- private final static boolean VERBOSE_DEFAULT = false;
- private DistanceMatrix _d;
- private DistanceMatrix _m;
- private double[] _r;
- private int _n;
- private PhylogenyNodeI[] _external_nodes;
- private int[] _mappings;
- private boolean _verbose;
-
- public NeighborJoining() {
- init();
- }
-
- private void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
- for( int i = 0; i < _n; ++i ) {
- if ( ( i == otu1 ) || ( i == otu2 ) ) {
- continue;
- }
- final double nd = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2;
- setValueInD( nd, otu1, i );
- }
- }
+ private final static DecimalFormat DF = new DecimalFormat( "0.00000" );
+ private BasicSymmetricalDistanceMatrix _d;
+ private double[][] _d_values;
+ private final DecimalFormat _df;
+ private PhylogenyNode[] _external_nodes;
+ private int[] _mappings;
+ private int _n;
+ private double[] _r;
+ private final boolean _verbose;
+ private int _min_i;
+ private int _min_j;