import java.util.Date;
import java.util.List;
-import org.forester.archaeopteryx.Archaeopteryx;
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;
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();
}
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<String> matrix_0 = new BasicCharacterStateMatrix<String>( 4, 8 );
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;
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 );
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" );
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() );
+ nj = NeighborJoining.createInstance( false, 6 );
final Phylogeny p2 = nj.execute( m );
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" );
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 ) {
}
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 <= 13; ++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" );
}
}
}
git://source.jalview.org / jalview.git / blobdiff