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 static DecimalFormat DF = new DecimalFormat( "0.00000" );
private BasicSymmetricalDistanceMatrix _d;
- private float[][] _d_values;
+ private double[][] _d_values;
private final DecimalFormat _df;
private PhylogenyNode[] _external_nodes;
private int[] _mappings;
private int _n;
- private float[] _r;
+ private double[] _r;
private final boolean _verbose;
private int _min_i;
private int _min_j;
- private S _s;
- private float _d_min; //TODO remove me
+ private Sarray _s;
+ private double _d_min; //TODO remove me
private int[] _rev_mappings;
+ private double _umax;
+ private double _rmax;
private NeighborJoiningR() {
_verbose = false;
reset( distance );
final Phylogeny phylogeny = new Phylogeny();
while ( _n > 2 ) {
- System.out.println( "N=" + _n );
- System.out.println();
+ if ( _verbose ) {
+ System.out.println( "N=" + _n );
+ System.out.println();
+ }
// 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;
- System.out.println( _min_i + " " + _min_j + " => " + DF.format( m ) + " (" + DF.format( _d_min ) + ")" );
+ //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 ] );
+ // System.out.println( "mapped otu 2 " + _mappings[ otu2 ] );
+ // }
final PhylogenyNode node = new PhylogenyNode();
//final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] );
- final float d = _d_values[ otu1 ][ _mappings[ otu2 ] ];
- final float d1 = ( d / 2 ) + ( ( _r[ _rev_mappings[ otu1 ] ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
- final float d2 = d - d1;
+ final double d = _d_values[ otu1 ][ _mappings[ otu2 ] ];
+ final double d1 = ( d / 2 ) + ( ( _r[ _rev_mappings[ otu1 ] ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
+ final double d2 = d - d1;
if ( _df == null ) {
_external_nodes[ otu1 ].setDistanceToParent( d1 );
getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 );
if ( _verbose ) {
printProgress( otu1, otu2, node );
}
- System.out.println( "otu1=" + otu1 );
- System.out.println( "otu2=" + otu2 );
+ if ( _verbose ) {
+ System.out.println( "otu1=" + otu1 );
+ System.out.println( "otu2=" + otu2 );
+ }
calculateDistancesFromNewNode( otu1, otu2, d );
// _external_nodes[ _mappings[ otu1 ] ] = node;
_external_nodes[ otu1 ] = node;
updateMappings( otu2 );
--_n;
- System.out.println( "" );
- System.out.println( "----------------------------------------------------------------------------------" );
- System.out.println( "" );
+ if ( _verbose ) {
+ System.out.println( "" );
+ System.out
+ .println( "----------------------------------------------------------------------------------" );
+ System.out.println( "" );
+ }
}
- final float d = getDvalue( 0, 1 ) / 2;
+ final double d = getDvalue( 0, 1 ) / 2;
if ( _df == null ) {
getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
}
else {
- final float dd = Float.parseFloat( _df.format( d ) );
+ final double dd = Double.parseDouble( _df.format( d ) );
getExternalPhylogenyNode( 0 ).setDistanceToParent( dd );
getExternalPhylogenyNode( 1 ).setDistanceToParent( dd );
}
return pl;
}
- private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final float d ) {
+ private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
for( int j = 0; j < _n; ++j ) {
if ( ( j == otu2 ) || ( j == _rev_mappings[ otu1 ] ) ) {
continue;
}
updateDvalue( otu1, otu2, j, d );
}
- System.out.println();
+ if ( _verbose ) {
+ System.out.println();
+ }
}
- private final void updateDvalue( final int otu1, final int otu2, final int j, final float d ) {
- final float new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2;
+ private final void updateDvalue( final int otu1, final int otu2, final int j, final double d ) {
+ final int mj = _mappings[ j ];
+ // 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 < _mappings[ j ] ) {
- // System.out.println( " otu1=" + otu1 );
- // System.out.println( " otu2=" + otu2 );
- // System.out.println( "motu1=" + _mappings[ otu1 ] );
- // System.out.println( "motu2=" + _mappings[ otu2 ] );
- // System.out.println( " j=" + j );
- // System.out.println( "mj=" + _mappings[ j ] );
- // System.out.println( "d=" + DF.format( getDvalueUnmapped( otu1, _mappings[ j ] ) ) );
- _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), otu1, _mappings[ j ] );
+ if ( otu1 < mj ) {
+ _s.removePairing( _d_values[ otu1 ][ mj ], otu1, mj );
}
else {
- // System.out.println( " otu1=" + otu1 );
- // System.out.println( " otu2=" + otu2 );
- // System.out.println( "motu1=" + _mappings[ otu1 ] );
- // System.out.println( "motu2=" + _mappings[ otu2 ] );
- // System.out.println( " j=" + j );
- // System.out.println( "mj=" + _mappings[ j ] );
- // System.out.println( "d=" + DF.format( getDvalueUnmapped( otu1, _mappings[ j ] ) ) );
- _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), _mappings[ j ], otu1 );
+ _s.removePairing( _d_values[ mj ][ otu1 ], mj, otu1 );
}
- if ( _mappings[ otu2 ] < _mappings[ j ] ) {
- _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], _mappings[ j ] );
+ if ( _mappings[ otu2 ] < mj ) {
+ _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], mj );
}
else {
- _s.removePairing( getDvalue( j, otu2 ), _mappings[ j ], _mappings[ otu2 ] );
+ _s.removePairing( getDvalue( j, otu2 ), mj, _mappings[ otu2 ] );
}
- if ( otu1 < _mappings[ j ] ) {
- _s.addPairing( new_d, otu1, _mappings[ j ] );
+ double new_d;
+ if ( otu1 < mj ) {
+ new_d = ( _d_values[ otu1 ][ mj ] + getDvalue( j, otu2 ) - d ) / 2;
+ _s.addPairing( new_d, otu1, mj );
+ _d_values[ otu1 ][ mj ] = new_d;
}
else {
- _s.addPairing( new_d, _mappings[ j ], otu1 );
- }
- setDvalueU( otu1, j, new_d );
- }
-
- private void setDvalueU( final int i, final int j, final float d ) {
- if ( i < _mappings[ j ] ) {
- _d_values[ i ][ _mappings[ j ] ] = d;
+ new_d = ( _d_values[ mj ][ otu1 ] + getDvalue( j, otu2 ) - d ) / 2;
+ _s.addPairing( new_d, mj, otu1 );
+ _d_values[ mj ][ otu1 ] = new_d;
}
- _d_values[ _mappings[ j ] ][ i ] = d;
}
- private float getDvalue( final int i, final int j ) {
+ private double getDvalue( final int i, final int j ) {
if ( i < j ) {
return _d_values[ _mappings[ i ] ][ _mappings[ j ] ];
}
return _d_values[ _mappings[ j ] ][ _mappings[ i ] ];
}
- private float 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 ];
+ }
}
}
- private float calculateNetDivergence( final int i ) {
+ private double calculateNetDivergence( final int i ) {
float d = 0;
for( int n = 0; n < _n; ++n ) {
if ( i != n ) {
private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
_n = distances.getSize();
_d = distances;
- _r = new float[ _n ];
+ _r = new double[ _n ];
_mappings = new int[ _n ];
_rev_mappings = new int[ _n ];
- _d_values = new float[ distances.getSize() ][ distances.getSize() ];
- for( int i = 0; i < distances.getSize(); ++i ) {
- for( int j = 0; j < distances.getSize(); ++j ) {
- _d_values[ i ][ j ] = ( float ) distances.getValue( i, j );
- }
- }
- _s = new S();
+ _d_values = distances.getValues();
+ _s = new Sarray();
_s.initialize( distances );
initExternalNodes();
- System.out.println();
- printM();
- System.out.println( "----------------------------------------------------------------------------------" );
- System.out.println();
- System.out.println();
+ if ( _verbose ) {
+ System.out.println();
+ printM();
+ System.out.println( "----------------------------------------------------------------------------------" );
+ System.out.println();
+ System.out.println();
+ }
}
final private void printM() {
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;
_min_j = -1;
final int n_minus_2 = _n - 2;
- printM();
- for( int j = 1; j < _n; ++j ) {
+ if ( _verbose ) {
+ printM();
+ }
+ //
+ X: for( int j = 1; j < _n; ++j ) {
final double r_j = _r[ j ];
final int m_j = _mappings[ j ];
- 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() ) {
- System.out.print( sorted_i + " " );
- System.out.print( "(" + DF.format( getDvalueUnmapped( sorted_i, m_j ) ) + ") " );
- final double m = getDvalueUnmapped( sorted_i, m_j )
+ final double m = _d_values[ 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;
}
- System.out.println();
- for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
+ }
+ //
+ 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() ) {
- System.out.print( sorted_i );
- System.out.print( "->" );
- System.out.print( DF.format( _r[ sorted_i ] ) );
- System.out.print( " " );
+ 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, int[]> entry : _s.getSentrySet( m_j ) ) {
+ for( final int sorted_i : entry.getValue() ) {
+ System.out.print( sorted_i );
+ System.out.print( "->" );
+ System.out.print( DF.format( _r[ sorted_i ] ) );
+ System.out.print( " " );
+ }
+ }
+ System.out.println();
+ }
+ }
+ if ( _verbose ) {
System.out.println();
}
- System.out.println();
- return min_m;
}
// otu2 will, in effect, be "deleted" from the matrix.
git://source.jalview.org / jalview.git / blobdiff