X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2FTestPhylogenyReconstruction.java;h=a9c16e9ffa657969d185678cc0a159ef81a07fa9;hb=09a8c723e9ab220999f25c6be635282f18186be7;hp=60739851ccc9552d0059f023d7d47d281bcc1597;hpb=2eb16fa8fc6fa40a6f9829a5d624ada26b026fcc;p=jalview.git diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index 6073985..a9c16e9 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -32,10 +32,14 @@ import java.io.FileInputStream; import java.io.StringWriter; import java.util.Date; import java.util.List; +import java.util.Set; -import org.forester.archaeopteryx.Archaeopteryx; import org.forester.evoinference.distance.NeighborJoining; +import org.forester.evoinference.distance.NeighborJoiningF; +import org.forester.evoinference.distance.NeighborJoiningR; import org.forester.evoinference.distance.PairwiseDistanceCalculator; +import org.forester.evoinference.distance.Sarray; +import org.forester.evoinference.distance.Sset; import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix; import org.forester.evoinference.matrix.character.CharacterStateMatrix; import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates; @@ -56,13 +60,45 @@ import org.forester.util.ForesterUtil; public class TestPhylogenyReconstruction { private final static double ZERO_DIFF = 1.0E-9; - private final static boolean TIME = false; + private final static boolean VERBOSE = false; public static boolean isEqual( final double a, final double b ) { return ( ( Math.abs( a - b ) ) < ZERO_DIFF ); } + public static boolean isUnequal( final double a, final double b ) { + return !isEqual( a, b ); + } + public static void main( final String[] args ) { + System.out.println( "NJ" ); + if ( testNeighborJoining( VERBOSE ) ) { + System.out.println( " OK." ); + } + else { + System.out.println( " failed." ); + } + System.out.println( "S" ); + if ( testS() ) { + System.out.println( " OK." ); + } + else { + System.out.println( " failed." ); + } + System.out.println( "Sarray" ); + if ( testSarray() ) { + System.out.println( " OK." ); + } + else { + System.out.println( " failed." ); + } + System.out.println( "NJR" ); + if ( testNeighborJoiningR() ) { + System.out.println( " OK." ); + } + else { + System.out.println( " failed." ); + } timeNeighborJoining(); } @@ -91,8 +127,14 @@ public class TestPhylogenyReconstruction { return false; } System.out.println( "OK." ); + System.out.print( " Datastructure S: " ); + if ( !testS() ) { + System.out.println( "failed." ); + return false; + } + System.out.println( "OK." ); System.out.print( " Neighbor Joining: " ); - if ( !testNeighborJoining() ) { + if ( !testNeighborJoining( VERBOSE ) ) { System.out.println( "failed." ); return false; } @@ -118,27 +160,6 @@ public class TestPhylogenyReconstruction { return true; } - private static boolean testDistanceCalculationMethods( final File test_dir ) { - try { - final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR - + "bcl.aln" ) ); - final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 ); - if ( pwd0.getSize() != 120 ) { - return false; - } - for( int i = 0; i < pwd0.getSize(); ++i ) { - if ( !isEqual( pwd0.getValue( i, i ), 0.0 ) ) { - return false; - } - } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - private static boolean testBasicCharacterStateMatrix() { try { final CharacterStateMatrix matrix_0 = new BasicCharacterStateMatrix( 4, 8 ); @@ -414,6 +435,27 @@ public class TestPhylogenyReconstruction { return true; } + private static boolean testDistanceCalculationMethods( final File test_dir ) { + try { + final Msa msa0 = GeneralMsaParser.parseMsa( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR + + "bcl.aln" ) ); + final DistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 ); + if ( pwd0.getSize() != 120 ) { + return false; + } + for( int i = 0; i < pwd0.getSize(); ++i ) { + if ( !isEqual( pwd0.getValue( i, i ), 0.0 ) ) { + return false; + } + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testDolloParsimony() { try { final BinaryStates PRESENT = BinaryStates.PRESENT; @@ -1911,8 +1953,66 @@ public class TestPhylogenyReconstruction { return true; } - private static boolean testNeighborJoining() { + private static boolean testNeighborJoining( final boolean verbose ) { try { + NeighborJoining nj = NeighborJoining.createInstance(); + final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 ); + m0.setIdentifier( 0, "A" ); + m0.setIdentifier( 1, "B" ); + m0.setIdentifier( 2, "C" ); + m0.setIdentifier( 3, "D" ); + m0.setRow( "5 ", 1 ); + m0.setRow( "3 6 ", 2 ); + m0.setRow( "7.5 10.5 5.5", 3 ); + final Phylogeny p0 = nj.execute( m0 ); + p0.reRoot( p0.getNode( "D" ) ); + if ( isUnequal( p0.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "B" ).getDistanceToParent(), 4 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "C" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) { + return false; + } + nj = NeighborJoining.createInstance(); + final BasicSymmetricalDistanceMatrix m00 = new BasicSymmetricalDistanceMatrix( 4 ); + m00.setIdentifier( 0, "A" ); + m00.setIdentifier( 1, "B" ); + m00.setIdentifier( 2, "C" ); + m00.setIdentifier( 3, "D" ); + m00.setRow( "2.01 ", 1 ); + m00.setRow( "3 3.01 ", 2 ); + m00.setRow( "3.01 3.02 1.01", 3 ); + final Phylogeny p00 = nj.execute( m00 ); + p00.reRoot( p00.getNode( "D" ) ); + if ( isUnequal( p00.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p00.getNode( "B" ).getDistanceToParent(), 1.01 ) ) { + return false; + } + if ( isUnequal( p00.getNode( "C" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( isUnequal( p00.getNode( "D" ).getDistanceToParent(), 0.255 ) ) { + return false; + } + if ( isUnequal( p00.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) { + return false; + } + if ( isUnequal( p00.getNode( "A" ).getParent().getParent().getDistanceToParent(), 0.255 ) ) { + return false; + } BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 ); m.setRow( "5", 1 ); m.setRow( "4 7", 2 ); @@ -1925,8 +2025,45 @@ public class TestPhylogenyReconstruction { m.setIdentifier( 3, "D" ); m.setIdentifier( 4, "E" ); m.setIdentifier( 5, "F" ); - final NeighborJoining nj = NeighborJoining.createInstance(); - nj.execute( m ); + nj = NeighborJoining.createInstance(); + final Phylogeny p1 = nj.execute( m ); + p1.reRoot( p1.getNode( "F" ) ); + if ( isUnequal( p1.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "B" ).getDistanceToParent(), 4 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "C" ).getDistanceToParent(), 2 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "D" ).getDistanceToParent(), 3 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "E" ).getDistanceToParent(), 2 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "F" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "A" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getParent().getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "B" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "D" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "E" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } m = new BasicSymmetricalDistanceMatrix( 7 ); m.setIdentifier( 0, "Bovine" ); m.setIdentifier( 1, "Mouse" ); @@ -1942,13 +2079,52 @@ public class TestPhylogenyReconstruction { m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 ); m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 ); m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 ); - System.out.println( m.toString() ); + //NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 ); + nj = NeighborJoining.createInstance( verbose, 6 ); final Phylogeny p2 = nj.execute( m ); + //Archaeopteryx.createApplication( p2 ); p2.reRoot( p2.getNode( "Bovine" ) ); - System.out.println( p2.toString() ); - // from phylip Neighbor-Joining/UPGMA method version 3.69: - // ((((((Chimp:0.15167,Human:0.11753):0.03982,Gorilla:0.15393):0.02696,Orang:0.28469):0.04648,Gibbon:0.35793):0.42027,Mouse:0.76891):0.458845,Bovine:0.458845); - Archaeopteryx.createApplication( p2 ); + if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.117525 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153932 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.284694 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Gibbon" ).getDistanceToParent(), 0.357931 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.039819 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Human" ).getParent().getDistanceToParent(), 0.039819 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.026956 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.046481 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getDistanceToParent(), + 0.420269 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() + .getDistanceToParent(), 0.458845 ) ) { + return false; + } m = new BasicSymmetricalDistanceMatrix( 4 ); m.setIdentifier( 0, "A" ); m.setIdentifier( 1, "B" ); @@ -1959,29 +2135,619 @@ public class TestPhylogenyReconstruction { m.setRow( "0.17 1.02 0.00 1.01", 2 ); m.setRow( "0.98 1.83 1.01 0.00", 3 ); final Phylogeny p3 = nj.execute( m ); + p3.reRoot( p3.getNode( "C" ) ); + if ( isUnequal( p3.getNode( "A" ).getDistanceToParent(), 0.05 ) ) { + return false; + } + if ( isUnequal( p3.getNode( "B" ).getDistanceToParent(), 0.90 ) ) { + return false; + } + if ( !isEqual( p3.getNode( "C" ).getDistanceToParent(), 0.05 ) ) { + return false; + } + if ( !isEqual( p3.getNode( "D" ).getDistanceToParent(), 0.91 ) ) { + return false; + } + if ( isUnequal( p3.getNode( "A" ).getParent().getDistanceToParent(), 0.02 ) ) { + return false; + } + if ( isUnequal( p3.getNode( "A" ).getParent().getParent().getDistanceToParent(), 0.05 ) ) { + return false; + } // - // -- A 0.05 - // - |0.01 - // ----------------------- B 0.90 + NeighborJoiningF njf = NeighborJoiningF.createInstance(); + final BasicSymmetricalDistanceMatrix m0f = new BasicSymmetricalDistanceMatrix( 4 ); + m0f.setIdentifier( 0, "A" ); + m0f.setIdentifier( 1, "B" ); + m0f.setIdentifier( 2, "C" ); + m0f.setIdentifier( 3, "D" ); + m0f.setRow( "5 ", 1 ); + m0f.setRow( "3 6 ", 2 ); + m0f.setRow( "7.5 10.5 5.5", 3 ); + final Phylogeny p0f = njf.execute( m0f ); + p0f.reRoot( p0f.getNode( "D" ) ); + if ( isUnequal( p0f.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "B" ).getDistanceToParent(), 4 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "C" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) { + return false; + } // - // --- C 0.10 - // - |0.01 - // ------------------------- D 0.91 - p3.reRoot( p3.getNode( "C" ).getParent() ); - if ( !isEqual( p3.getNode( "A" ).getDistanceToParent(), 0.05 ) ) { + m = new BasicSymmetricalDistanceMatrix( 7 ); + m.setIdentifier( 0, "Bovine" ); + m.setIdentifier( 1, "Mouse" ); + m.setIdentifier( 2, "Gibbon" ); + m.setIdentifier( 3, "Orang" ); + m.setIdentifier( 4, "Gorilla" ); + m.setIdentifier( 5, "Chimp" ); + m.setIdentifier( 6, "Human" ); + m.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 ); + m.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 ); + m.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 ); + m.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 ); + m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 ); + m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 ); + m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 ); + njf = NeighborJoiningF.createInstance( verbose, 5 ); + final Phylogeny p2f = njf.execute( m ); + p2f.reRoot( p2f.getNode( "Bovine" ) ); + if ( isUnequal( p2f.getNode( "Chimp" ).getDistanceToParent(), 0.15168 ) ) { return false; } - if ( !isEqual( p3.getNode( "B" ).getDistanceToParent(), 0.90 ) ) { + if ( isUnequal( p2f.getNode( "Human" ).getDistanceToParent(), 0.11752 ) ) { return false; } - if ( !isEqual( p3.getNode( "C" ).getDistanceToParent(), 0.10 ) ) { + if ( isUnequal( p2f.getNode( "Gorilla" ).getDistanceToParent(), 0.15393 ) ) { return false; } - if ( !isEqual( p3.getNode( "D" ).getDistanceToParent(), 0.91 ) ) { + if ( isUnequal( p2f.getNode( "Orang" ).getDistanceToParent(), 0.28469 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Gibbon" ).getDistanceToParent(), 0.35793 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.03982 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Human" ).getParent().getDistanceToParent(), 0.03982 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.02696 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.04648 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent() + .getDistanceToParent(), 0.42027 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() + .getDistanceToParent(), 0.458845 ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testS() { + try { + final Sset s0 = new Sset(); + s0.initialize( 1 ); + s0.addPairing( 0, 1, 0 ); + s0.addPairing( 7, 8, 0 ); + s0.addPairing( 4, 55, 0 ); + s0.addPairing( 2, 3, 0 ); + s0.addPairing( 4, 5, 0 ); + s0.addPairing( 5, 6666, 0 ); + s0.addPairing( 5, 666, 0 ); + s0.addPairing( 5, 66, 0 ); + s0.addPairing( 5, 6, 0 ); + s0.addPairing( 6, 7, 0 ); + s0.addPairing( 3, 4, 0 ); + s0.addPairing( 1, 2, 0 ); + if ( s0.size() != 1 ) { return false; } - if ( TIME ) { - timeNeighborJoining(); + if ( s0.getS( 0 ).size() != 8 ) { + return false; + } + if ( s0.getValues( 0, 0 ).size() != 1 ) { + return false; + } + if ( s0.getValues( 1, 0 ).size() != 1 ) { + return false; + } + if ( s0.getValues( 2, 0 ).size() != 1 ) { + return false; + } + if ( s0.getValues( 3, 0 ).size() != 1 ) { + return false; + } + if ( s0.getValues( 4, 0 ).size() != 2 ) { + return false; + } + if ( s0.getValues( 5, 0 ).size() != 4 ) { + return false; + } + if ( s0.getValues( 6, 0 ).size() != 1 ) { + return false; + } + if ( s0.getValues( 7, 0 ).size() != 1 ) { + return false; + } + if ( !s0.getValues( 0, 0 ).contains( 1 ) ) { + return false; + } + if ( !s0.getValues( 5, 0 ).contains( 6 ) ) { + return false; + } + if ( !s0.getValues( 5, 0 ).contains( 66 ) ) { + return false; + } + if ( !s0.getValues( 5, 0 ).contains( 666 ) ) { + return false; + } + if ( !s0.getValues( 5, 0 ).contains( 6666 ) ) { + return false; + } + s0.removePairing( 5, 6666, 0 ); + if ( s0.getValues( 5, 0 ).contains( 6666 ) ) { + return false; + } + s0.removePairing( 5, 666, 0 ); + if ( s0.getValues( 5, 0 ).contains( 666 ) ) { + return false; + } + s0.removePairing( 5, 66, 0 ); + if ( s0.getValues( 5, 0 ).contains( 66 ) ) { + return false; + } + if ( s0.getValues( 5, 0 ).size() != 1 ) { + return false; + } + if ( s0.getS( 0 ).size() != 8 ) { + return false; + } + s0.removePairing( 5, 6, 0 ); + if ( s0.getS( 0 ).size() != 7 ) { + return false; + } + s0.addPairing( 5, 6, 0 ); + if ( s0.getS( 0 ).size() != 8 ) { + return false; + } + if ( s0.getValues( 5, 0 ).size() != 1 ) { + return false; + } + if ( !s0.getValues( 5, 0 ).contains( 6 ) ) { + return false; + } + s0.addPairing( 5, 403, 0 ); + if ( s0.getValues( 5, 0 ).size() != 2 ) { + return false; + } + if ( !s0.getValues( 5, 0 ).contains( 403 ) ) { + return false; + } + s0.addPairing( 693, 100, 0 ); + s0.addPairing( 693, 101, 0 ); + if ( s0.getValues( 693, 0 ).size() != 2 ) { + return false; + } + s0.addPairing( 2, 33, 0 ); + s0.addPairing( 2, 333, 0 ); + final Set[] a = s0.toArray( 0 ); + if ( !a[ 0 ].contains( 1 ) ) { + return false; + } + if ( a[ 0 ].size() != 1 ) { + return false; + } + if ( !a[ 1 ].contains( 2 ) ) { + return false; + } + if ( a[ 1 ].size() != 1 ) { + return false; + } + if ( !a[ 2 ].contains( 3 ) ) { + return false; + } + if ( !a[ 2 ].contains( 33 ) ) { + return false; + } + if ( !a[ 2 ].contains( 333 ) ) { + return false; + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testSarray() { + try { + final Sarray s0 = new Sarray(); + s0.initialize( 1 ); + s0.addPairing( 0, 1, 0 ); + s0.addPairing( 7, 8, 0 ); + s0.addPairing( 4, 55, 0 ); + s0.addPairing( 2, 3, 0 ); + s0.addPairing( 4, 5, 0 ); + s0.addPairing( 5, 6666, 0 ); + s0.addPairing( 5, 666, 0 ); + s0.addPairing( 5, 66, 0 ); + s0.addPairing( 5, 6, 0 ); + s0.addPairing( 6, 7, 0 ); + s0.addPairing( 3, 4, 0 ); + s0.addPairing( 1, 2, 0 ); + if ( s0.size() != 1 ) { + return false; + } + if ( s0.getS( 0 ).size() != 8 ) { + return false; + } + if ( s0.getValues( 0, 0 ).length != 1 ) { + return false; + } + if ( s0.getValues( 1, 0 ).length != 1 ) { + return false; + } + if ( s0.getValues( 2, 0 ).length != 1 ) { + return false; + } + if ( s0.getValues( 3, 0 ).length != 1 ) { + return false; + } + if ( s0.getValues( 4, 0 ).length != 2 ) { + return false; + } + if ( s0.getValues( 5, 0 ).length != 4 ) { + return false; + } + if ( s0.getValues( 6, 0 ).length != 1 ) { + return false; + } + if ( s0.getValues( 7, 0 ).length != 1 ) { + return false; + } + if ( s0.getValues( 0, 0 )[ 0 ] != 1 ) { + return false; + } + if ( s0.getValues( 5, 0 )[ 3 ] != 6 ) { + return false; + } + if ( s0.getValues( 5, 0 )[ 2 ] != 66 ) { + return false; + } + if ( s0.getValues( 5, 0 )[ 1 ] != 666 ) { + return false; + } + if ( s0.getValues( 5, 0 )[ 0 ] != 6666 ) { + return false; + } + s0.removePairing( 5, 6666, 0 ); + if ( s0.getValues( 5, 0 ).length != 3 ) { + System.out.println( s0.getValues( 5, 0 ).length ); + return false; + } + // if ( s0.getValues( 5, 0 ).contains( 6666 ) ) { + // return false; + // } + // s0.removePairing( 5, 666, 0 ); + // if ( s0.getValues( 5, 0 ).contains( 666 ) ) { + // return false; + // } + // s0.removePairing( 5, 66, 0 ); + // if ( s0.getValues( 5, 0 ).contains( 66 ) ) { + // return false; + // } + // if ( s0.getValues( 5, 0 ).size() != 1 ) { + // return false; + // } + // if ( s0.getS( 0 ).size() != 8 ) { + // return false; + // } + // s0.removePairing( 5, 6, 0 ); + // if ( s0.getS( 0 ).size() != 7 ) { + // return false; + // } + // s0.addPairing( 5, 6, 0 ); + // if ( s0.getS( 0 ).size() != 8 ) { + // return false; + // } + // if ( s0.getValues( 5, 0 ).size() != 1 ) { + // return false; + // } + // if ( !s0.getValues( 5, 0 ).contains( 6 ) ) { + // return false; + // } + // s0.addPairing( 5, 403, 0 ); + // if ( s0.getValues( 5, 0 ).size() != 2 ) { + // return false; + // } + // if ( !s0.getValues( 5, 0 ).contains( 403 ) ) { + // return false; + // } + // s0.addPairing( 693, 100, 0 ); + // s0.addPairing( 693, 101, 0 ); + // if ( s0.getValues( 693, 0 ).size() != 2 ) { + // return false; + // } + // s0.addPairing( 2, 33, 0 ); + // s0.addPairing( 2, 333, 0 ); + // final Set[] a = s0.toArray( 0 ); + // if ( !a[ 0 ].contains( 1 ) ) { + // return false; + // } + // if ( a[ 0 ].size() != 1 ) { + // return false; + // } + // if ( !a[ 1 ].contains( 2 ) ) { + // return false; + // } + // if ( a[ 1 ].size() != 1 ) { + // return false; + // } + // if ( !a[ 2 ].contains( 3 ) ) { + // return false; + // } + // if ( !a[ 2 ].contains( 33 ) ) { + // return false; + // } + // if ( !a[ 2 ].contains( 333 ) ) { + // return false; + // } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + + private static boolean testNeighborJoiningR() { + try { + final NeighborJoiningR nj0 = NeighborJoiningR.createInstance(); + final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 ); + m0.setIdentifier( 0, "A" ); + m0.setIdentifier( 1, "B" ); + m0.setIdentifier( 2, "C" ); + m0.setIdentifier( 3, "D" ); + m0.setRow( "5 ", 1 ); + m0.setRow( "3 6 ", 2 ); + m0.setRow( "7.5 10.5 5.5", 3 ); + final Phylogeny p0 = nj0.execute( m0 ); + p0.reRoot( p0.getNode( "D" ) ); + if ( isUnequal( p0.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "B" ).getDistanceToParent(), 4 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "C" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) { + return false; + } + if ( isUnequal( p0.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) { + return false; + } + final BasicSymmetricalDistanceMatrix m1 = new BasicSymmetricalDistanceMatrix( 6 ); + m1.setRow( "5", 1 ); + m1.setRow( "4 7", 2 ); + m1.setRow( "7 10 7", 3 ); + m1.setRow( "6 9 6 5", 4 ); + m1.setRow( "8 11 8 9 8", 5 ); + m1.setIdentifier( 0, "A" ); + m1.setIdentifier( 1, "B" ); + m1.setIdentifier( 2, "C" ); + m1.setIdentifier( 3, "D" ); + m1.setIdentifier( 4, "E" ); + m1.setIdentifier( 5, "F" ); + final NeighborJoiningR nj1 = NeighborJoiningR.createInstance(); + final Phylogeny p1 = nj1.execute( m1 ); + p1.reRoot( p1.getNode( "F" ) ); + if ( isUnequal( p1.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "B" ).getDistanceToParent(), 4 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "C" ).getDistanceToParent(), 2 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "D" ).getDistanceToParent(), 3 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "E" ).getDistanceToParent(), 2 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "F" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "A" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "A" ).getParent().getParent().getParent().getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "B" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "D" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p1.getNode( "E" ).getParent().getDistanceToParent(), 1 ) ) { + return false; + } + final BasicSymmetricalDistanceMatrix m2 = new BasicSymmetricalDistanceMatrix( 7 ); + m2.setIdentifier( 0, "Bovine" ); + m2.setIdentifier( 1, "Mouse" ); + m2.setIdentifier( 2, "Gibbon" ); + m2.setIdentifier( 3, "Orang" ); + m2.setIdentifier( 4, "Gorilla" ); + m2.setIdentifier( 5, "Chimp" ); + m2.setIdentifier( 6, "Human" ); + m2.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 ); + m2.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 ); + m2.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 ); + m2.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 ); + m2.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 ); + m2.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 ); + m2.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 ); + final NeighborJoiningR nj2 = NeighborJoiningR.createInstance( true, 6 ); + final Phylogeny p2 = nj2.execute( m2 ); + // Archaeopteryx.createApplication( p2 ); + p2.reRoot( p2.getNode( "Bovine" ) ); + if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) { + System.out.println( p2.getNode( "Chimp" ).getDistanceToParent() ); + return false; + } + if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.117525 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153931 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.284694 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Gibbon" ).getDistanceToParent(), 0.357931 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.039819 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Human" ).getParent().getDistanceToParent(), 0.039819 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.026956 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.046481 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getDistanceToParent(), + 0.420269 ) ) { + return false; + } + if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() + .getDistanceToParent(), 0.458845 ) ) { + return false; + } + // + // System.exit( 1 ); + final BasicSymmetricalDistanceMatrix m3 = new BasicSymmetricalDistanceMatrix( 20 ); + m3.setIdentifier( 0, "F_MOUSE" ); + m3.setIdentifier( 1, "11_RAT" ); + m3.setIdentifier( 2, "A_CAVPO" ); + m3.setIdentifier( 3, "D_HUMAN" ); + m3.setIdentifier( 4, "E_HUMAN" ); + m3.setIdentifier( 5, "F_HUMAN" ); + m3.setIdentifier( 6, "C_HUMAN" ); + m3.setIdentifier( 7, "6_FELCA" ); + m3.setIdentifier( 8, "D_MOUSE" ); + m3.setIdentifier( 9, "E_MOUSE" ); + m3.setIdentifier( 10, "E_RAT " ); + m3.setIdentifier( 11, "C_MOUSE" ); + m3.setIdentifier( 12, "10_RAT" ); + m3.setIdentifier( 13, "3_TAEGU" ); + m3.setIdentifier( 14, "2_SACKO" ); + m3.setIdentifier( 15, "2_PANTR" ); + m3.setIdentifier( 16, "3_CANFA" ); + m3.setIdentifier( 17, "9_HUMAN" ); + m3.setIdentifier( 18, "A_HUMAN" ); + m3.setIdentifier( 19, "B_HUMAN" ); + m3.setRow( "0.000000 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376 ", + 0 ); + m3.setRow( "0.000010 0.000000 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 1 ); + m3.setRow( "0.020875 0.020875 0.000000 0.031503 0.031503 0.031503 0.031503 0.031477 0.020875 0.020875 0.020875 0.020875 0.020875 0.096983 0.768150 0.031503 0.031503 0.031503 0.031503 0.031503", + 2 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000000 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000010", + 3 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000000 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000010", + 4 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000000 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000010", + 5 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000000 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000010", + 6 ); + m3.setRow( "0.010368 0.010368 0.031477 0.010375 0.010375 0.010375 0.010375 0.000000 0.010368 0.010368 0.010368 0.010368 0.010368 0.098591 0.745047 0.010375 0.010375 0.010375 0.010375 0.010375", + 7 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000000 0.000010 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 8 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000000 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 9 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000000 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 10 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000000 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 11 ); + m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000010 0.000000 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376", + 12 ); + m3.setRow( "0.087165 0.087165 0.096983 0.098678 0.098678 0.098678 0.098678 0.098591 0.087165 0.087165 0.087165 0.087165 0.087165 0.000000 0.720387 0.098678 0.098678 0.098678 0.098678 0.098678", + 13 ); + m3.setRow( "0.743570 0.743570 0.768150 0.741282 0.741282 0.741282 0.741282 0.745047 0.743570 0.743570 0.743570 0.743570 0.743570 0.720387 0.000000 0.741282 0.741282 0.741282 0.741282 0.741282", + 14 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000000 0.000010 0.000010 0.000010 0.000010", + 15 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000000 0.000010 0.000010 0.000010", + 16 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000000 0.000010 0.000010", + 17 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000000 0.000010", + 18 ); + m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000000", + 19 ); + final NeighborJoiningR nj3 = NeighborJoiningR.createInstance( false, 6 ); + final Phylogeny p3 = nj3.execute( m3 ); + //Archaeopteryx.createApplication( p3 ); + //// + final int size = 10; + for( int n = 0; n <= 100; ++n ) { + final NeighborJoiningR njn = NeighborJoiningR.createInstance( false, 6 ); + final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( size ); + mt.randomize( new Date().getTime() ); + final long start_time = new Date().getTime(); + njn.execute( mt ); + System.out.println( "Size: " + size + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } } catch ( final Exception e ) { @@ -2352,18 +3118,32 @@ public class TestPhylogenyReconstruction { } private static void timeNeighborJoining() { + final NeighborJoiningR njr = NeighborJoiningR.createInstance(); + for( int n = 3; n <= 10; ++n ) { + final int x = ( int ) Math.pow( 2, n ); + final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x ); + mt.randomize( new Date().getTime() ); + final long start_time = new Date().getTime(); + njr.execute( mt ); + System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); + } + final NeighborJoiningF njf = NeighborJoiningF.createInstance(); + for( int n = 3; n <= 10; ++n ) { + final int x = ( int ) Math.pow( 2, n ); + final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x ); + mt.randomize( new Date().getTime() ); + final long start_time = new Date().getTime(); + njf.execute( mt ); + System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); + } final NeighborJoining nj = NeighborJoining.createInstance(); - for( int n = 3; n <= 13; ++n ) { + for( int n = 3; n <= 10; ++n ) { final int x = ( int ) Math.pow( 2, n ); final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x ); mt.randomize( new Date().getTime() ); - // for( int i = 0; i < mt.getSize(); i++ ) { - // mt.setIdentifier( i, i + "i" ); - // } - // System.out.println( mt.toStringBuffer( Format.PHYLIP ) ); final long start_time = new Date().getTime(); nj.execute( mt ); - System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms." ); + System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } } }