// 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;
import java.io.StringWriter;
import java.util.Date;
import java.util.List;
+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.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;
public class TestPhylogenyReconstruction {
private final static double ZERO_DIFF = 1.0E-9;
- private final static boolean TIME = false;
+ private final static boolean VERBOSE = false;
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 ) {
+ System.out.println( "NJ" );
+ if ( testNeighborJoining( VERBOSE ) ) {
+ System.out.println( " OK." );
+ }
+ else {
+ System.out.println( " failed." );
+ }
+ System.out.println( "S" );
+ if ( testS() ) {
+ System.out.println( " OK." );
+ }
+ 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." );
+ }
+ else {
+ System.out.println( " failed." );
+ }
timeNeighborJoining();
}
return false;
}
System.out.println( "OK." );
+ System.out.print( " Datastructure S: " );
+ if ( !testS() ) {
+ System.out.println( "failed." );
+ return false;
+ }
+ System.out.println( "OK." );
System.out.print( " Neighbor Joining: " );
- if ( !testNeighborJoining() ) {
+ if ( !testNeighborJoining( VERBOSE ) ) {
System.out.println( "failed." );
return false;
}
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.parseMsa( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR
+ + "bcl.aln" ) );
+ final DistanceMatrix 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;
return true;
}
- private static boolean testNeighborJoining() {
+ private static boolean testNeighborJoining( final boolean verbose ) {
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 );
- nj.execute( m );
+ //NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 );
+ nj = NeighborJoining.createInstance( verbose, 6 );
+ final Phylogeny p2 = nj.execute( m );
+ //Archaeopteryx.createApplication( p2 );
+ 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.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( verbose, 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 ( TIME ) {
- timeNeighborJoining();
+ 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 ( 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 ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
+ private static boolean testS() {
+ try {
+ final Sset s0 = new Sset();
+ 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 ).size() != 1 ) {
+ return false;
+ }
+ if ( s0.getValues( 1, 0 ).size() != 1 ) {
+ return false;
+ }
+ if ( s0.getValues( 2, 0 ).size() != 1 ) {
+ return false;
+ }
+ if ( s0.getValues( 3, 0 ).size() != 1 ) {
+ return false;
+ }
+ if ( s0.getValues( 4, 0 ).size() != 2 ) {
+ return false;
+ }
+ if ( s0.getValues( 5, 0 ).size() != 4 ) {
+ return false;
+ }
+ if ( s0.getValues( 6, 0 ).size() != 1 ) {
+ return false;
+ }
+ if ( s0.getValues( 7, 0 ).size() != 1 ) {
+ return false;
+ }
+ if ( !s0.getValues( 0, 0 ).contains( 1 ) ) {
+ return false;
+ }
+ if ( !s0.getValues( 5, 0 ).contains( 6 ) ) {
+ return false;
+ }
+ if ( !s0.getValues( 5, 0 ).contains( 66 ) ) {
+ return false;
+ }
+ if ( !s0.getValues( 5, 0 ).contains( 666 ) ) {
+ return false;
+ }
+ if ( !s0.getValues( 5, 0 ).contains( 6666 ) ) {
+ return false;
+ }
+ s0.removePairing( 5, 6666, 0 );
+ 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<Integer>[] 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 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<Integer>[] 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();
+ 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 = nj0.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;
+ }
+ final BasicSymmetricalDistanceMatrix m1 = new BasicSymmetricalDistanceMatrix( 6 );
+ m1.setRow( "5", 1 );
+ m1.setRow( "4 7", 2 );
+ m1.setRow( "7 10 7", 3 );
+ m1.setRow( "6 9 6 5", 4 );
+ m1.setRow( "8 11 8 9 8", 5 );
+ m1.setIdentifier( 0, "A" );
+ m1.setIdentifier( 1, "B" );
+ m1.setIdentifier( 2, "C" );
+ m1.setIdentifier( 3, "D" );
+ m1.setIdentifier( 4, "E" );
+ m1.setIdentifier( 5, "F" );
+ final NeighborJoiningR nj1 = NeighborJoiningR.createInstance();
+ final Phylogeny p1 = nj1.execute( m1 );
+ 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;
+ }
+ final BasicSymmetricalDistanceMatrix m2 = new BasicSymmetricalDistanceMatrix( 7 );
+ m2.setIdentifier( 0, "Bovine" );
+ m2.setIdentifier( 1, "Mouse" );
+ m2.setIdentifier( 2, "Gibbon" );
+ m2.setIdentifier( 3, "Orang" );
+ m2.setIdentifier( 4, "Gorilla" );
+ m2.setIdentifier( 5, "Chimp" );
+ m2.setIdentifier( 6, "Human" );
+ m2.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 );
+ m2.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 );
+ m2.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 );
+ m2.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 );
+ m2.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 );
+ m2.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 );
+ 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 ) ) {
+ return false;
+ }
+ if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153931 ) ) {
+ 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;
+ }
+ //
+ // System.exit( 1 );
+ final BasicSymmetricalDistanceMatrix m3 = new BasicSymmetricalDistanceMatrix( 20 );
+ m3.setIdentifier( 0, "F_MOUSE" );
+ m3.setIdentifier( 1, "11_RAT" );
+ m3.setIdentifier( 2, "A_CAVPO" );
+ m3.setIdentifier( 3, "D_HUMAN" );
+ m3.setIdentifier( 4, "E_HUMAN" );
+ m3.setIdentifier( 5, "F_HUMAN" );
+ m3.setIdentifier( 6, "C_HUMAN" );
+ m3.setIdentifier( 7, "6_FELCA" );
+ m3.setIdentifier( 8, "D_MOUSE" );
+ m3.setIdentifier( 9, "E_MOUSE" );
+ m3.setIdentifier( 10, "E_RAT " );
+ m3.setIdentifier( 11, "C_MOUSE" );
+ m3.setIdentifier( 12, "10_RAT" );
+ m3.setIdentifier( 13, "3_TAEGU" );
+ m3.setIdentifier( 14, "2_SACKO" );
+ m3.setIdentifier( 15, "2_PANTR" );
+ m3.setIdentifier( 16, "3_CANFA" );
+ m3.setIdentifier( 17, "9_HUMAN" );
+ m3.setIdentifier( 18, "A_HUMAN" );
+ m3.setIdentifier( 19, "B_HUMAN" );
+ m3.setRow( "0.000000 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376 ",
+ 0 );
+ m3.setRow( "0.000010 0.000000 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376",
+ 1 );
+ m3.setRow( "0.020875 0.020875 0.000000 0.031503 0.031503 0.031503 0.031503 0.031477 0.020875 0.020875 0.020875 0.020875 0.020875 0.096983 0.768150 0.031503 0.031503 0.031503 0.031503 0.031503",
+ 2 );
+ m3.setRow( "0.010376 0.010376 0.031503 0.000000 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 0.000010",
+ 3 );
+ m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000000 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 0.000010",
+ 4 );
+ m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000000 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 0.000010",
+ 5 );
+ m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000000 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000010",
+ 6 );
+ m3.setRow( "0.010368 0.010368 0.031477 0.010375 0.010375 0.010375 0.010375 0.000000 0.010368 0.010368 0.010368 0.010368 0.010368 0.098591 0.745047 0.010375 0.010375 0.010375 0.010375 0.010375",
+ 7 );
+ m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000000 0.000010 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376",
+ 8 );
+ m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000000 0.000010 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376",
+ 9 );
+ m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000000 0.000010 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376",
+ 10 );
+ m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000000 0.000010 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376",
+ 11 );
+ m3.setRow( "0.000010 0.000010 0.020875 0.010376 0.010376 0.010376 0.010376 0.010368 0.000010 0.000010 0.000010 0.000010 0.000000 0.087165 0.743570 0.010376 0.010376 0.010376 0.010376 0.010376",
+ 12 );
+ m3.setRow( "0.087165 0.087165 0.096983 0.098678 0.098678 0.098678 0.098678 0.098591 0.087165 0.087165 0.087165 0.087165 0.087165 0.000000 0.720387 0.098678 0.098678 0.098678 0.098678 0.098678",
+ 13 );
+ m3.setRow( "0.743570 0.743570 0.768150 0.741282 0.741282 0.741282 0.741282 0.745047 0.743570 0.743570 0.743570 0.743570 0.743570 0.720387 0.000000 0.741282 0.741282 0.741282 0.741282 0.741282",
+ 14 );
+ 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 0.000000 0.000010 0.000010 0.000010 0.000010",
+ 15 );
+ 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 0.000000 0.000010 0.000010 0.000010",
+ 16 );
+ 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 0.000000 0.000010 0.000010",
+ 17 );
+ 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 0.000000 0.000010",
+ 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( 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 ) {
}
private static void timeNeighborJoining() {
+ final NeighborJoiningR njr = NeighborJoiningR.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() );
+ final long start_time = new Date().getTime();
+ njr.execute( mt );
+ System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
+ }
+ final NeighborJoiningF njf = NeighborJoiningF.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() );
+ 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 <= 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();
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