import java.util.ArrayList;
import java.util.List;
import java.util.Map.Entry;
-import java.util.Set;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.phylogeny.Phylogeny;
private final boolean _verbose;
private int _min_i;
private int _min_j;
- private S _s;
+ private Sarray _s;
private double _d_min; //TODO remove me
private int[] _rev_mappings;
private double _umax;
if ( _verbose ) {
System.out.println( "" );
System.out
- .println( "----------------------------------------------------------------------------------" );
+ .println( "----------------------------------------------------------------------------------" );
System.out.println( "" );
}
}
}
double new_d;
if ( otu1 < mj ) {
- new_d = ( _d_values[ otu1 ][ mj ] + getDvalue( j, otu2 ) - d ) / 2;
+ new_d = ( ( _d_values[ otu1 ][ mj ] + getDvalue( j, otu2 ) ) - d ) / 2;
_s.addPairing( new_d, otu1, mj );
_d_values[ otu1 ][ mj ] = new_d;
}
else {
- new_d = ( _d_values[ mj ][ otu1 ] + getDvalue( j, otu2 ) - d ) / 2;
+ new_d = ( ( _d_values[ mj ][ otu1 ] + getDvalue( j, otu2 ) ) - d ) / 2;
_s.addPairing( new_d, mj, otu1 );
_d_values[ mj ][ otu1 ] = new_d;
}
+ " ("
+ ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1()
.getName() )
- + "+"
- + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
- .getName() ) + ")";
+ + "+"
+ + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
+ .getName() ) + ")";
}
// only the values in the lower triangle are used.
_mappings = new int[ _n ];
_rev_mappings = new int[ _n ];
_d_values = distances.getValues();
- _s = new S();
+ _s = new Sarray();
_s.initialize( distances );
initExternalNodes();
if ( _verbose ) {
System.out.print( " " );
}
System.out.print( "\t\t" );
- for( final Entry<Integer, Set<Integer>> entry : _s.getSentrySet( _mappings[ j ] ) ) {
- System.out.print( DF.format( ( double ) entry.getKey() / S.FACTOR ) + "=" );
+ for( final Entry<Integer, int[]> entry : _s.getSentrySet( _mappings[ j ] ) ) {
+ System.out.print( DF.format( ( double ) entry.getKey() / Sarray.FACTOR ) + "=" );
boolean first = true;
for( final int v : entry.getValue() ) {
if ( !first ) {
X: for( int j = 1; j < _n; ++j ) {
final double r_j = _r[ j ];
final int m_j = _mappings[ j ];
- for( final Entry<Integer, Set<Integer>> entry : _s.getSentrySet( m_j ) ) {
+ for( final Entry<Integer, int[]> entry : _s.getSentrySet( m_j ) ) {
for( final int sorted_i : entry.getValue() ) {
final double m = _d_values[ sorted_i ][ m_j ]
- ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 );
final double r_j = _r[ j ];
final int m_j = _mappings[ j ];
boolean first = true;
- for( final Entry<Integer, Set<Integer>> entry : _s.getSentrySet( m_j ) ) {
+ for( final Entry<Integer, int[]> entry : _s.getSentrySet( m_j ) ) {
if ( first ) {
first = false;
continue;
}
if ( _verbose ) {
System.out.println();
- for( final Entry<Integer, Set<Integer>> entry : _s.getSentrySet( m_j ) ) {
+ for( final Entry<Integer, int[]> entry : _s.getSentrySet( m_j ) ) {
for( final int sorted_i : entry.getValue() ) {
System.out.print( sorted_i );
System.out.print( "->" );