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;
else {
System.out.println( " failed." );
}
- //timeNeighborJoining();
+ // timeNeighborJoining();
}
public static boolean test( final File test_dir ) {
final S s0 = new S();
s0.initialize( 1 );
s0.addPairing( 0, 1, 0 );
- s0.addPairing( 7.0000001, 8, 0 );
- s0.addPairing( 7.00000011, 9, 0 );
- s0.addPairing( 7.000000111, 10, 0 );
- s0.addPairing( 7.000000111, 101, 0 );
+ s0.addPairing( 7, 8, 0 );
s0.addPairing( 4, 55, 0 );
s0.addPairing( 2, 3, 0 );
s0.addPairing( 4, 5, 0 );
if ( s0.size() != 1 ) {
return false;
}
- if ( s0.getS( 0 ).size() != 10 ) {
+ if ( s0.getS( 0 ).size() != 8 ) {
return false;
}
if ( s0.getValues( 0, 0 ).size() != 1 ) {
if ( s0.getValues( 6, 0 ).size() != 1 ) {
return false;
}
- if ( s0.getValues( 7.0000001, 0 ).size() != 1 ) {
- return false;
- }
- if ( s0.getValues( 7.00000011, 0 ).size() != 1 ) {
- return false;
- }
- if ( s0.getValues( 7.000000111, 0 ).size() != 2 ) {
+ if ( s0.getValues( 7, 0 ).size() != 1 ) {
return false;
}
if ( !s0.getValues( 0, 0 ).contains( 1 ) ) {
if ( s0.getValues( 5, 0 ).size() != 1 ) {
return false;
}
- if ( s0.getS( 0 ).size() != 10 ) {
+ if ( s0.getS( 0 ).size() != 8 ) {
return false;
}
s0.removePairing( 5, 6, 0 );
- if ( s0.getS( 0 ).size() != 9 ) {
+ if ( s0.getS( 0 ).size() != 7 ) {
return false;
}
s0.addPairing( 5, 6, 0 );
- if ( s0.getS( 0 ).size() != 10 ) {
+ if ( s0.getS( 0 ).size() != 8 ) {
return false;
}
if ( s0.getValues( 5, 0 ).size() != 1 ) {
if ( !s0.getValues( 5, 0 ).contains( 403 ) ) {
return false;
}
- s0.addPairing( 693.539324, 100, 0 );
- s0.addPairing( 693.539324, 101, 0 );
- if ( s0.getValues( 693.539324, 0 ).size() != 2 ) {
+ s0.addPairing( 693, 100, 0 );
+ s0.addPairing( 693, 101, 0 );
+ if ( s0.getValues( 693, 0 ).size() != 2 ) {
return false;
}
s0.addPairing( 2, 33, 0 );
if ( !a[ 2 ].contains( 333 ) ) {
return false;
}
- if ( a[ 2 ].size() != 3 ) {
- return false;
- }
- if ( a[ 8 ].size() != 1 ) {
- return false;
- }
- if ( !a[ 8 ].contains( 9 ) ) {
- return false;
- }
- if ( a[ 9 ].size() != 2 ) {
- return false;
- }
- if ( !a[ 9 ].contains( 10 ) ) {
- return false;
- }
- if ( !a[ 9 ].contains( 101 ) ) {
- return false;
- }
- if ( !a[ 10 ].contains( 100 ) ) {
- return false;
- }
- if ( !a[ 10 ].contains( 101 ) ) {
- return false;
- }
- if ( a[ 4 ].size() != 2 ) {
- return false;
- }
- if ( !a[ 4 ].contains( 5 ) ) {
- return false;
- }
- if ( !a[ 4 ].contains( 55 ) ) {
- return false;
- }
}
catch ( final Exception e ) {
e.printStackTrace( System.out );
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 );
+ Archaeopteryx.createApplication( p2 );
p2.reRoot( p2.getNode( "Bovine" ) );
if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) {
return false;
}
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 <= 9; ++n ) {
final int x = ( int ) Math.pow( 2, n );