import java.util.ArrayList;
import java.util.List;
import java.util.Map.Entry;
-import java.util.SortedSet;
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;
+ private double _rmax;
private NeighborJoiningR() {
_verbose = false;
}
// Calculates the minimal distance.
// If more than one minimal distances, always the first found is used
- final double m = updateM();
+ updateM();
final int otu1 = _min_i;
final int otu2 = _min_j;
- if ( _verbose ) {
- System.out.println( _min_i + " " + _min_j + " => " + DF.format( m ) + " (" + DF.format( _d_min ) + ")" );
- // It is a condition that otu1 < otu2.
- //System.out.println( "mapped 1 " + _mappings[ otu1 ] );
- System.out.println( "mapped otu 2 " + _mappings[ otu2 ] );
- }
+ //if ( _verbose ) {
+ // System.out.println( _min_i + " " + _min_j + " => " + DF.format( m ) + " (" + DF.format( _d_min ) + ")" );
+ // It is a condition that otu1 < otu2.
+ //System.out.println( "mapped 1 " + _mappings[ otu1 ] );
+ // System.out.println( "mapped otu 2 " + _mappings[ otu2 ] );
+ // }
final PhylogenyNode node = new PhylogenyNode();
//final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] );
final double d = _d_values[ otu1 ][ _mappings[ otu2 ] ];
if ( _verbose ) {
System.out.println( "" );
System.out
- .println( "----------------------------------------------------------------------------------" );
+ .println( "----------------------------------------------------------------------------------" );
System.out.println( "" );
}
}
// 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 );
}
else {
- _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 );
}
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;
}
return _d_values[ _mappings[ j ] ][ _mappings[ i ] ];
}
- private double getDvalueUnmapped( final int i, final int j ) {
- if ( i < j ) {
- return _d_values[ i ][ j ];
- }
- return _d_values[ j ][ i ];
- }
-
private final void calculateNetDivergences() {
+ _rmax = -Double.MAX_VALUE;
for( int i = 0; i < _n; ++i ) {
_r[ i ] = calculateNetDivergence( i );
+ if ( _r[ i ] > _rmax ) {
+ _rmax = _r[ i ];
+ }
}
}
+ " ("
+ ( 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, SortedSet<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 ) {
}
}
- private final double updateM() {
+ private final void updateM() {
calculateNetDivergences();
Double min_m = Double.MAX_VALUE;
_min_i = -1;
if ( _verbose ) {
printM();
}
- for( int j = 1; j < _n; ++j ) {
+ //
+ X: for( int j = 1; j < _n; ++j ) {
final double r_j = _r[ j ];
final int m_j = _mappings[ j ];
- if ( _verbose ) {
- System.out.print( "j=" + j + " mj=" + m_j + ": " );
- }
- for( final Entry<Integer, SortedSet<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 m = getDvalueUnmapped( sorted_i, m_j )
- // - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 );
if ( ( m < min_m ) ) {
- // _d_min = getDvalueUnmapped( sorted_i, m_j );
+ min_m = m;
+ _min_i = sorted_i;
+ _min_j = j;
+ }
+ }
+ continue X;
+ }
+ }
+ //
+ J: for( int j = 1; j < _n; ++j ) {
+ //System.out.println( "~~~~~~~~~~~~~ min_m=" + min_m );
+ final double r_j = _r[ j ];
+ final int m_j = _mappings[ j ];
+ boolean first = true;
+ for( final Entry<Integer, int[]> entry : _s.getSentrySet( m_j ) ) {
+ if ( first ) {
+ first = false;
+ continue;
+ }
+ for( final int sorted_i : entry.getValue() ) {
+ final double d = _d_values[ sorted_i ][ m_j ];
+ if ( ( d - ( ( _umax + r_j ) / n_minus_2 ) ) > min_m ) {
+ continue J;
+ }
+ final double m = d - ( ( _r[ _rev_mappings[ sorted_i ] ] + r_j ) / n_minus_2 );
+ if ( ( m < min_m ) ) {
min_m = m;
_min_i = sorted_i;
_min_j = j;
}
if ( _verbose ) {
System.out.println();
- for( final Entry<Integer, SortedSet<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( "->" );
if ( _verbose ) {
System.out.println();
}
- return min_m;
}
// otu2 will, in effect, be "deleted" from the matrix.