X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Frio%2FTestRIO.java;h=5d2c34e23f0a46858f57d44c98d9eaf51e5d78fc;hb=8dbaf0f253f5ec2721b540d1f4ad06ffb35b66b6;hp=81d2db283bf1b1e641dc46aed01db1f4be170756;hpb=99c1b5211c817dbe35a646589d9c4dbf508b8d50;p=jalview.git

diff --git a/forester/java/src/org/forester/rio/TestRIO.java b/forester/java/src/org/forester/rio/TestRIO.java
index 81d2db2..5d2c34e 100644
--- a/forester/java/src/org/forester/rio/TestRIO.java
+++ b/forester/java/src/org/forester/rio/TestRIO.java
@@ -1,6 +1,8 @@
 
 package org.forester.rio;
 
+import java.io.File;
+
 import org.forester.datastructures.IntMatrix;
 import org.forester.io.parsers.nhx.NHXParser;
 import org.forester.phylogeny.Phylogeny;
@@ -22,6 +24,9 @@ public final class TestRIO {
         if ( !testRIO_GSDIR() ) {
             System.out.println( "testRIO GSDIR failed" );
         }
+        if ( !testRIO_GSDIR_Iterating() ) {
+            System.out.println( "testRIO GSDIR iterating failed" );
+        }
         else {
             System.out.println( "OK" );
         }
@@ -31,32 +36,293 @@ public final class TestRIO {
         if ( !testRIO_GSDIR() ) {
             return false;
         }
+        if ( !testRIO_GSDIR_Iterating() ) {
+            return false;
+        }
         return true;
     }
 
-    private static boolean testRIO_GSDIR() {
+    private static boolean testRIO_GSDIR_Iterating() {
         try {
             final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
             final NHXParser nhx = new NHXParser();
             nhx.setReplaceUnderscores( false );
             nhx.setIgnoreQuotes( true );
-            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.YES );
+            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE );
             final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
                     + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
                     + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";
-            final Phylogeny[] gene_trees_1 = factory.create( gene_trees_1_str, nhx );
+            nhx.setSource( gene_trees_1_str );
             final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);";
             final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ];
             species_tree_1.setRooted( true );
             PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true );
             //Archaeopteryx.createApplication( species_trees_1 );
-            RIO rio = RIO.executeAnalysis( gene_trees_1,
+            RIO rio = RIO.executeAnalysis( nhx,
                                            species_tree_1,
                                            ALGORITHM.GSDIR,
                                            REROOTING.BY_ALGORITHM,
                                            "",
                                            true,
                                            false );
+            if ( rio.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
+                return false;
+            }
+            if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
+                return false;
+            }
+            if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            IntMatrix m = rio.getOrthologTable();
+            //System.out.println( m.toString() );
+            if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,3,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,3,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,3,3,5,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
+                return false;
+            }
+            //
+            final String species_trees_2_str = "((((MOUSE,RAT,HUMAN),CAEEL),YEAST),ARATH);";
+            final Phylogeny species_tree_2 = factory.create( species_trees_2_str, new NHXParser() )[ 0 ];
+            species_tree_2.setRooted( true );
+            PhylogenyMethods.transferNodeNameToField( species_tree_2, PhylogenyNodeField.TAXONOMY_CODE, true );
+            rio = RIO.executeAnalysis( nhx, species_tree_2, ALGORITHM.GSDIR, REROOTING.BY_ALGORITHM, "", true, false );
+            m = rio.getOrthologTable();
+            // System.out.println( m.toString() );
+            if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "CAEEL,5,5,5,5,5,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 2, ',' ).equals( "HUMAN,5,5,5,5,5,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 3, ',' ).equals( "MOUSE,5,5,5,5,5,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 4, ',' ).equals( "RAT,5,5,5,5,5,5" ) ) {
+                return false;
+            }
+            if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
+                return false;
+            }
+        }
+        catch ( final Exception e ) {
+            e.printStackTrace( System.out );
+            return false;
+        }
+        return true;
+    }
+
+    private static boolean testRIO_GSDIR() {
+        try {
+            final PhylogenyFactory factory = ParserBasedPhylogenyFactory.getInstance();
+            final NHXParser nhx = new NHXParser();
+            nhx.setReplaceUnderscores( false );
+            nhx.setIgnoreQuotes( true );
+            nhx.setTaxonomyExtraction( NHXParser.TAXONOMY_EXTRACTION.AGRESSIVE );
+            //
+            final String gene_trees_00_str = "(MOUSE,RAT);(MOUSE,RAT);(MOUSE,RAT);(RAT,MOUSE);";
+            final Phylogeny[] gene_trees_00 = factory.create( gene_trees_00_str, nhx );
+            final String species_trees_00_str = "(MOUSE,RAT);";
+            final Phylogeny species_tree_00 = factory.create( species_trees_00_str, new NHXParser() )[ 0 ];
+            species_tree_00.setRooted( true );
+            PhylogenyMethods.transferNodeNameToField( species_tree_00, PhylogenyNodeField.TAXONOMY_CODE, true );
+            RIO rio = RIO.executeAnalysis( gene_trees_00,
+                                           species_tree_00,
+                                           ALGORITHM.GSDIR,
+                                           REROOTING.BY_ALGORITHM,
+                                           "",
+                                           true,
+                                           false );
+            if ( rio.getAnalyzedGeneTrees().length != 4 ) {
+                return false;
+            }
+            if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+                return false;
+            }
+            if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
+                return false;
+            }
+            if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE,4,4" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "RAT,4,4" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            //
+            final String gene_trees_000_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
+            final Phylogeny[] gene_trees_000 = factory.create( gene_trees_000_str, nhx );
+            final String species_trees_000_str = "[&&NHX:S=MOUSE];";
+            final Phylogeny species_tree_000 = factory.create( species_trees_000_str, new NHXParser() )[ 0 ];
+            species_tree_000.setRooted( true );
+            rio = RIO.executeAnalysis( gene_trees_000,
+                                       species_tree_000,
+                                       ALGORITHM.GSDIR,
+                                       REROOTING.BY_ALGORITHM,
+                                       "",
+                                       true,
+                                       false );
+            if ( rio.getAnalyzedGeneTrees().length != 2 ) {
+                return false;
+            }
+            if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+                return false;
+            }
+            if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,2,0" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,2" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            //
+            //
+            final String gene_trees_0000_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE]);(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
+            final Phylogeny[] gene_trees_0000 = factory.create( gene_trees_0000_str, nhx );
+            final String species_trees_0000_str = "([&&NHX:S=MOUSE]);";
+            final Phylogeny species_tree_0000 = factory.create( species_trees_0000_str, new NHXParser() )[ 0 ];
+            species_tree_0000.setRooted( true );
+            rio = RIO.executeAnalysis( gene_trees_0000,
+                                       species_tree_0000,
+                                       ALGORITHM.GSDIR,
+                                       REROOTING.BY_ALGORITHM,
+                                       "",
+                                       true,
+                                       false );
+            if ( rio.getAnalyzedGeneTrees().length != 3 ) {
+                return false;
+            }
+            if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+                return false;
+            }
+            if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,3,0" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,3" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            //
+            final String gene_trees_x_str = "(MOUSE1[&&NHX:S=MOUSE],MOUSE2[&&NHX:S=MOUSE])";
+            final Phylogeny[] gene_trees_x = factory.create( gene_trees_x_str, nhx );
+            final String species_trees_x_str = "[&&NHX:S=MOUSE];";
+            final Phylogeny species_tree_x = factory.create( species_trees_x_str, new NHXParser() )[ 0 ];
+            species_tree_x.setRooted( true );
+            rio = RIO.executeAnalysis( gene_trees_x,
+                                       species_tree_x,
+                                       ALGORITHM.GSDIR,
+                                       REROOTING.BY_ALGORITHM,
+                                       "",
+                                       true,
+                                       false );
+            if ( rio.getAnalyzedGeneTrees().length != 1 ) {
+                return false;
+            }
+            if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+                return false;
+            }
+            if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,1,0" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "MOUSE2,0,1" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            //
+            final String gene_trees_xx_str = "(MOUSE1[&&NHX:S=MOUSE],RAT1[&&NHX:S=RAT])";
+            final Phylogeny[] gene_trees_xx = factory.create( gene_trees_xx_str, nhx );
+            final String species_trees_xx_str = "([&&NHX:S=MOUSE],[&&NHX:S=RAT]);";
+            final Phylogeny species_tree_xx = factory.create( species_trees_xx_str, new NHXParser() )[ 0 ];
+            species_tree_xx.setRooted( true );
+            rio = RIO.executeAnalysis( gene_trees_xx,
+                                       species_tree_xx,
+                                       ALGORITHM.GSDIR,
+                                       REROOTING.BY_ALGORITHM,
+                                       "",
+                                       true,
+                                       false );
+            if ( rio.getAnalyzedGeneTrees().length != 1 ) {
+                return false;
+            }
+            if ( rio.getExtNodesOfAnalyzedGeneTrees() != 2 ) {
+                return false;
+            }
+            if ( rio.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "MOUSE1,1,1" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "RAT1,1,1" ) ) {
+                System.out.println( m.toString() );
+                return false;
+            }
+            //
+            final String gene_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);"
+                    + "((((MOUSE,RAT),HUMAN),(ARATH,YEAST)),CAEEL);" + "((MOUSE,RAT),(((ARATH,YEAST),CAEEL),HUMAN));"
+                    + "(((((MOUSE,HUMAN),RAT),CAEEL),YEAST),ARATH);" + "((((HUMAN,MOUSE),RAT),(ARATH,YEAST)),CAEEL);";
+            final Phylogeny[] gene_trees_1 = factory.create( gene_trees_1_str, nhx );
+            final String species_trees_1_str = "(((((MOUSE,RAT),HUMAN),CAEEL),YEAST),ARATH);";
+            final Phylogeny species_tree_1 = factory.create( species_trees_1_str, new NHXParser() )[ 0 ];
+            species_tree_1.setRooted( true );
+            PhylogenyMethods.transferNodeNameToField( species_tree_1, PhylogenyNodeField.TAXONOMY_CODE, true );
+            rio = RIO.executeAnalysis( gene_trees_1,
+                                       species_tree_1,
+                                       ALGORITHM.GSDIR,
+                                       REROOTING.BY_ALGORITHM,
+                                       "",
+                                       true,
+                                       false );
             if ( rio.getAnalyzedGeneTrees().length != 5 ) {
                 return false;
             }
@@ -69,7 +335,7 @@ public final class TestRIO {
             if ( rio.getRemovedGeneTreeNodes().size() != 0 ) {
                 return false;
             }
-            IntMatrix m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
+            m = RIO.calculateOrthologTable( rio.getAnalyzedGeneTrees(), true );
             // System.out.println( m.toString() );
             if ( !m.getRowAsString( 0, ',' ).equals( "ARATH,5,5,5,5,5,5" ) ) {
                 return false;
@@ -116,6 +382,422 @@ public final class TestRIO {
             if ( !m.getRowAsString( 5, ',' ).equals( "YEAST,5,5,5,5,5,5" ) ) {
                 return false;
             }
+            //
+            RIO r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode.run1.t" ),
+                                          new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
+                                          ALGORITHM.GSDIR,
+                                          REROOTING.BY_ALGORITHM,
+                                          "",
+                                          -1,
+                                          -1,
+                                          true,
+                                          false );
+            if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
+                return false;
+            }
+            if ( r0.getAnalyzedGeneTrees().length != 201 ) {
+                return false;
+            }
+            if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
+                return false;
+            }
+            if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
+                return false;
+            }
+            if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE,201,201,200,200,200,200" ) ) {
+                System.out.println( m.getRowAsString( 0, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN,201,201,200,200,200,43" ) ) {
+                System.out.println( m.getRowAsString( 1, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) {
+                System.out.println( m.getRowAsString( 2, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_CIOSA,200,200,201,201,201,201" ) ) {
+                System.out.println( m.getRowAsString( 3, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE,200,200,201,201,201,43" ) ) {
+                System.out.println( m.getRowAsString( 4, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR,200,43,43,201,43,201" ) ) {
+                System.out.println( m.getRowAsString( 5, ',' ) );
+                return false;
+            }
+            //
+            r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxid.run1.t" ),
+                                      new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
+                                      ALGORITHM.GSDIR,
+                                      REROOTING.BY_ALGORITHM,
+                                      "",
+                                      -1,
+                                      -1,
+                                      true,
+                                      false );
+            if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.ID ) {
+                return false;
+            }
+            if ( r0.getAnalyzedGeneTrees().length != 201 ) {
+                return false;
+            }
+            if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
+                return false;
+            }
+            if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
+                return false;
+            }
+            if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_45351,201,200,201,200,200,200" ) ) {
+                System.out.println( m.getRowAsString( 0, ',' ) );
+                return false;
+            }
+            //mouse
+            if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_10090,200,201,200,201,201,43" ) ) {
+                System.out.println( m.getRowAsString( 1, ',' ) );
+                return false;
+            }
+            //human
+            if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_9606,201,200,201,200,200,43" ) ) {
+                System.out.println( m.getRowAsString( 2, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_51511,200,201,200,201,201,201" ) ) {
+                System.out.println( m.getRowAsString( 3, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_7955,200,201,200,201,201,43" ) ) {
+                System.out.println( m.getRowAsString( 4, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_8364,200,43,43,201,43,201" ) ) {
+                System.out.println( m.getRowAsString( 5, ',' ) );
+                return false;
+            }
+            r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
+                                      new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
+                                      ALGORITHM.GSDIR,
+                                      REROOTING.BY_ALGORITHM,
+                                      "",
+                                      -1,
+                                      -1,
+                                      true,
+                                      false );
+            if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( r0.getAnalyzedGeneTrees().length != 201 ) {
+                return false;
+            }
+            if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
+                return false;
+            }
+            if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
+                return false;
+            }
+            if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,200,200,200" ) ) {
+                System.out.println( m.getRowAsString( 0, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,200,200,43" ) ) {
+                System.out.println( m.getRowAsString( 1, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,201,201,43" ) ) {
+                System.out.println( m.getRowAsString( 2, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,200,200,201,201,201,201" ) ) {
+                System.out.println( m.getRowAsString( 3, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,201,201,43" ) ) {
+                System.out.println( m.getRowAsString( 4, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,201,43,201" ) ) {
+                System.out.println( m.getRowAsString( 5, ',' ) );
+                return false;
+            }
+            //
+            r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
+                                      new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
+                                      ALGORITHM.GSDIR,
+                                      REROOTING.MIDPOINT,
+                                      "",
+                                      -1,
+                                      -1,
+                                      true,
+                                      false );
+            if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( r0.getAnalyzedGeneTrees().length != 201 ) {
+                return false;
+            }
+            if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
+                return false;
+            }
+            if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
+                return false;
+            }
+            if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,94,93,160,93,93" ) ) {
+                System.out.println( m.getRowAsString( 0, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,94,201,200,53,200,43" ) ) {
+                System.out.println( m.getRowAsString( 1, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,93,200,201,53,201,43" ) ) {
+                System.out.println( m.getRowAsString( 2, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,160,53,53,201,53,53" ) ) {
+                System.out.println( m.getRowAsString( 3, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,93,200,201,53,201,43" ) ) {
+                System.out.println( m.getRowAsString( 4, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,93,43,43,53,43,201" ) ) {
+                System.out.println( m.getRowAsString( 5, ',' ) );
+                return false;
+            }
+            //
+            r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
+                                      new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
+                                      ALGORITHM.GSDIR,
+                                      REROOTING.OUTGROUP,
+                                      "H2ZH97_Ciona_savignyi",
+                                      -1,
+                                      -1,
+                                      true,
+                                      false );
+            if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( r0.getAnalyzedGeneTrees().length != 201 ) {
+                return false;
+            }
+            if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
+                return false;
+            }
+            if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
+                return false;
+            }
+            if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 2 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,201,201,200,0,200,200" ) ) {
+                System.out.println( m.getRowAsString( 0, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,201,201,200,0,200,43" ) ) {
+                System.out.println( m.getRowAsString( 1, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,200,200,201,0,201,43" ) ) {
+                System.out.println( m.getRowAsString( 2, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,0,0,0,201,0,0" ) ) {
+                System.out.println( m.getRowAsString( 3, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,200,200,201,0,201,43" ) ) {
+                System.out.println( m.getRowAsString( 4, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,200,43,43,0,43,201" ) ) {
+                System.out.println( m.getRowAsString( 5, ',' ) );
+                return false;
+            }
+            //
+            //
+            r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxsn.run1.t" ),
+                                      new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
+                                      ALGORITHM.GSDIR,
+                                      REROOTING.NONE,
+                                      null,
+                                      10,
+                                      19,
+                                      true,
+                                      false );
+            if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.SCIENTIFIC_NAME ) {
+                return false;
+            }
+            if ( r0.getAnalyzedGeneTrees().length != 10 ) {
+                return false;
+            }
+            if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
+                return false;
+            }
+            if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
+                return false;
+            }
+            if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 4 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_Nematostella_vectensis,10,0,0,10,0,0" ) ) {
+                System.out.println( m.getRowAsString( 0, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_Homo_sapiens,0,10,0,0,0,0" ) ) {
+                System.out.println( m.getRowAsString( 1, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_Mus_musculus,0,0,10,0,0,0" ) ) {
+                System.out.println( m.getRowAsString( 2, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 3, ',' ).equals( "H2ZH97_Ciona_savignyi,10,0,0,10,0,0" ) ) {
+                System.out.println( m.getRowAsString( 3, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_Danio_rerio,0,0,0,0,10,0" ) ) {
+                System.out.println( m.getRowAsString( 4, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_Xenopus_tropicalis,0,0,0,0,0,10" ) ) {
+                System.out.println( m.getRowAsString( 5, ',' ) );
+                return false;
+            }
+            //
+            r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_1.run1.t" ),
+                                      new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
+                                      ALGORITHM.GSDIR,
+                                      REROOTING.BY_ALGORITHM,
+                                      "",
+                                      -1,
+                                      -1,
+                                      true,
+                                      false );
+            if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
+                return false;
+            }
+            if ( r0.getAnalyzedGeneTrees().length != 201 ) {
+                return false;
+            }
+            if ( r0.getExtNodesOfAnalyzedGeneTrees() != 3 ) {
+                return false;
+            }
+            if ( r0.getIntNodesOfAnalyzedGeneTrees() != 2 ) {
+                return false;
+            }
+            if ( r0.getRemovedGeneTreeNodes().size() != 3 ) {
+                return false;
+            }
+            if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 0 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "BCDO2_HUMAN,201,201,201" ) ) {
+                System.out.println( m.getRowAsString( 0, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "Q1RLW1_DANRE,201,201,201" ) ) {
+                System.out.println( m.getRowAsString( 1, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 2, ',' ).equals( "Q6DIN7_XENTR,201,201,201" ) ) {
+                System.out.println( m.getRowAsString( 2, ',' ) );
+                return false;
+            }
+            //
+            //
+            r0 = RIO.executeAnalysis( new File( PATH_TO_TEST_DATA + "rio_mb_taxcode_2.run1.t" ),
+                                      new File( PATH_TO_TEST_DATA + "rio_tol_1.xml" ),
+                                      ALGORITHM.GSDIR,
+                                      REROOTING.BY_ALGORITHM,
+                                      "",
+                                      -1,
+                                      -1,
+                                      true,
+                                      false );
+            if ( r0.getGSDIRtaxCompBase() != TaxonomyComparisonBase.CODE ) {
+                return false;
+            }
+            if ( r0.getAnalyzedGeneTrees().length != 201 ) {
+                return false;
+            }
+            if ( r0.getExtNodesOfAnalyzedGeneTrees() != 6 ) {
+                return false;
+            }
+            if ( r0.getIntNodesOfAnalyzedGeneTrees() != 5 ) {
+                return false;
+            }
+            if ( r0.getRemovedGeneTreeNodes().size() != 0 ) {
+                return false;
+            }
+            if ( ForesterUtil.roundToInt( r0.getDuplicationsStatistics().median() ) != 1 ) {
+                return false;
+            }
+            m = RIO.calculateOrthologTable( r0.getAnalyzedGeneTrees(), true );
+            if ( !m.getRowAsString( 0, ',' ).equals( "A7SHU1_NEMVE&1,201,201,200,200,200,200" ) ) {
+                System.out.println( m.getRowAsString( 0, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 1, ',' ).equals( "BCDO2_HUMAN+,201,201,200,200,200,43" ) ) {
+                System.out.println( m.getRowAsString( 1, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 2, ',' ).equals( "BCDO2_MOUSE,200,200,201,201,201,43" ) ) {
+                System.out.println( m.getRowAsString( 2, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 3, ',' ).equals( "CIOSA,200,200,201,201,201,201" ) ) {
+                System.out.println( m.getRowAsString( 3, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 4, ',' ).equals( "Q1RLW1_DANRE/12-45,200,200,201,201,201,43" ) ) {
+                System.out.println( m.getRowAsString( 4, ',' ) );
+                return false;
+            }
+            if ( !m.getRowAsString( 5, ',' ).equals( "Q6DIN7_XENTR-LOUSE,200,43,43,201,43,201" ) ) {
+                System.out.println( m.getRowAsString( 5, ',' ) );
+                return false;
+            }
+            //
         }
         catch ( final Exception e ) {
             e.printStackTrace( System.out );