeAnalysis4() {
 724         try {
 725             final File intreefile1 = new File( PATH_TO_TEST_DATA + "pplacer_2.tre" );
 726             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 727             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 728             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 729             Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
 730             Result2 res = Analysis2.execute( p1, query, "." );
 731
 732             res.analyzeGreatestCommonPrefixes( 0.3 );
 733             System.out.print( res.toString());
 734             System.out.println( "------------------------- ");
 735             System.out.println();
 736
 737            // Result res = Analysis.execute( p1, "A.1.1.1", "." );
 738            /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
 739                 return false;
 740             }
 741             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 742                 return false;
 743             }
 744             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
 745                 return false;
 746             }
 747             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 748                 return false;
 749             }
 750             if ( res.getTreeSize() != 25 ) {
 751                 return false;
 752             }
 753             if ( res.getWarnings().size() != 0 ) {
 754                 return false;
 755             }*/
 756
 757         }
 758         catch ( final Exception e ) {
 759             e.printStackTrace( System.out );
 760             return false;
 761         }
 762         return true;
 763     }
 764 }