import java.io.StringWriter;
import java.util.Date;
import java.util.List;
-import java.util.SortedSet;
+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.S;
+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;
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();
+ timeNeighborJoining();
}
public static boolean test( final File test_dir ) {
private static boolean testDistanceCalculationMethods( final File test_dir ) {
try {
final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR
- + "bcl.aln" ) );
+ + "bcl.aln" ) );
final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 );
if ( pwd0.getSize() != 120 ) {
return false;
final String p1_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
- 1 );
+ 1 );
m1.setIdentifier( 0, "a" );
m1.setIdentifier( 1, "b" );
m1.setIdentifier( 2, "c" );
final String p2_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h,i)gi)ai,((j,k,l)jl,(m,n,o)mo,(p,q,r)pr)jr)root";
final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 18,
- 4 );
+ 4 );
m2.setIdentifier( 0, "a" );
m2.setIdentifier( 1, "b" );
m2.setIdentifier( 2, "c" );
final String p10_str = "((((((a,b)ab,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
final Phylogeny p10 = factory10.create( p10_str, new NHXParser() )[ 0 ];
final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m10 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 9,
- 1 );
+ 1 );
m10.setIdentifier( 0, "a" );
m10.setIdentifier( 1, "b" );
m10.setIdentifier( 2, "c" );
final String p1_str = "((((((a,b,y)aby,c)ac,d)ad,(e,f)ef)af,(g,h)gh)ah,i)r";
final Phylogeny p1 = factory1.create( p1_str, new NHXParser() )[ 0 ];
final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m1 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
- 1 );
+ 1 );
m1.setIdentifier( 0, "a" );
m1.setIdentifier( 1, "b" );
m1.setIdentifier( 2, "y" );
final String p2_str = "((((((a,b,y)aby,c,d)cad,e,f)af,(g,h)gh)ah,i))r";
final Phylogeny p2 = factory2.create( p2_str, new NHXParser() )[ 0 ];
final CharacterStateMatrix<CharacterStateMatrix.BinaryStates> m2 = new BasicCharacterStateMatrix<CharacterStateMatrix.BinaryStates>( 10,
- 1 );
+ 1 );
m2.setIdentifier( 0, "a" );
m2.setIdentifier( 1, "b" );
m2.setIdentifier( 2, "y" );
//NeighborJoiningR njr = NeighborJoiningR.createInstance( true, 6 );
nj = NeighborJoining.createInstance( true, 6 );
final Phylogeny p2 = nj.execute( m );
- // Archaeopteryx.createApplication( p2 );
+ //Archaeopteryx.createApplication( p2 );
p2.reRoot( p2.getNode( "Bovine" ) );
if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) {
return false;
return false;
}
if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
- .getDistanceToParent(), 0.458845 ) ) {
+ .getDistanceToParent(), 0.458845 ) ) {
return false;
}
m = new BasicSymmetricalDistanceMatrix( 4 );
return false;
}
if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent()
- .getDistanceToParent(), 0.42027 ) ) {
+ .getDistanceToParent(), 0.42027 ) ) {
return false;
}
if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
- .getDistanceToParent(), 0.458845 ) ) {
+ .getDistanceToParent(), 0.458845 ) ) {
return false;
}
}
private static boolean testS() {
try {
- final S s0 = new S();
+ final Sset s0 = new Sset();
s0.initialize( 1 );
s0.addPairing( 0, 1, 0 );
s0.addPairing( 7, 8, 0 );
}
s0.addPairing( 2, 33, 0 );
s0.addPairing( 2, 333, 0 );
- final SortedSet<Integer>[] a = s0.toArray( 0 );
+ final Set<Integer>[] a = s0.toArray( 0 );
if ( !a[ 0 ].contains( 1 ) ) {
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();
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( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
- .getDistanceToParent(), 0.458845 ) ) {
+ .getDistanceToParent(), 0.458845 ) ) {
return false;
}
//
+ // System.exit( 1 );
final BasicSymmetricalDistanceMatrix m3 = new BasicSymmetricalDistanceMatrix( 20 );
m3.setIdentifier( 0, "F_MOUSE" );
m3.setIdentifier( 1, "11_RAT" );
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( true, 6 );
+ 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 ) {
e.printStackTrace( System.out );
private static void timeNeighborJoining() {
final NeighborJoiningR njr = NeighborJoiningR.createInstance();
- for( int n = 3; n <= 9; ++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( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
}
final NeighborJoiningF njf = NeighborJoiningF.createInstance();
- for( int n = 3; n <= 9; ++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( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" );
}
final NeighborJoining nj = NeighborJoining.createInstance();
- for( int n = 3; n <= 9; ++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() );
git://source.jalview.org / jalview.git / blobdiff