public final class NeighborJoiningR {
- private final static DecimalFormat DF = new DecimalFormat( "0.00" );
+ private final static DecimalFormat DF = new DecimalFormat( "0.00000" );
private BasicSymmetricalDistanceMatrix _d;
private double[][] _d_values;
private final DecimalFormat _df;
private int _min_i;
private int _min_j;
private S _s;
- private double _d_min; //TODO remove me
+ private double _d_min; //TODO remove me
+ private int[] _rev_mappings;
private NeighborJoiningR() {
_verbose = false;
final int otu2 = _min_j;
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 = getDvalue( otu1, otu2 );
- final double d1 = ( d / 2 ) + ( ( _r[ otu1 ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
+ //final double d = getDvalueUnmapped( otu1, _mappings[ otu2 ] );
+ 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 ) {
- getExternalPhylogenyNode( otu1 ).setDistanceToParent( d1 );
+ _external_nodes[ otu1 ].setDistanceToParent( d1 );
getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 );
}
else {
// yes, yes, slow but only grows with n (and not n^2 or worse)...
- getExternalPhylogenyNode( otu1 ).setDistanceToParent( Double.parseDouble( _df.format( d1 ) ) );
+ _external_nodes[ otu1 ].setDistanceToParent( Double.parseDouble( _df.format( d1 ) ) );
getExternalPhylogenyNode( otu2 ).setDistanceToParent( Double.parseDouble( _df.format( d2 ) ) );
}
- node.addAsChild( getExternalPhylogenyNode( otu1 ) );
+ node.addAsChild( _external_nodes[ otu1 ] );
node.addAsChild( getExternalPhylogenyNode( otu2 ) );
if ( _verbose ) {
- printProgress( otu1, otu2 );
+ printProgress( otu1, otu2, node );
}
+ System.out.println( "otu1=" + otu1 );
+ System.out.println( "otu2=" + otu2 );
calculateDistancesFromNewNode( otu1, otu2, d );
- _external_nodes[ _mappings[ otu1 ] ] = node;
+ // _external_nodes[ _mappings[ otu1 ] ] = node;
+ _external_nodes[ otu1 ] = node;
updateMappings( otu2 );
--_n;
- System.out.println( "-------------------------------------------------------------" );
+ System.out.println( "" );
+ System.out.println( "----------------------------------------------------------------------------------" );
System.out.println( "" );
}
final double d = getDvalue( 0, 1 ) / 2;
root.addAsChild( getExternalPhylogenyNode( 0 ) );
root.addAsChild( getExternalPhylogenyNode( 1 ) );
if ( _verbose ) {
- printProgress( 0, 1 );
+ printProgress( 0, 1, root );
}
phylogeny.setRoot( root );
phylogeny.setRooted( false );
}
private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
- for( int i = 0; i < _n; ++i ) {
- if ( ( i == otu1 ) || ( i == otu2 ) ) {
+ System.out.print( "new D values: " );
+ for( int j = 0; j < _n; ++j ) {
+ if ( j == otu2 ) {
continue;
}
- updateDvalue( otu1, otu2, i, d );
+ if ( otu1 < _mappings[ j ] ) {
+ updateDvalue( otu1, otu2, j, d );
+ }
}
+ System.out.println();
}
- private final void updateDvalue( final int otu1, final int otu2, final int i, final double d ) {
- setDvalue( otu1, i, ( getDvalue( otu1, i ) + getDvalue( i, otu2 ) - d ) / 2 );
+ private final void updateDvalue( final int otu1, final int otu2, final int j, final double d ) {
+ final double new_d = ( getDvalueUnmapped( otu1, _mappings[ j ] ) + getDvalue( j, otu2 ) - d ) / 2;
+ System.out.print( DF.format( new_d ) + " " );
+ // System.out.println( "going to remove: " + getDvalueUnmapped( otu1, _mappings[ j ] ) + ", " + otu1 + ", "
+ // + _mappings[ j ] );
+
+ if ( otu1< _mappings[ j ] ) {
+ _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), otu1, _mappings[ j ] );
+ }
+ else {
+ _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), _mappings[ j ] , otu1 );
+ }
+
+
+ // System.out.println( "going to remove: " + getDvalue( j, otu2 ) + ", " +_mappings[ otu2 ] + ", "
+ // + _mappings[ j ] );
+
+ if ( _mappings[ otu2 ] < _mappings[ j ] ) {
+ _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ] , _mappings[ j ] );
+ }
+ else {
+ _s.removePairing( getDvalue( j, otu2 ) , _mappings[ j ], _mappings[ otu2 ] );
+
+ }
+
+ _s.addPairing( new_d, otu1, _mappings[ j ] );
+ setDvalueU( otu1, j, new_d );
}
- private void setDvalue( final int i, final int j, final double d ) {
- if ( i < j ) {
- _d_values[ _mappings[ i ] ][ _mappings[ j ] ] = d;
+ private void setDvalueU( final int i, final int j, final double d ) {
+ if ( i < _mappings[ j ] ) {
+ _d_values[ i ][ _mappings[ j ] ] = d;
}
- _d_values[ _mappings[ j ] ][ _mappings[ i ] ] = d;
+ _d_values[_mappings[ j] ][ i ] = d;
}
private double getDvalue( final int i, final int j ) {
_external_nodes[ i ].setName( Integer.toString( i ) );
}
_mappings[ i ] = i;
+ _rev_mappings[ i ] = i;
}
}
- private final void printProgress( final int otu1, final int otu2 ) {
- System.out.println( "Node " + printProgressNodeToString( getExternalPhylogenyNode( otu1 ) ) + " joins "
- + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) );
+ private final void printProgress( final int otu1, final int otu2, final PhylogenyNode node ) {
+ System.out.println( "Node " + printProgressNodeToString( _external_nodes[ otu1 ] ) + " joins "
+ + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) + " [resulting in node "
+ + ( printProgressNodeToString( node ) ) + "]" );
}
private final String printProgressNodeToString( final PhylogenyNode n ) {
_d = distances;
_r = new double[ _n ];
_mappings = new int[ _n ];
+ _rev_mappings = new int[ _n ];
_d_values = _d.getValues();
_s = new S();
_s.initialize( distances );
initExternalNodes();
+ System.out.println();
printM();
+ System.out.println( "----------------------------------------------------------------------------------" );
+ System.out.println();
+ System.out.println();
}
final private void printM() {
- for( int j = 1; j < _n; ++j ) {
+ for( int j = 0; j < _d_values.length; ++j ) {
+ System.out.print( _external_nodes[ j ] );
+ System.out.print( "\t\t" );
+ for( int i = 0; i < _d_values[ j ].length; ++i ) {
+ System.out.print( DF.format( _d_values[ i ][ j ] ) );
+ System.out.print( " " );
+ }
+ System.out.println();
+ }
+ for( int j = 0; j < _n; ++j ) {
+ System.out.print( getExternalPhylogenyNode( j ) );
+ System.out.print( "\t\t" );
for( int i = 0; i < _n; ++i ) {
System.out.print( DF.format( _d_values[ _mappings[ i ] ][ _mappings[ j ] ] ) );
System.out.print( " " );
}
- System.out.print( " " );
- for( final Entry<Double, SortedSet<Integer>> entry : _s.getSentrySet( _mappings[ j ] ) ) {
- final double key = entry.getKey();
- final SortedSet<Integer> value = entry.getValue();
- System.out.print( DF.format( key ) + "=" );
+ 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 ) + "=" );
boolean first = true;
- for( final Integer v : value ) {
+ for( final int v : entry.getValue() ) {
if ( !first ) {
System.out.print( "," );
}
}
private final double updateM() {
- printM();
calculateNetDivergences();
- Double min = Double.MAX_VALUE;
+ 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 ) {
final double r_j = _r[ j ];
final int m_j = _mappings[ j ];
- int counter = 0;
- int counter_all = 0;
- X: for( final Entry<Double, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
+ System.out.print( "j=" + j + " mj=" + m_j + ": " );
+ for( final Entry<Integer, SortedSet<Integer>> entry : _s.getSentrySet( m_j ) ) {
for( final int sorted_i : entry.getValue() ) {
- //if ( counter_all >= j ) {
- // break X;
- //}
- if ( _mappings[ counter ] == counter_all ) {
- System.out.print( sorted_i + " " );
- System.out.print( "(" + DF.format( getDvalueUnmapped( sorted_i, m_j ) ) + ") " );
- final double m = getDvalueUnmapped( sorted_i, m_j ) - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 );
- if ( m < min ) {
- _d_min = getDvalueUnmapped( sorted_i, m_j );
- min = m;
- _min_i = sorted_i;
- _min_j = j;
- }
- ++counter;
+ System.out.print( sorted_i + " " );
+ System.out.print( "(" + DF.format( getDvalueUnmapped( sorted_i, m_j ) ) + ") " );
+ 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;
}
- ++counter_all;
+ }
+ }
+ System.out.println();
+ for( final Entry<Integer, SortedSet<Integer>> 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();
}*/
}
System.out.println();
- return min;
+ return min_m;
}
// 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 ] );
+ }
+ for( int i = 0; i < _n; ++i ) {
+ _rev_mappings[ _mappings[ i ] ] = i;
}
}
git://source.jalview.org / jalview.git / blobdiff