+ 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.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" );
+ 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.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;
+ }