X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2FTestPhylogenyReconstruction.java;h=0e554f875160fedc31cd95c012587f5b62bedb38;hb=761719f91261eb049fada546ba363d4693a3bfa7;hp=3f989a0eee17c95e98328bbabad7ac5eb437c021;hpb=e893d04cff700c7c75f26e88e1d945b3c2ae5981;p=jalview.git diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index 3f989a0..0e554f8 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -32,13 +32,14 @@ import java.io.FileInputStream; import java.io.StringWriter; import java.util.Date; import java.util.List; -import java.util.SortedSet; +import java.util.Set; 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.S; +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; @@ -83,6 +84,13 @@ public class TestPhylogenyReconstruction { 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." ); @@ -90,7 +98,7 @@ public class TestPhylogenyReconstruction { else { System.out.println( " failed." ); } - //timeNeighborJoining(); + timeNeighborJoining(); } public static boolean test( final File test_dir ) { @@ -429,7 +437,7 @@ public class TestPhylogenyReconstruction { private static boolean testDistanceCalculationMethods( final File test_dir ) { try { final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR - + "bcl.aln" ) ); + + "bcl.aln" ) ); final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 ); if ( pwd0.getSize() != 120 ) { return false; @@ -457,7 +465,7 @@ public class TestPhylogenyReconstruction { final String p1_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r"; final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ]; CharacterStateMatrix m1 = new BasicCharacterStateMatrix( 9, - 1 ); + 1 ); m1.setIdentifier( 0, "a" ); m1.setIdentifier( 1, "b" ); m1.setIdentifier( 2, "c" ); @@ -530,7 +538,7 @@ public class TestPhylogenyReconstruction { final String p2_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h,i)gi)ai,((j,k,l)jl,(m,n,o)mo,(p,q,r)pr)jr)root"; final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ]; final CharacterStateMatrix m2 = new BasicCharacterStateMatrix( 18, - 4 ); + 4 ); m2.setIdentifier( 0, "a" ); m2.setIdentifier( 1, "b" ); m2.setIdentifier( 2, "c" ); @@ -839,7 +847,7 @@ public class TestPhylogenyReconstruction { final String p10_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r"; final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ]; final CharacterStateMatrix m10 = new BasicCharacterStateMatrix( 9, - 1 ); + 1 ); m10.setIdentifier( 0, "a" ); m10.setIdentifier( 1, "b" ); m10.setIdentifier( 2, "c" ); @@ -882,7 +890,7 @@ public class TestPhylogenyReconstruction { final String p1_str = "((((((a,b,y)aby,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r"; final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ]; final CharacterStateMatrix m1 = new BasicCharacterStateMatrix( 10, - 1 ); + 1 ); m1.setIdentifier( 0, "a" ); m1.setIdentifier( 1, "b" ); m1.setIdentifier( 2, "y" ); @@ -953,7 +961,7 @@ public class TestPhylogenyReconstruction { final String p2_str = "((((((a,b,y)aby,c,d)cad,e,f)af,(g,h)gh)ah,i))r"; final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ]; final CharacterStateMatrix m2 = new BasicCharacterStateMatrix( 10, - 1 ); + 1 ); m2.setIdentifier( 0, "a" ); m2.setIdentifier( 1, "b" ); m2.setIdentifier( 2, "y" ); @@ -2073,7 +2081,7 @@ public class TestPhylogenyReconstruction { //NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 ); nj = NeighborJoining.createInstance( true, 6 ); final Phylogeny p2 = nj.execute( m ); - // Archaeopteryx.createApplication( p2 ); + //Archaeopteryx.createApplication( p2 ); p2.reRoot( p2.getNode( "Bovine" ) ); if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) { return false; @@ -2113,7 +2121,7 @@ public class TestPhylogenyReconstruction { return false; } if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() - .getDistanceToParent(), 0.458845 ) ) { + .getDistanceToParent(), 0.458845 ) ) { return false; } m = new BasicSymmetricalDistanceMatrix( 4 ); @@ -2228,11 +2236,11 @@ public class TestPhylogenyReconstruction { return false; } if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent() - .getDistanceToParent(), 0.42027 ) ) { + .getDistanceToParent(), 0.42027 ) ) { return false; } if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() - .getDistanceToParent(), 0.458845 ) ) { + .getDistanceToParent(), 0.458845 ) ) { return false; } } @@ -2245,7 +2253,7 @@ public class TestPhylogenyReconstruction { private static boolean testS() { try { - final S s0 = new S(); + final Sset s0 = new Sset(); s0.initialize( 1 ); s0.addPairing( 0, 1, 0 ); s0.addPairing( 7, 8, 0 ); @@ -2350,7 +2358,7 @@ public class TestPhylogenyReconstruction { } s0.addPairing( 2, 33, 0 ); s0.addPairing( 2, 333, 0 ); - final SortedSet[] a = s0.toArray( 0 ); + final Set[] a = s0.toArray( 0 ); if ( !a[ 0 ].contains( 1 ) ) { return false; } @@ -2380,6 +2388,147 @@ public class TestPhylogenyReconstruction { 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(); @@ -2479,8 +2628,10 @@ public class TestPhylogenyReconstruction { 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 ) ) { @@ -2518,10 +2669,11 @@ public class TestPhylogenyReconstruction { return false; } if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() - .getDistanceToParent(), 0.458845 ) ) { + .getDistanceToParent(), 0.458845 ) ) { return false; } // + // System.exit( 1 ); final BasicSymmetricalDistanceMatrix m3 = new BasicSymmetricalDistanceMatrix( 20 ); m3.setIdentifier( 0, "F_MOUSE" ); m3.setIdentifier( 1, "11_RAT" ); @@ -2583,8 +2735,19 @@ public class TestPhylogenyReconstruction { 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( true, 6 ); + 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 ) { e.printStackTrace( System.out ); @@ -2955,7 +3118,7 @@ public class TestPhylogenyReconstruction { private static void timeNeighborJoining() { final NeighborJoiningR njr = NeighborJoiningR.createInstance(); - for( int n = 3; n <= 9; ++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() ); @@ -2964,7 +3127,7 @@ public class TestPhylogenyReconstruction { System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } final NeighborJoiningF njf = NeighborJoiningF.createInstance(); - for( int n = 3; n <= 9; ++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() ); @@ -2973,7 +3136,7 @@ public class TestPhylogenyReconstruction { System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } final NeighborJoining nj = NeighborJoining.createInstance(); - for( int n = 3; n <= 9; ++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() );