// final double new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2;
// System.out.println( "\nnew d value: " + DF.format( new_d ) );
if ( otu1 < mj ) {
// final double new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2;
// System.out.println( "\nnew d value: " + DF.format( new_d ) );
if ( otu1 < mj ) {
- _s.removePairing( getDvalueUnmapped( otu1, mj ), otu1, mj );
+ _s.removePairing( _d_values[ otu1][ mj ] , otu1, mj );
- _s.removePairing( getDvalueUnmapped( otu1, mj ), mj, otu1 );
+ _s.removePairing( _d_values[ mj ][ otu1 ], mj, otu1 );
}
if ( _mappings[ otu2 ] < mj ) {
_s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], mj );
}
if ( _mappings[ otu2 ] < mj ) {
_s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], mj );
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 m = getDvalueUnmapped( 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 );
//final double m = getDvalueUnmapped( sorted_i, m_j )
// - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 );