// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
package org.forester.evoinference.distance;
public final class NeighborJoining {
private BasicSymmetricalDistanceMatrix _d;
- private BasicSymmetricalDistanceMatrix _m;
+ // private BasicSymmetricalDistanceMatrix _m;
+ private double[][] _d_values;
+ private double[][] _m_values;
private double[] _r;
private int _n;
private PhylogenyNode[] _external_nodes;
}
private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
+ final int otu1_m = _mappings[ otu1 ];
+ final int otu2_m = _mappings[ otu2 ];
+ int i_m;
for( int i = 0; i < _n; ++i ) {
if ( ( i == otu1 ) || ( i == otu2 ) ) {
continue;
}
- //final double nd = ;
- // setValueInD( nd, otu1, i );
- // _d.setValue( _mappings[ otu1 ],
- // _mappings[ i ],
- // ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2 );
- _d._values[ _mappings[ otu1 ] ][ _mappings[ i ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2;
+ _d_values[ _mappings[ otu1 ] ][ _mappings[ i ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2;
+ //i_m = _mappings[ i ];
+ //_d_values[ otu1_m ][ i_m ] = ( ( _d_values[ otu1_m ][ i_m ] + _d_values[ i_m ][ otu2_m ] ) - 2 ) / 2;
}
}
private final void calculateNetDivergences() {
double d;
+ int i_m;
for( int i = 0; i < _n; ++i ) {
d = 0;
+ i_m = _mappings[ i ];
for( int n = 0; n < _n; ++n ) {
+ //d += _d_values[ i_m ][ _mappings[ n ] ];
d += getValueFromD( i, n );
}
_r[ i ] = d;
final Phylogeny phylogeny = new Phylogeny();
while ( _n > 2 ) {
updateM();
- //final int[] s = findMinimalDistance();
// Calculates the minimal distance.
// If more than one minimal distances, always the first found is used
// could randomize this, so that any would be returned in a randomized fashion...
int otu2 = -1;
for( int j = 1; j < _n; ++j ) {
for( int i = 0; i < j; ++i ) {
- // if ( _m.getValue( i, j ) < minimum ) {
- if ( _m._values[ i ][ j ] < minimum ) {
- //minimum = _m.getValue( i, j );
- minimum = _m._values[ i ][ j ];
+ if ( _m_values[ i ][ j ] < minimum ) {
+ minimum = _m_values[ i ][ j ];
otu1 = i;
otu2 = j;
}
}
}
- //
- // final int otu1 = s[ 0 ];
- // final int otu2 = s[ 1 ];
// It is a condition that otu1 < otu2.
if ( DEBUG ) {
if ( otu1 > otu2 ) {
- throw new RuntimeException( "NJ code is faulty: otu1 > otu2" );
+ throw new RuntimeException( "faulty NJ code: otu1 > otu2" );
}
}
final PhylogenyNode node = new PhylogenyNode();
printProgress( otu1, otu2 );
}
calculateDistancesFromNewNode( otu1, otu2, d );
- //setExternalPhylogenyNode( node, otu1 );
_external_nodes[ _mappings[ otu1 ] ] = node;
updateMappings( otu2 );
--_n;
return pl;
}
- // private int[] findMinimalDistance() {
- // // if more than one minimal distances, always the first found is
- // // returned
- // // i could randomize this, so that any would be returned in a randomized
- // // fashion...
- // double minimum = Double.MAX_VALUE;
- // int otu_1 = -1;
- // int otu_2 = -1;
- // for( int j = 1; j < _n; ++j ) {
- // for( int i = 0; i < j; ++i ) {
- // if ( _m.getValue( i, j ) < minimum ) {
- // minimum = _m.getValue( i, j );
- // otu_1 = i;
- // otu_2 = j;
- // }
- // }
- // }
- // return new int[] { otu_1, otu_2 };
- // }
private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
return _external_nodes[ _mappings[ i ] ];
}
private final double getValueFromD( final int otu1, final int otu2 ) {
- //return _d.getValue( _mappings[ otu1 ], _mappings[ otu2 ] );
- return _d._values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ];
+ return _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ];
}
private final void initExternalNodes() {
_external_nodes = new PhylogenyNode[ _n ];
+ String id;
for( int i = 0; i < _n; ++i ) {
_external_nodes[ i ] = new PhylogenyNode();
- final String id = _d.getIdentifier( i );
+ id = _d.getIdentifier( i );
if ( id != null ) {
_external_nodes[ i ].setName( id );
}
private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
_n = distances.getSize();
_d = distances;
- _m = new BasicSymmetricalDistanceMatrix( _n );
_r = new double[ _n ];
_mappings = new int[ _n ];
+ _d_values = _d.getValues();
+ _m_values = new double[ _n ][ _n ];
initExternalNodes();
}
- // private final void setExternalPhylogenyNode( final PhylogenyNode node, final int i ) {
- // _external_nodes[ _mappings[ i ] ] = node;
- // }
- // private final void setValueInD( final double d, final int otu1, final int otu2 ) {
- // _d.setValue( _mappings[ otu1 ], _mappings[ otu2 ], d );
- // }
private final void updateM() {
calculateNetDivergences();
+ double r_j;
+ int j_m;
+ final int _n_2 = _n - 2;
for( int j = 1; j < _n; ++j ) {
+ r_j = _r[ j ];
+ j_m = _mappings[ j ];
for( int i = 0; i < j; ++i ) {
- //_m.setValue( i, j, calculateM( i, j ) );
- //_m.setValue( i, j, getValueFromD( i, j ) - ( _r[ i ] + _r[ j ] ) / ( _n - 2 ) );
- _m._values[ i ][ j ] = getValueFromD( i, j ) - ( _r[ i ] + _r[ j ] ) / ( _n - 2 );
+ _m_values[ i ][ j ] = getValueFromD( i, j ) - ( _r[ i ] + r_j ) / ( _n - 2 );
+ //_m_values[ i ][ j ] = _d_values[ _mappings[ i ] ][ j_m ] - ( ( _r[ i ] + r_j ) / ( _n_2 ) );
}
}
}
- //private double calculateM( final int i, final int j ) {
- // return getValueFromD( i, j ) - ( _r[ i ] + _r[ j ] ) / ( _n - 2 );
- //}
+ // private final double getValueFromD( final int otu1, final int otu2 ) {
+ // return _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ];
+ // }
// 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 ) {
+ for( int i = otu2; i < ( _mappings.length - 1 ); ++i ) {
_mappings[ i ] = _mappings[ i + 1 ];
}
}
git://source.jalview.org / jalview.git / blobdiff