import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.phylogeny.Phylogeny;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
import org.forester.phylogeny.Phylogeny;
_s.addPairing( new_d, otu1, mj );
_d_values[ otu1 ][ mj ] = new_d;
}
else {
_s.addPairing( new_d, otu1, mj );
_d_values[ otu1 ][ mj ] = new_d;
}
else {
_s.addPairing( new_d, mj, otu1 );
_d_values[ mj ][ otu1 ] = new_d;
}
_s.addPairing( new_d, mj, otu1 );
_d_values[ mj ][ otu1 ] = new_d;
}
_mappings = new int[ _n ];
_rev_mappings = new int[ _n ];
_d_values = distances.getValues();
_mappings = new int[ _n ];
_rev_mappings = new int[ _n ];
_d_values = distances.getValues();
- 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 ) + "=" );
X: for( int j = 1; j < _n; ++j ) {
final double r_j = _r[ j ];
final int m_j = _mappings[ j ];
X: for( int j = 1; j < _n; ++j ) {
final double r_j = _r[ j ];
final int m_j = _mappings[ 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 );
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 );
for( final int sorted_i : entry.getValue() ) {
System.out.print( sorted_i );
System.out.print( "->" );
for( final int sorted_i : entry.getValue() ) {
System.out.print( sorted_i );
System.out.print( "->" );