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 4 failed" );
  36             failed = true;
  37         }
  38         if ( !testCladeAnalysis5() ) {
  39             System.out.println( "Clade analysis 5 failed" );
  40             failed = true;
  41         }
  42         if ( !testCladeAnalysis6() ) {
  43             System.out.println( "Clade analysis 6 failed" );
  44             failed = true;
  45         }
  46         if ( !failed ) {
  47             System.out.println( "OK" );
  48         }
  49     }
  50
  51     public static boolean test() {
  52         if ( !testCladeAnalysis1() ) {
  53             return false;
  54         }
  55         if ( !testCladeAnalysis2() ) {
  56             return false;
  57         }
  58         if ( !testCladeAnalysis3() ) {
  59             return false;
  60         }
  61         if ( !testCladeAnalysis4() ) {
  62             return false;
  63         }
  64         if ( !testCladeAnalysis5() ) {
  65             return false;
  66         }
  67         if ( !testCladeAnalysis6() ) {
  68             return false;
  69         }
  70         return true;
  71     }
  72
  73     private static boolean testCladeAnalysis1() {
  74         try {
  75             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_1.xml" );
  76             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
  77             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
  78             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
  79             Result res = Analysis.execute( p1, "A.1.1.1", "." );
  80             if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
  81                 return false;
  82             }
  83             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
  84                 return false;
  85             }
  86             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
  87                 return false;
  88             }
  89             if ( res.getLeastEncompassingCladeSize() != 4 ) {
  90                 return false;
  91             }
  92             if ( res.getTreeSize() != 25 ) {
  93                 return false;
  94             }
  95             if ( res.getWarnings().size() != 0 ) {
  96                 return false;
  97             }
  98             res = Analysis.execute( p1, "A.1.1.2", "." );
  99             if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
 100                 return false;
 101             }
 102             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 103                 return false;
 104             }
 105             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
 106                 return false;
 107             }
 108             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 109                 return false;
 110             }
 111             if ( res.getTreeSize() != 25 ) {
 112                 return false;
 113             }
 114             if ( res.getWarnings().size() != 0 ) {
 115                 return false;
 116             }
 117             res = Analysis.execute( p1, "A.1.1.3", "." );
 118             if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
 119                 return false;
 120             }
 121             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 122                 return false;
 123             }
 124             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
 125                 return false;
 126             }
 127             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 128                 return false;
 129             }
 130             if ( res.getTreeSize() != 25 ) {
 131                 return false;
 132             }
 133             if ( res.getWarnings().size() != 0 ) {
 134                 return false;
 135             }
 136             res = Analysis.execute( p1, "A.1.1.4", "." );
 137             if ( !res.getGreatestCommonPrefix().equals( "A.1.1" ) ) {
 138                 return false;
 139             }
 140             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 141                 return false;
 142             }
 143             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.1" ) ) {
 144                 return false;
 145             }
 146             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 147                 return false;
 148             }
 149             if ( res.getTreeSize() != 25 ) {
 150                 return false;
 151             }
 152             if ( res.getWarnings().size() != 0 ) {
 153                 return false;
 154             }
 155             res = Analysis.execute( p1, "A.1.2.1", "." );
 156             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 157                 return false;
 158             }
 159             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 160                 return false;
 161             }
 162             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 163                 return false;
 164             }
 165             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 166                 return false;
 167             }
 168             if ( res.getTreeSize() != 25 ) {
 169                 return false;
 170             }
 171             if ( res.getWarnings().size() != 0 ) {
 172                 return false;
 173             }
 174             res = Analysis.execute( p1, "A.2.1.1", "." );
 175             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 176                 return false;
 177             }
 178             if ( !res.getGreatestCommonPrefixDown().equals( "A.2.1.2" ) ) {
 179                 return false;
 180             }
 181             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 182                 return false;
 183             }
 184             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 185                 return false;
 186             }
 187             if ( res.getTreeSize() != 25 ) {
 188                 return false;
 189             }
 190             if ( res.getWarnings().size() != 0 ) {
 191                 return false;
 192             }
 193             res = Analysis.execute( p1, "A.2.1.2", "." );
 194             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 195                 return false;
 196             }
 197             if ( !res.getGreatestCommonPrefixDown().equals( "A.2.1.1" ) ) {
 198                 return false;
 199             }
 200             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 201                 return false;
 202             }
 203             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 204                 return false;
 205             }
 206             if ( res.getTreeSize() != 25 ) {
 207                 return false;
 208             }
 209             if ( res.getWarnings().size() != 0 ) {
 210                 return false;
 211             }
 212             res = Analysis.execute( p1, "A.3.1.1", "." );
 213             if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
 214                 return false;
 215             }
 216             if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1.2" ) ) {
 217                 return false;
 218             }
 219             if ( !res.getGreatestCommonPrefixUp().equals( "A.3.2.1" ) ) {
 220                 return false;
 221             }
 222             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 223                 return false;
 224             }
 225             if ( res.getTreeSize() != 25 ) {
 226                 return false;
 227             }
 228             if ( res.getWarnings().size() != 0 ) {
 229                 return false;
 230             }
 231             res = Analysis.execute( p1, "A.3.1.2", "." );
 232             if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
 233                 return false;
 234             }
 235             if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1.1" ) ) {
 236                 return false;
 237             }
 238             if ( !res.getGreatestCommonPrefixUp().equals( "A.3.2.1" ) ) {
 239                 return false;
 240             }
 241             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 242                 return false;
 243             }
 244             if ( res.getTreeSize() != 25 ) {
 245                 return false;
 246             }
 247             if ( res.getWarnings().size() != 0 ) {
 248                 return false;
 249             }
 250             res = Analysis.execute( p1, "A.3.2.1", "." );
 251             if ( !res.getGreatestCommonPrefix().equals( "A.3" ) ) {
 252                 return false;
 253             }
 254             if ( !res.getGreatestCommonPrefixDown().equals( "A.3.1" ) ) {
 255                 return false;
 256             }
 257             if ( !res.getGreatestCommonPrefixUp().equals( "A.3.3.1" ) ) {
 258                 return false;
 259             }
 260             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 261                 return false;
 262             }
 263             if ( res.getTreeSize() != 25 ) {
 264                 return false;
 265             }
 266             if ( res.getWarnings().size() != 0 ) {
 267                 return false;
 268             }
 269             res = Analysis.execute( p1, "A.3.3.1", "." );
 270             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 271                 return false;
 272             }
 273             if ( !res.getGreatestCommonPrefixDown().equals( "A.3" ) ) {
 274                 return false;
 275             }
 276             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 277                 return false;
 278             }
 279             if ( res.getLeastEncompassingCladeSize() != 10 ) {
 280                 return false;
 281             }
 282             if ( res.getTreeSize() != 25 ) {
 283                 return false;
 284             }
 285             if ( res.getWarnings().size() != 0 ) {
 286                 return false;
 287             }
 288             res = Analysis.execute( p1, "A.4.1.1", "." );
 289             if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
 290                 return false;
 291             }
 292             if ( !res.getGreatestCommonPrefixDown().equals( "A.4.1.1.a" ) ) {
 293                 return false;
 294             }
 295             if ( !res.getGreatestCommonPrefixUp().equals( "A.4.1.2" ) ) {
 296                 return false;
 297             }
 298             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 299                 return false;
 300             }
 301             if ( res.getTreeSize() != 25 ) {
 302                 return false;
 303             }
 304             if ( res.getWarnings().size() != 0 ) {
 305                 return false;
 306             }
 307             res = Analysis.execute( p1, "A.4.1.1.a", "." );
 308             if ( !res.getGreatestCommonPrefix().equals( "A.4.1" ) ) {
 309                 return false;
 310             }
 311             if ( !res.getGreatestCommonPrefixDown().equals( "A.4.1.1" ) ) {
 312                 return false;
 313             }
 314             if ( !res.getGreatestCommonPrefixUp().equals( "A.4.1.2" ) ) {
 315                 return false;
 316             }
 317             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 318                 return false;
 319             }
 320             if ( res.getTreeSize() != 25 ) {
 321                 return false;
 322             }
 323             if ( res.getWarnings().size() != 0 ) {
 324                 return false;
 325             }
 326             res = Analysis.execute( p1, "A.4.1.2", "." );
 327             res = Analysis.execute( p1, "A.4.1.2.a", "." );
 328             res = Analysis.execute( p1, "A.5.1.1", "." );
 329             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 330                 return false;
 331             }
 332             if ( !res.getGreatestCommonPrefixDown().equals( "A.5.1.2" ) ) {
 333                 return false;
 334             }
 335             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 336                 return false;
 337             }
 338             if ( res.getLeastEncompassingCladeSize() != 10 ) {
 339                 return false;
 340             }
 341             if ( res.getTreeSize() != 25 ) {
 342                 return false;
 343             }
 344             if ( res.getWarnings().size() != 0 ) {
 345                 return false;
 346             }
 347             res = Analysis.execute( p1, "A.5.1.2", "." );
 348             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 349                 return false;
 350             }
 351             if ( !res.getGreatestCommonPrefixDown().equals( "A.5.1.1" ) ) {
 352                 return false;
 353             }
 354             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 355                 return false;
 356             }
 357             if ( res.getLeastEncompassingCladeSize() != 10 ) {
 358                 return false;
 359             }
 360             if ( res.getTreeSize() != 25 ) {
 361                 return false;
 362             }
 363             if ( res.getWarnings().size() != 0 ) {
 364                 return false;
 365             }
 366             res = Analysis.execute( p1, "A.6.3.12", "." );
 367             if ( !res.getGreatestCommonPrefix().equals( "A" ) ) {
 368                 return false;
 369             }
 370             if ( !res.getGreatestCommonPrefixDown().equals( "A" ) ) {
 371                 return false;
 372             }
 373             if ( !res.getGreatestCommonPrefixUp().equals( "A" ) ) {
 374                 return false;
 375             }
 376             if ( res.getLeastEncompassingCladeSize() != 17 ) {
 377                 return false;
 378             }
 379             if ( res.getTreeSize() != 25 ) {
 380                 return false;
 381             }
 382             if ( res.getWarnings().size() != 0 ) {
 383                 return false;
 384             }
 385             res = Analysis.execute( p1, "B.1.1.1", "." );
 386             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 387                 return false;
 388             }
 389             if ( !res.getGreatestCommonPrefixDown().equals( "B.1.234.3" ) ) {
 390                 return false;
 391             }
 392             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 393                 return false;
 394             }
 395             if ( res.getLeastEncompassingCladeSize() != 25 ) {
 396                 return false;
 397             }
 398             if ( res.getTreeSize() != 25 ) {
 399                 return false;
 400             }
 401             if ( res.getWarnings().size() != 2 ) {
 402                 return false;
 403             }
 404             res = Analysis.execute( p1, "B.1.234.3", "." );
 405             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 406                 return false;
 407             }
 408             if ( !res.getGreatestCommonPrefixDown().equals( "B.1.1.1" ) ) {
 409                 return false;
 410             }
 411             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 412                 return false;
 413             }
 414             if ( res.getLeastEncompassingCladeSize() != 25 ) {
 415                 return false;
 416             }
 417             if ( res.getTreeSize() != 25 ) {
 418                 return false;
 419             }
 420             if ( res.getWarnings().size() != 2 ) {
 421                 return false;
 422             }
 423             res = Analysis.execute( p1, "C.1.1.1", "." );
 424             if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
 425                 return false;
 426             }
 427             if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1.2" ) ) {
 428                 return false;
 429             }
 430             if ( !res.getGreatestCommonPrefixUp().equals( "C.1.2.1" ) ) {
 431                 return false;
 432             }
 433             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 434                 return false;
 435             }
 436             if ( res.getTreeSize() != 25 ) {
 437                 return false;
 438             }
 439             if ( res.getWarnings().size() != 0 ) {
 440                 return false;
 441             }
 442             res = Analysis.execute( p1, "C.1.1.2", "." );
 443             if ( !res.getGreatestCommonPrefix().equals( "C.1" ) ) {
 444                 return false;
 445             }
 446             if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1.1" ) ) {
 447                 return false;
 448             }
 449             if ( !res.getGreatestCommonPrefixUp().equals( "C.1.2.1" ) ) {
 450                 return false;
 451             }
 452             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 453                 return false;
 454             }
 455             if ( res.getTreeSize() != 25 ) {
 456                 return false;
 457             }
 458             if ( res.getWarnings().size() != 0 ) {
 459                 return false;
 460             }
 461             res = Analysis.execute( p1, "C.1.2.1", "." );
 462             if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
 463                 return false;
 464             }
 465             if ( !res.getGreatestCommonPrefixDown().equals( "C.1.1" ) ) {
 466                 return false;
 467             }
 468             if ( !res.getGreatestCommonPrefixUp().equals( "C.2.1" ) ) {
 469                 return false;
 470             }
 471             if ( res.getLeastEncompassingCladeSize() != 3 ) {
 472                 return false;
 473             }
 474             if ( res.getTreeSize() != 25 ) {
 475                 return false;
 476             }
 477             if ( res.getWarnings().size() != 0 ) {
 478                 return false;
 479             }
 480             res = Analysis.execute( p1, "C.2.1", "." );
 481             if ( !res.getGreatestCommonPrefix().equals( "C" ) ) {
 482                 return false;
 483             }
 484             if ( !res.getGreatestCommonPrefixDown().equals( "C.1" ) ) {
 485                 return false;
 486             }
 487             if ( !res.getGreatestCommonPrefixUp().equals( "C.3" ) ) {
 488                 return false;
 489             }
 490             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 491                 return false;
 492             }
 493             if ( res.getTreeSize() != 25 ) {
 494                 return false;
 495             }
 496             if ( res.getWarnings().size() != 0 ) {
 497                 return false;
 498             }
 499             res = Analysis.execute( p1, "C.3", "." );
 500             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 501                 return false;
 502             }
 503             if ( !res.getGreatestCommonPrefixDown().equals( "C" ) ) {
 504                 return false;
 505             }
 506             if ( !res.getGreatestCommonPrefixUp().equals( "QE.1.1.1.2.1" ) ) {
 507                 return false;
 508             }
 509             if ( res.getLeastEncompassingCladeSize() != 5 ) {
 510                 return false;
 511             }
 512             if ( res.getTreeSize() != 25 ) {
 513                 return false;
 514             }
 515             if ( res.getWarnings().size() != 1 ) {
 516                 return false;
 517             }
 518             res = Analysis.execute( p1, "QE.1.1.1.2.1", "." );
 519             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 520                 return false;
 521             }
 522             if ( !res.getGreatestCommonPrefixDown().equals( "C" ) ) {
 523                 return false;
 524             }
 525             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 526                 return false;
 527             }
 528             if ( res.getLeastEncompassingCladeSize() != 25 ) {
 529                 return false;
 530             }
 531             if ( res.getTreeSize() != 25 ) {
 532                 return false;
 533             }
 534             if ( res.getWarnings().size() != 2 ) {
 535                 return false;
 536             }
 537         }
 538         catch ( final Exception e ) {
 539             e.printStackTrace( System.out );
 540             return false;
 541         }
 542         return true;
 543     }
 544
 545     private static boolean testCladeAnalysis2() {
 546         try {
 547             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_2.xml" );
 548             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 549             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 550             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 551             Result res = Analysis.execute( p1, "6_DQ278891", null );
 552             if ( !res.getGreatestCommonPrefix().equals( "6_" ) ) {
 553                 return false;
 554             }
 555             if ( !res.getGreatestCommonPrefixDown().equals( "6_DQ278893" ) ) {
 556                 return false;
 557             }
 558             if ( !res.getGreatestCommonPrefixUp().equals( "6_JX183550" ) ) {
 559                 return false;
 560             }
 561             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 562                 return false;
 563             }
 564             if ( res.getTreeSize() != 219 ) {
 565                 return false;
 566             }
 567             if ( res.getWarnings().size() != 0 ) {
 568                 return false;
 569             }
 570             res = Analysis.execute( p1, "6xa_EU408330", null );
 571             if ( !res.getGreatestCommonPrefix().equals( "6xa_EU40833" ) ) {
 572                 return false;
 573             }
 574             if ( !res.getGreatestCommonPrefixDown().equals( "6xa_EU408331" ) ) {
 575                 return false;
 576             }
 577             if ( !res.getGreatestCommonPrefixUp().equals( "6xa_EU408332" ) ) {
 578                 return false;
 579             }
 580             if ( res.getLeastEncompassingCladeSize() != 2 ) {
 581                 return false;
 582             }
 583             if ( res.getTreeSize() != 219 ) {
 584                 return false;
 585             }
 586             if ( res.getWarnings().size() != 0 ) {
 587                 return false;
 588             }
 589             res = Analysis.execute( p1, "7a_EF108306", null );
 590             if ( !res.getGreatestCommonPrefix().equals( "" ) ) {
 591                 return false;
 592             }
 593             if ( !res.getGreatestCommonPrefixDown().equals( "2" ) ) {
 594                 return false;
 595             }
 596             if ( !res.getGreatestCommonPrefixUp().equals( "" ) ) {
 597                 return false;
 598             }
 599             if ( res.getLeastEncompassingCladeSize() != 219 ) {
 600                 return false;
 601             }
 602             if ( res.getTreeSize() != 219 ) {
 603                 return false;
 604             }
 605             if ( res.getWarnings().size() != 2 ) {
 606                 return false;
 607             }
 608         }
 609         catch ( final Exception e ) {
 610             e.printStackTrace( System.out );
 611             return false;
 612         }
 613         return true;
 614     }
 615
 616     private static boolean testCladeAnalysis3() {
 617         try {
 618             final Result2 res1 = new Result2();
 619             res1.addGreatestCommonPrefix( "A.1.1", 0.3 );
 620             res1.addGreatestCommonPrefix( "A.1.2", 0.3 );
 621             res1.addGreatestCommonPrefix( "A.1.3", 0.3 );
 622             res1.addGreatestCommonPrefix( "B.1", 0.1 );
 623             res1.analyzeGreatestCommonPrefixes( 0.3 );
 624             System.out.print( res1.toString());
 625             System.out.println( "------------------------- ");
 626             System.out.println();
 627
 628             final Result2 res2 = new Result2( "." );
 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.analyzeGreatestCommonPrefixes( 0.3 );
 634             System.out.print( res2.toString());
 635             System.out.println( "------------------------- ");
 636             System.out.println();
 637
 638             final Result2 res3 = new Result2( "." );
 639             res3.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
 640             res3.addGreatestCommonPrefix( "A.1.1.1.1", 0.6 );
 641             res3.addGreatestCommonPrefix( "A.1", 0.1 );
 642             res3.addGreatestCommonPrefix( "A.1.2", 0.1 );
 643             res3.addGreatestCommonPrefix( "B.1", 0.1 );
 644             res3.analyzeGreatestCommonPrefixes( 0.3 );
 645             System.out.print( res3.toString());
 646             System.out.println( "------------------------- ");
 647             System.out.println();
 648
 649             final Result2 res33 = new Result2( "." );
 650             res33.addGreatestCommonPrefix( "A.1.1.1", 0.1 );
 651             res33.addGreatestCommonPrefix( "A.1.1.1.1", 0.3 );
 652             res33.addGreatestCommonPrefix( "A.1", 0.1 );
 653             res33.addGreatestCommonPrefix( "A.1.2", 0.1 );
 654             res33.addGreatestCommonPrefix( "B.1", 0.1 );
 655             res33.addGreatestCommonPrefix( "B.1.1.1", 0.3 );
 656             res33.analyzeGreatestCommonPrefixes( 0.3 );
 657             System.out.print( res33.toString());
 658             System.out.println( "------------------------- ");
 659             System.out.println();
 660
 661             final Result2 res4 = new Result2();
 662             res4.addGreatestCommonPrefix( "A.1.1.1.1", 0.35 );
 663             res4.addGreatestCommonPrefix( "A.1.1.1.2", 0.35 );
 664             res4.addGreatestCommonPrefix( "A.1", 0.1 );
 665             res4.addGreatestCommonPrefix( "A.1.2", 0.1 );
 666             res4.addGreatestCommonPrefix( "B.1", 0.1 );
 667             res4.analyzeGreatestCommonPrefixes( 0.3 );
 668             System.out.print( res4.toString());
 669             System.out.println( "------------------------- ");
 670             System.out.println();
 671
 672             final Result2 res5 = new Result2();
 673             res5.addGreatestCommonPrefix( "A.1.1.1.1", 0.2 );
 674             res5.addGreatestCommonPrefix( "C.2.3", 0.2 );
 675             res5.addGreatestCommonPrefix( "A.1.5", 0.1 );
 676             res5.addGreatestCommonPrefix( "A.3.1.4", 0.2 );
 677             res5.addGreatestCommonPrefix( "B.1.1", 0.2 );
 678             res5.addGreatestCommonPrefix( "B.1.2", 0.09 );
 679             res5.addGreatestCommonPrefix( "D.1.1.1.1", 0.01 );
 680             res5.analyzeGreatestCommonPrefixes( 0.3 );
 681             System.out.print( res5.toString());
 682             System.out.println( "------------------------- ");
 683             System.out.println();
 684
 685             final Result2 res6 = new Result2();
 686             res6.addGreatestCommonPrefix( "A.1.1.1", 0.05 );
 687             res6.addGreatestCommonPrefix( "A.1.1.1.1", 0.65 );
 688             res6.addGreatestCommonPrefix( "A.1", 0.1 );
 689             res6.addGreatestCommonPrefix( "A.1.2", 0.1 );
 690             res6.addGreatestCommonPrefix( "B.1", 0.1 );
 691             res6.analyzeGreatestCommonPrefixes( 0.3 );
 692             System.out.print( res6.toString());
 693             System.out.println( "------------------------- ");
 694             System.out.println();
 695
 696             final Result2 res7 = new Result2();
 697             res7.addGreatestCommonPrefix( "A.1.1.1", 0.07 );
 698             res7.addGreatestCommonPrefix( "A.1.1.1.1", 0.9 );
 699             res7.addGreatestCommonPrefix( "A.1", 0.01 );
 700             res7.addGreatestCommonPrefix( "A.1.2", 0.01 );
 701             res7.addGreatestCommonPrefix( "B.1", 0.01 );
 702             res7.analyzeGreatestCommonPrefixes( 0.3 );
 703             System.out.print( res7.toString());
 704             System.out.println( "------------------------- ");
 705             System.out.println();
 706
 707             final Result2 res8 = new Result2( "_/_" );
 708             res8.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
 709             res8.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.9 );
 710             res8.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
 711             res8.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
 712             res8.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
 713             res8.analyzeGreatestCommonPrefixes( 0.3 );
 714             System.out.print( res8.toString());
 715             System.out.println( "------------------------- ");
 716             System.out.println();
 717
 718             final Result2 res9 = new Result2( "_/_" );
 719             res9.addGreatestCommonPrefix( "AA_/_abc_/_def", 0.07 );
 720             res9.addGreatestCommonPrefix( "AA_/_abc_/_sfc", 0.6 );
 721             res9.addGreatestCommonPrefix( "AA_/_abc_/_xcd", 0.01 );
 722             res9.addGreatestCommonPrefix( "AA_/_abc_/_memr", 0.01 );
 723             res9.addGreatestCommonPrefix( "AA_/_abc_/_fkem_/_odem", 0.01 );
 724             res9.addGreatestCommonPrefix( "BB_/_fke_/_dme_/_nx2", 0.3 );
 725             res9.analyzeGreatestCommonPrefixes( 0.3 );
 726             System.out.print( res9.toString());
 727             System.out.println( "------------------------- ");
 728             System.out.println();
 729         }
 730         catch ( final Exception e ) {
 731             e.printStackTrace( System.out );
 732             return false;
 733         }
 734         return true;
 735     }
 736
 737     private static boolean testCladeAnalysis4() {
 738         try {
 739             final File intreefile1 = new File( PATH_TO_TEST_DATA + "pplacer_2.tre" );
 740             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 741             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 742             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 743             Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
 744             Result2 res = Analysis2.execute( p1, query, "." );
 745
 746             res.analyzeGreatestCommonPrefixes( 0.3 );
 747             System.out.print( res.toString());
 748             System.out.println( "------------------------- ");
 749             System.out.println();
 750
 751            // Result res = Analysis.execute( p1, "A.1.1.1", "." );
 752            /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
 753                 return false;
 754             }
 755             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 756                 return false;
 757             }
 758             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
 759                 return false;
 760             }
 761             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 762                 return false;
 763             }
 764             if ( res.getTreeSize() != 25 ) {
 765                 return false;
 766             }
 767             if ( res.getWarnings().size() != 0 ) {
 768                 return false;
 769             }*/
 770
 771         }
 772         catch ( final Exception e ) {
 773             e.printStackTrace( System.out );
 774             return false;
 775         }
 776         return true;
 777     }
 778
 779     private static boolean testCladeAnalysis5() {
 780         try {
 781             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_3.xml" );
 782             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 783             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 784             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 785             Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
 786             Result2 res = Analysis2.execute( p1, query, "." );
 787
 788             res.analyzeGreatestCommonPrefixes( 0.3 );
 789             System.out.print( res.toString());
 790             System.out.println( "------------------------- ");
 791             System.out.println();
 792
 793            // Result res = Analysis.execute( p1, "A.1.1.1", "." );
 794            /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
 795                 return false;
 796             }
 797             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 798                 return false;
 799             }
 800             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
 801                 return false;
 802             }
 803             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 804                 return false;
 805             }
 806             if ( res.getTreeSize() != 25 ) {
 807                 return false;
 808             }
 809             if ( res.getWarnings().size() != 0 ) {
 810                 return false;
 811             }*/
 812
 813         }
 814         catch ( final Exception e ) {
 815             e.printStackTrace( System.out );
 816             return false;
 817         }
 818         return true;
 819     }
 820
 821     private static boolean testCladeAnalysis6() {
 822         try {
 823             final File intreefile1 = new File( PATH_TO_TEST_DATA + "clade_analysis_test_4.xml" );
 824             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
 825             final PhylogenyParser pp = ParserUtils.createParserDependingOnFileType( intreefile1, true );
 826             final Phylogeny p1 = factory.create( intreefile1, pp )[ 0 ];
 827             Pattern query = Pattern.compile(".+#\\d+_M=(.+)");
 828             Result2 res = Analysis2.execute( p1, query, "." );
 829
 830             res.analyzeGreatestCommonPrefixes( 0.45 );
 831             System.out.print( res.toString());
 832             System.out.println( "------------------------- ");
 833             System.out.println();
 834
 835            // Result res = Analysis.execute( p1, "A.1.1.1", "." );
 836            /* if ( !res.getGreatestCommonPrefix().equals( "A.1" ) ) {
 837                 return false;
 838             }
 839             if ( !res.getGreatestCommonPrefixDown().equals( "A.1.1" ) ) {
 840                 return false;
 841             }
 842             if ( !res.getGreatestCommonPrefixUp().equals( "A.1.2.1" ) ) {
 843                 return false;
 844             }
 845             if ( res.getLeastEncompassingCladeSize() != 4 ) {
 846                 return false;
 847             }
 848             if ( res.getTreeSize() != 25 ) {
 849                 return false;
 850             }
 851             if ( res.getWarnings().size() != 0 ) {
 852                 return false;
 853             }*/
 854
 855         }
 856         catch ( final Exception e ) {
 857             e.printStackTrace( System.out );
 858             return false;
 859         }
 860         return true;
 861     }
 862 }