else {
System.out.println( " failed." );
}
- // timeNeighborJoining();
+ //timeNeighborJoining();
}
public static boolean test( final File test_dir ) {
final NeighborJoining nj = NeighborJoining.createInstance( true, 6 );
//nj = NeighborJoining.createInstance( true, 6 );
final Phylogeny pnj = nj.execute( m );
+ pnj.reRoot( pnj.getNode( "Bovine" ) );
Archaeopteryx.createApplication( pnj );
//
m = new BasicSymmetricalDistanceMatrix( 7 );
final NeighborJoiningR nj2 = NeighborJoiningR.createInstance( true, 6 );
//nj = NeighborJoining.createInstance( true, 6 );
final Phylogeny p2 = nj2.execute( m );
- Archaeopteryx.createApplication( p2 );
p2.reRoot( p2.getNode( "Bovine" ) );
- if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.151675 ) ) {
+ Archaeopteryx.createApplication( p2 );
+ if ( isUnequal( p2.getNode( "Chimp" ).getDistanceToParent(), 0.15168 ) ) {
return false;
}
- if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.117525 ) ) {
+ if ( isUnequal( p2.getNode( "Human" ).getDistanceToParent(), 0.11752 ) ) {
return false;
}
- if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.153932 ) ) {
+ if ( isUnequal( p2.getNode( "Gorilla" ).getDistanceToParent(), 0.15393 ) ) {
return false;
}
- if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.284694 ) ) {
+ if ( isUnequal( p2.getNode( "Orang" ).getDistanceToParent(), 0.28469 ) ) {
return false;
}
- if ( isUnequal( p2.getNode( "Gibbon" ).getDistanceToParent(), 0.357931 ) ) {
+ if ( isUnequal( p2.getNode( "Gibbon" ).getDistanceToParent(), 0.35793 ) ) {
return false;
}
if ( isUnequal( p2.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) {
if ( isUnequal( p2.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) {
return false;
}
- if ( isUnequal( p2.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.039819 ) ) {
+ if ( isUnequal( p2.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.03982 ) ) {
return false;
}
- if ( isUnequal( p2.getNode( "Human" ).getParent().getDistanceToParent(), 0.039819 ) ) {
+ if ( isUnequal( p2.getNode( "Human" ).getParent().getDistanceToParent(), 0.03982 ) ) {
return false;
}
- if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.026956 ) ) {
+ if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.02696 ) ) {
return false;
}
- if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.046481 ) ) {
+ if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.04648 ) ) {
return false;
}
if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getDistanceToParent(),
- 0.420269 ) ) {
+ 0.42027 ) ) {
return false;
}
if ( isUnequal( p2.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent()
+++ /dev/null
-// $Id:
-// FORESTER -- software libraries and applications
-// for evolutionary biology research and applications.
-//
-// Copyright (C) 2014 Christian M. Zmasek
-// All rights reserved
-//
-// This library is free software; you can redistribute it and/or
-// modify it under the terms of the GNU Lesser General Public
-// License as published by the Free Software Foundation; either
-// version 2.1 of the License, or (at your option) any later version.
-//
-// This library is distributed in the hope that it will be useful,
-// but WITHOUT ANY WARRANTY; without even the implied warranty of
-// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
-// Lesser General Public License for more details.
-//
-// You should have received a copy of the GNU Lesser General Public
-// License along with this library; if not, write to the Free Software
-// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
-//
-// Contact: phylosoft @ gmail . com
-// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
-
-package org.forester.evoinference.distance;
-
-import java.math.RoundingMode;
-import java.text.DecimalFormat;
-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;
-import org.forester.phylogeny.PhylogenyNode;
-import org.forester.util.ForesterUtil;
-
-public final class CopyOfNeighborJoiningR {
-
- private final static DecimalFormat DF = new DecimalFormat( "0.00000" );
- private BasicSymmetricalDistanceMatrix _d;
- private double[][] _d_values;
- private final DecimalFormat _df;
- private PhylogenyNode[] _external_nodes;
- private int[] _mappings;
- private int _n;
- private double[] _r;
- private final boolean _verbose;
- private int _min_i;
- private int _min_j;
- private S _s;
- private double _d_min; //TODO remove me
-
- private CopyOfNeighborJoiningR() {
- _verbose = false;
- _df = null;
- }
-
- private CopyOfNeighborJoiningR( final boolean verbose, final int maximum_fraction_digits_for_distances ) {
- if ( ( maximum_fraction_digits_for_distances < 1 ) || ( maximum_fraction_digits_for_distances > 9 ) ) {
- throw new IllegalArgumentException( "maximum fraction digits for distances is out of range: "
- + maximum_fraction_digits_for_distances );
- }
- _verbose = verbose;
- _df = new DecimalFormat();
- _df.setMaximumFractionDigits( maximum_fraction_digits_for_distances );
- _df.setRoundingMode( RoundingMode.HALF_UP );
- }
-
- public final Phylogeny execute( final BasicSymmetricalDistanceMatrix distance ) {
- reset( distance );
- final Phylogeny phylogeny = new Phylogeny();
- while ( _n > 2 ) {
- 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();
- final int otu1 = _min_i;
- 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 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 d2 = d - d1;
- if ( _df == null ) {
- getExternalPhylogenyNode( 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 ) ) );
- getExternalPhylogenyNode( otu2 ).setDistanceToParent( Double.parseDouble( _df.format( d2 ) ) );
- }
- node.addAsChild( getExternalPhylogenyNode( otu1 ) );
- node.addAsChild( getExternalPhylogenyNode( otu2 ) );
- if ( _verbose ) {
- printProgress( otu1, otu2, node );
- printProgress( _mappings[ otu1 ], _mappings[ otu2 ], node );
- }
- System.out.println( "otu1=" + otu1 );
- System.out.println( "otu2=" + otu2 );
- calculateDistancesFromNewNode( otu1, otu2, d );
- _external_nodes[ _mappings[ otu1 ] ] = node;
- updateMappings( otu2 );
- --_n;
- System.out.println( "" );
- System.out.println( "----------------------------------------------------------------------------------" );
- System.out.println( "" );
- }
- final double d = getDvalue( 0, 1 ) / 2;
- if ( _df == null ) {
- getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
- getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
- }
- else {
- final double dd = Double.parseDouble( _df.format( d ) );
- getExternalPhylogenyNode( 0 ).setDistanceToParent( dd );
- getExternalPhylogenyNode( 1 ).setDistanceToParent( dd );
- }
- final PhylogenyNode root = new PhylogenyNode();
- root.addAsChild( getExternalPhylogenyNode( 0 ) );
- root.addAsChild( getExternalPhylogenyNode( 1 ) );
- if ( _verbose ) {
- printProgress( 0, 1, root );
- }
- phylogeny.setRoot( root );
- phylogeny.setRooted( false );
- return phylogeny;
- }
-
- public final List<Phylogeny> execute( final List<BasicSymmetricalDistanceMatrix> distances_list ) {
- final List<Phylogeny> pl = new ArrayList<Phylogeny>();
- for( final BasicSymmetricalDistanceMatrix distances : distances_list ) {
- pl.add( execute( distances ) );
- }
- return pl;
- }
-
- private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
- System.out.print( "new D values: " );
- for( int j = 0; j < _n; ++j ) {
- if ( ( j == otu1 ) || ( j == otu2 ) ) {
- continue;
- }
- updateDvalue( otu1, otu2, j, d );
- }
- System.out.println();
- }
-
- private final void updateDvalue( final int otu1, final int otu2, final int j, final double d ) {
- final double new_d = ( getDvalue( otu1, j ) + getDvalue( j, otu2 ) - d ) / 2;
- System.out.print( DF.format( new_d ) + " " );
- System.out.println( "going to remove: " + getDvalue( otu1, j ) + ", " + _mappings[ otu1 ] + ", "
- + _mappings[ j ] );
- _s.removePairing( getDvalue( otu1, j ), _mappings[ otu1 ], _mappings[ j ] );
- System.out.println( "going to remove: " + getDvalue( j, otu2 ) + ", " + _mappings[ otu2 ] + ", "
- + _mappings[ j ] );
- _s.removePairing( getDvalue( j, otu2 ), _mappings[ otu2 ], _mappings[ j ] );
- _s.addPairing( new_d, otu1, _mappings[ j ] );
- setDvalue( 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;
- }
- _d_values[ _mappings[ j ] ][ _mappings[ i ] ] = d;
- }
-
- 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 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() {
- for( int i = 0; i < _n; ++i ) {
- _r[ i ] = calculateNetDivergence( i );
- }
- }
-
- private double calculateNetDivergence( final int i ) {
- double d = 0;
- for( int n = 0; n < _n; ++n ) {
- if ( i != n ) {
- d += getDvalue( n, i );
- }
- }
- return d;
- }
-
- private final PhylogenyNode getExternalPhylogenyNode( final int i ) {
- return _external_nodes[ _mappings[ i ] ];
- }
-
- private final void initExternalNodes() {
- _external_nodes = new PhylogenyNode[ _n ];
- String id;
- for( int i = 0; i < _n; ++i ) {
- _external_nodes[ i ] = new PhylogenyNode();
- id = _d.getIdentifier( i );
- if ( id != null ) {
- _external_nodes[ i ].setName( id );
- }
- else {
- _external_nodes[ i ].setName( Integer.toString( i ) );
- }
- _mappings[ i ] = i;
- }
- }
-
- private final void printProgress( final int otu1, final int otu2, final PhylogenyNode node ) {
- System.out.println( "Node " + printProgressNodeToString( getExternalPhylogenyNode( otu1 ) ) + " joins "
- + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) + " [resulting in node "
- + ( printProgressNodeToString( node ) ) + "]" );
- }
-
- private final String printProgressNodeToString( final PhylogenyNode n ) {
- if ( n.isExternal() ) {
- if ( ForesterUtil.isEmpty( n.getName() ) ) {
- return Long.toString( n.getId() );
- }
- return n.getName();
- }
- return n.getId()
- + " ("
- + ( ForesterUtil.isEmpty( n.getChildNode1().getName() ) ? n.getChildNode1().getId() : n.getChildNode1()
- .getName() )
- + "+"
- + ( ForesterUtil.isEmpty( n.getChildNode2().getName() ) ? n.getChildNode2().getId() : n.getChildNode2()
- .getName() ) + ")";
- }
-
- // only the values in the lower triangle are used.
- // !matrix values will be changed!
- private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
- _n = distances.getSize();
- _d = distances;
- _r = new double[ _n ];
- _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 = 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( "\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 int v : entry.getValue() ) {
- if ( !first ) {
- System.out.print( "," );
- }
- first = false;
- System.out.print( v );
- }
- System.out.print( " " );
- }
- System.out.println();
- }
- }
-
- private final double updateM() {
- calculateNetDivergences();
- Double min = 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 ];
- 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( "(" + DF.format( getDvalueUnmapped( sorted_i, m_j ) ) + ") " );
- final double m = getDvalue( sorted_i, j ) - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 );
- if ( ( m < min ) && ( sorted_i != j ) ) {
- _d_min = getDvalueUnmapped( sorted_i, m_j );
- min = m;
- _min_i = sorted_i;
- _min_j = j;
- }
- }
- }
- System.out.println();
- /*
- for( int i = 0; i < j; ++i ) {
- final double m = getDvalue( i, j ) - ( ( _r[ i ] + r_j ) / n_minus_2 );
- if ( m < min ) {
- min = m;
- _d_min = getDvalue( i, j );
- _min_i = i;
- _min_j = j;
- }
- }*/
- }
- System.out.println();
- return min;
- }
-
- // 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 ) {
- _mappings[ i ] = _mappings[ i + 1 ];
- }
- }
-
- public final static CopyOfNeighborJoiningR createInstance() {
- return new CopyOfNeighborJoiningR();
- }
-
- public final static CopyOfNeighborJoiningR createInstance( final boolean verbose,
- final int maximum_fraction_digits_for_distances ) {
- return new CopyOfNeighborJoiningR( verbose, maximum_fraction_digits_for_distances );
- }
-}
private final static DecimalFormat DF = new DecimalFormat( "0.00000" );
private BasicSymmetricalDistanceMatrix _d;
- private double[][] _d_values;
+ private float[][] _d_values;
private final DecimalFormat _df;
private PhylogenyNode[] _external_nodes;
private int[] _mappings;
private int _n;
- private double[] _r;
+ private float[] _r;
private final boolean _verbose;
private int _min_i;
private int _min_j;
private S _s;
- private double _d_min; //TODO remove me
+ private float _d_min; //TODO remove me
private int[] _rev_mappings;
private NeighborJoiningR() {
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 ] ];
- final double d1 = ( d / 2 ) + ( ( _r[ _rev_mappings[ otu1 ] ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) );
- final double d2 = d - d1;
+ 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;
if ( _df == null ) {
_external_nodes[ otu1 ].setDistanceToParent( d1 );
getExternalPhylogenyNode( otu2 ).setDistanceToParent( d2 );
System.out.println( "----------------------------------------------------------------------------------" );
System.out.println( "" );
}
- final double d = getDvalue( 0, 1 ) / 2;
+ final float d = getDvalue( 0, 1 ) / 2;
if ( _df == null ) {
getExternalPhylogenyNode( 0 ).setDistanceToParent( d );
getExternalPhylogenyNode( 1 ).setDistanceToParent( d );
}
else {
- final double dd = Double.parseDouble( _df.format( d ) );
+ final float dd = Float.parseFloat( _df.format( d ) );
getExternalPhylogenyNode( 0 ).setDistanceToParent( dd );
getExternalPhylogenyNode( 1 ).setDistanceToParent( dd );
}
return pl;
}
- private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) {
- System.out.print( "new D values: " );
+ private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final float d ) {
for( int j = 0; j < _n; ++j ) {
- if ( j == otu2 ) {
+ if ( ( j == otu2 ) || ( j == _rev_mappings[ otu1 ] ) ) {
continue;
}
- if ( otu1 < _mappings[ j ] ) {
- updateDvalue( otu1, otu2, j, d );
- }
- // else if ( otu1 > _mappings[ j ] ) {
- // updateDvalue( otu2, otu1, j, d );
- // }
+ updateDvalue( otu1, otu2, j, d );
}
System.out.println();
}
- 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 ] );
+ 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;
+ 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 ] );
}
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 );
}
- // 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 ] );
+ if ( otu1 < _mappings[ j ] ) {
+ _s.addPairing( new_d, otu1, _mappings[ j ] );
+ }
+ else {
+ _s.addPairing( new_d, _mappings[ j ], otu1 );
+ }
setDvalueU( otu1, j, new_d );
}
- private void setDvalueU( final int i, final int j, final double d ) {
+ private void setDvalueU( final int i, final int j, final float d ) {
if ( i < _mappings[ j ] ) {
_d_values[ i ][ _mappings[ j ] ] = d;
}
_d_values[ _mappings[ j ] ][ i ] = d;
}
- private double getDvalue( final int i, final int j ) {
+ private float 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 double getDvalueUnmapped( final int i, final int j ) {
+ private float getDvalueUnmapped( final int i, final int j ) {
if ( i < j ) {
return _d_values[ i ][ j ];
}
}
}
- private double calculateNetDivergence( final int i ) {
- double d = 0;
+ private float calculateNetDivergence( final int i ) {
+ float d = 0;
for( int n = 0; n < _n; ++n ) {
if ( i != n ) {
d += getDvalue( n, i );
private final void reset( final BasicSymmetricalDistanceMatrix distances ) {
_n = distances.getSize();
_d = distances;
- _r = new double[ _n ];
+ _r = new float[ _n ];
_mappings = new int[ _n ];
_rev_mappings = new int[ _n ];
- _d_values = _d.getValues();
+ _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();
_s.initialize( distances );
initExternalNodes();
git://source.jalview.org / jalview.git / commitdiff