import java.io.StringWriter;
import java.util.Date;
import java.util.List;
+import java.util.SortedSet;
+import org.forester.archaeopteryx.Archaeopteryx;
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.matrix.character.BasicCharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix;
import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
}
public static void main( final String[] args ) {
- if ( testNeighborJoining() ) {
- System.out.println( "OK." );
+ // System.out.println( "NJ" );
+ // if ( testNeighborJoining() ) {
+ // 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( " failed." );
+ }
+ System.out.println( "NJR" );
+ if ( testNeighborJoiningR() ) {
+ System.out.println( " OK." );
+ }
+ else {
+ System.out.println( " failed." );
}
- timeNeighborJoining();
+ // timeNeighborJoining();
}
public static boolean test( final File test_dir ) {
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() ) {
System.out.println( "failed." );
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 );
+ //NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 );
+ nj = NeighborJoining.createInstance( true, 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;
return true;
}
+ private static boolean testS() {
+ try {
+ final S s0 = new S();
+ 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 SortedSet<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" ) );
+ // // Archaeopteryx.createApplication( p0 );
+ // 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;
+ // }
+ BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 );
+ // m.setRow( "5", 1 );
+ // m.setRow( "4 7", 2 );
+ // m.setRow( "7 10 7", 3 );
+ // m.setRow( "6 9 6 5", 4 );
+ // m.setRow( "8 11 8 9 8", 5 );
+ // m.setIdentifier( 0, "A" );
+ // m.setIdentifier( 1, "B" );
+ // m.setIdentifier( 2, "C" );
+ // m.setIdentifier( 3, "D" );
+ // m.setIdentifier( 4, "E" );
+ // m.setIdentifier( 5, "F" );
+ // final NeighborJoiningR nj1 = NeighborJoiningR.createInstance();
+ // final Phylogeny p1 = nj1.execute( m );
+ // p1.reRoot( p1.getNode( "F" ) );
+ // Archaeopteryx.createApplication( p1 );
+ // 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 );
+ final NeighborJoining nj = NeighborJoining.createInstance( true, 6 );
+ //nj = NeighborJoining.createInstance( true, 6 );
+ final Phylogeny pnj = nj.execute( m );
+ Archaeopteryx.createApplication( pnj );
+ //
+ 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 );
+ final NeighborJoiningR nj2 = NeighborJoiningR.createInstance( true, 6 );
+ //nj = NeighborJoining.createInstance( true, 6 );
+ final Phylogeny p2 = nj2.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;
+ }
+ }
+ catch ( final Exception e ) {
+ e.printStackTrace( System.out );
+ return false;
+ }
+ return true;
+ }
+
private static boolean testSymmetricalDistanceMatrixParser() {
try {
final String l = ForesterUtil.getLineSeparator();
}
private static void timeNeighborJoining() {
+ final NeighborJoiningR njr = NeighborJoiningR.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();
+ njr.execute( mt );
+ System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
+ }
final NeighborJoiningF njf = NeighborJoiningF.createInstance();
- for( int n = 3; n <= 8; ++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() );
System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
}
final NeighborJoining nj = NeighborJoining.createInstance();
- for( int n = 3; n <= 8; ++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() );
git://source.jalview.org / jalview.git / blobdiff