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[jalview.git]
/
forester
/
java
/
src
/
org
/
forester
/
evoinference
/
distance
/
NeighborJoining.java
diff --git
a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
index
164599d
..
c624bff
100644
(file)
--- a/
forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
+++ b/
forester/java/src/org/forester/evoinference/distance/NeighborJoining.java
@@
-21,7
+21,7
@@
// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
//
// Contact: phylosoft @ gmail . com
// 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;
package org.forester.evoinference.distance;
@@
-36,7
+36,7
@@
import org.forester.util.ForesterUtil;
public final class NeighborJoining {
private BasicSymmetricalDistanceMatrix _d;
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 double[][] _d_values;
private double[][] _m_values;
private double[] _r;
@@
-60,7
+60,7
@@
public final class NeighborJoining {
}
// _d_values[ _mappings[ otu1 ] ][ _mappings[ i ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2;
i_m = _mappings[ i ];
}
// _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;
+ _d_values[ otu1_m ][ i_m ] = ( ( _d_values[ otu1_m ][ i_m ] + _d_values[ i_m ][ otu2_m ] ) - 2 ) / 2;
}
}
}
}
@@
-178,11
+178,10
@@
public final class NeighborJoining {
private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
_n = distances.getSize();
_d = distances;
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();
_r = new double[ _n ];
_mappings = new int[ _n ];
_d_values = _d.getValues();
- _m_values = _m.getValues();
+ _m_values = new double[ _n ][ _n ];
initExternalNodes();
}
initExternalNodes();
}
@@
-196,14
+195,14
@@
public final class NeighborJoining {
j_m = _mappings[ j ];
for( int i = 0; i < j; ++i ) {
// _m_values[ i ][ j ] = getValueFromD( i, j ) - ( _r[ i ] + r_j ) / ( _n - 2 );
j_m = _mappings[ j ];
for( int i = 0; i < j; ++i ) {
// _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 );
+ _m_values[ i ][ j ] = _d_values[ _mappings[ i ] ][ j_m ] - ( ( _r[ i ] + r_j ) / ( _n_2 ) );
}
}
}
// otu2 will, in effect, be "deleted" from the matrix.
private final void updateMappings( final int 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 ];
}
}
_mappings[ i ] = _mappings[ i + 1 ];
}
}