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;
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 ) {
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 );
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 );
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() );
// 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" );
}
}
}
git://source.jalview.org / jalview.git / blobdiff