X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fevoinference%2FTestPhylogenyReconstruction.java;h=e7eb3b1b9deace9d1fc0b1bc8d8a762c87651dc2;hb=5ffc54fe497b9b11663f629c8ed924de32d62925;hp=8f87d78ca9a06d43ec2573d9440e256ea5da7abc;hpb=e2785e20355846acd9e81d50cf9a8a56b04ec095;p=jalview.git diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index 8f87d78..e7eb3b1 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -23,7 +23,7 @@ // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA // // Contact: phylosoft @ gmail . com -// WWW: www.phylosoft.org/forester +// WWW: https://sites.google.com/site/cmzmasek/home/software/forester package org.forester.evoinference; @@ -34,6 +34,7 @@ import java.util.Date; import java.util.List; import org.forester.evoinference.distance.NeighborJoining; +import org.forester.evoinference.distance.NeighborJoiningF; import org.forester.evoinference.distance.PairwiseDistanceCalculator; import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix; import org.forester.evoinference.matrix.character.CharacterStateMatrix; @@ -54,14 +55,23 @@ 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 ) { + if ( testNeighborJoining() ) { + System.out.println( "OK." ); + } + else { + System.out.println( "failed." ); + } timeNeighborJoining(); } @@ -117,27 +127,6 @@ 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 ); @@ -413,6 +402,27 @@ 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 testDolloParsimony() { try { final BinaryStates PRESENT = BinaryStates.PRESENT; @@ -1912,6 +1922,64 @@ public class TestPhylogenyReconstruction { private static boolean testNeighborJoining() { 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 ); @@ -1924,8 +1992,45 @@ 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" ); @@ -1941,7 +2046,50 @@ 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 ); - nj.execute( m ); + 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" ); @@ -1952,29 +2100,114 @@ 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( false, 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 ( TIME ) { - timeNeighborJoining(); + 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 ) { @@ -2345,18 +2578,23 @@ public class TestPhylogenyReconstruction { } private static void timeNeighborJoining() { + final NeighborJoiningF njf = NeighborJoiningF.createInstance(); + for( int n = 3; n <= 9; ++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 <= 14; ++n ) { + for( int n = 3; n <= 9; ++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" ); } } }