X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2FTestPhylogenyReconstruction.java;h=a526e760fb41d1d4aee81fe91288aa2aa736236f;hb=88fadb6580a37c8c55e7062cc6dab09ee583a6fd;hp=19634919b80e41d797cbb5126ec25a6aaaa1a303;hpb=9b3e05726c435b3cbcf0bade91aec087b10c95be;p=jalview.git diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index 1963491..a526e76 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -33,8 +33,8 @@ import java.io.StringWriter; import java.util.Date; import java.util.List; -import org.forester.archaeopteryx.Archaeopteryx; import org.forester.evoinference.distance.NeighborJoining; +import org.forester.evoinference.distance.NeighborJoiningX; import org.forester.evoinference.distance.PairwiseDistanceCalculator; import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix; import org.forester.evoinference.matrix.character.CharacterStateMatrix; @@ -55,16 +55,24 @@ 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 double ZERO_DIFF = 1.0E-9; 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 ) { - testNeighborJoining(); - // timeNeighborJoining(); + if ( testNeighborJoining() ) { + System.out.println( "OK." ); + } + else { + System.out.println( "failed." ); + } + timeNeighborJoining(); } public static boolean test( final File test_dir ) { @@ -1914,19 +1922,64 @@ public class TestPhylogenyReconstruction { private static boolean testNeighborJoining() { try { - final NeighborJoining nj = NeighborJoining.createInstance(); - // 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 ); - // System.out.println( m0.toString() ); - // final Phylogeny p0 = nj.execute( m0 ); - // Archaeopteryx.createApplication( p0 ); - // + 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 ); @@ -1939,66 +1992,136 @@ public class TestPhylogenyReconstruction { m.setIdentifier( 3, "D" ); m.setIdentifier( 4, "E" ); m.setIdentifier( 5, "F" ); - System.out.println( m.toString() ); + nj = NeighborJoining.createInstance(); final Phylogeny p1 = nj.execute( m ); - Archaeopteryx.createApplication( p1 ); - // 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 ); - // System.out.println( m.toString() ); - // final Phylogeny p2 = nj.execute( m ); - // p2.reRoot( p2.getNode( "Bovine" ) ); - // System.out.println( p2.toString() ); - // Archaeopteryx.createApplication( p2 ); - // // 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 ); - // m = new BasicSymmetricalDistanceMatrix( 4 ); - // m.setIdentifier( 0, "A" ); - // m.setIdentifier( 1, "B" ); - // m.setIdentifier( 2, "C" ); - // m.setIdentifier( 3, "D" ); - // m.setRow( "0.00 0.95 0.17 0.98", 0 ); - // m.setRow( "0.95 0.00 1.02 1.83", 1 ); - // 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 ); - // // - // // -- A 0.05 - // // - |0.01 - // // ----------------------- B 0.90 - // // - // // --- C 0.10 - // // - |0.01 - // // ------------------------- D 0.91 - // p3.reRoot( p3.getNode( "C" ).getParent() ); - // if ( !isEqual( p3.getNode( "A" ).getDistanceToParent(), 0.05 ) ) { - // return false; - // } - // if ( !isEqual( p3.getNode( "B" ).getDistanceToParent(), 0.90 ) ) { - // return false; - // } - // if ( !isEqual( p3.getNode( "C" ).getDistanceToParent(), 0.10 ) ) { - // return false; - // } - // if ( !isEqual( p3.getNode( "D" ).getDistanceToParent(), 0.91 ) ) { - // return false; - // } - // if ( TIME ) { - // timeNeighborJoining(); - // } + 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" ); + 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 ); + nj = NeighborJoining.createInstance( false, 6 ); + final Phylogeny p2 = nj.execute( m ); + p2.reRoot( p2.getNode( "Bovine" ) ); + 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" ); + m.setIdentifier( 2, "C" ); + m.setIdentifier( 3, "D" ); + m.setRow( "0.00 0.95 0.17 0.98", 0 ); + m.setRow( "0.95 0.00 1.02 1.83", 1 ); + 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; + } + //if ( TIME ) { + // timeNeighborJoining(); + //} } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -2369,7 +2492,7 @@ public class TestPhylogenyReconstruction { private static void timeNeighborJoining() { final NeighborJoining nj = NeighborJoining.createInstance(); - for( int n = 3; n <= 6; ++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() ); @@ -2379,7 +2502,20 @@ public class TestPhylogenyReconstruction { // 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" ); + } + final NeighborJoiningX njx = NeighborJoiningX.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() ); + // 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(); + njx.execute( mt ); + System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } } }