updateM();
final int otu1 = _min_i;
final int otu2 = _min_j;
- System.out.println( _min_i + " " + _min_j );
+ //System.out.println( _min_i + " " + _min_j );
// It is a condition that otu1 < otu2.
final PhylogenyNode node = new PhylogenyNode();
final double d = _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ];
if ( otu1 < i ) {
if ( otu2 > i ) {
_d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2;
- System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) );
+ //System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) );
}
else {
_d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2;
- System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) );
+ //System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) );
}
}
else {
if ( otu2 > i ) {
_d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2;
- System.out.print( DF.format( _d_values[ m_i ][ m_otu1 ] ) );
+ //System.out.print( DF.format( _d_values[ m_i ][ m_otu1 ] ) );
}
else {
_d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2;
- System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) );
+ // System.out.print( DF.format( _d_values[ m_otu1 ][ m_i ] ) );
}
}
- System.out.print( " " );
+ //System.out.print( " " );
}
}
}
}
}
- for( int j = 1; j < _n; ++j ) {
- final double r_j = _r[ j ];
- final int m_j = _mappings[ j ];
- for( int i = 0; i < j; ++i ) {
- System.out.print( i );
- System.out.print( "->" );
- System.out.print( DF.format( _r[ i ] ) );
- System.out.print( " " );
- }
- System.out.println();
- }
+ // for( int j = 1; j < _n; ++j ) {
+ // final double r_j = _r[ j ];
+ // final int m_j = _mappings[ j ];
+ // for( int i = 0; i < j; ++i ) {
+ // System.out.print( i );
+ // System.out.print( "->" );
+ // System.out.print( DF.format( _r[ i ] ) );
+ // System.out.print( " " );
+ // }
+ // System.out.println();
+ // }
}
// otu2 will, in effect, be "deleted" from the matrix.
private final void updateMappings( final int otu2 ) {
for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) {
- System.out.print( _mappings[ i ] );
_mappings[ i ] = _mappings[ i + 1 ];
- System.out.println( "----->" + _mappings[ i ] );
- }
- for( int i = 0; i < _mappings.length; ++i ) {
- System.out.println( i + "-->" + _mappings[ i ] );
}
}