From: cmzmasek@gmail.com Date: Sat, 15 Mar 2014 00:25:33 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=73979ccd545aa73fa45321f7590f6d234b979e5e;p=jalview.git inprogress --- diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index 3f989a0..6db6453 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -90,7 +90,7 @@ public class TestPhylogenyReconstruction { else { System.out.println( " failed." ); } - //timeNeighborJoining(); + timeNeighborJoining(); } public static boolean test( final File test_dir ) { @@ -2583,8 +2583,19 @@ public class TestPhylogenyReconstruction { 18 ); m3.setRow( "0.010376 0.010376 0.031503 0.000010 0.000010 0.000010 0.000010 0.010375 0.010376 0.010376 0.010376 0.010376 0.010376 0.098678 0.741282 0.000010 0.000010 0.000010 0.000010 0.000000", 19 ); - final NeighborJoiningR nj3 = NeighborJoiningR.createInstance( true, 6 ); + final NeighborJoiningR nj3 = NeighborJoiningR.createInstance( false, 6 ); final Phylogeny p3 = nj3.execute( m3 ); + //Archaeopteryx.createApplication( p3 ); + //// + final int size = 100; + for( int n = 0; n <= 100; ++n ) { + final NeighborJoiningR njn = NeighborJoiningR.createInstance( false, 6 ); + final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( size ); + mt.randomize( new Date().getTime() ); + final long start_time = new Date().getTime(); + njn.execute( mt ); + System.out.println( "Size: " + size + " -> " + ( new Date().getTime() - start_time ) + "ms" ); + } } catch ( final Exception e ) { e.printStackTrace( System.out ); diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java index c8f9b2a..a0ffd60 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -40,17 +40,17 @@ public final class NeighborJoiningR { 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 double _d_min; //TODO remove me private int[] _rev_mappings; private NeighborJoiningR() { @@ -73,22 +73,26 @@ public final class NeighborJoiningR { 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(); 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 otu 2 " + _mappings[ otu2 ] ); + 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 ] ); + } 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 ); @@ -103,24 +107,29 @@ public final class NeighborJoiningR { 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 ); } @@ -143,69 +152,55 @@ public final class NeighborJoiningR { 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( getDvalueUnmapped( 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( getDvalueUnmapped( otu1, mj ), 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 ); + new_d = ( _d_values[ mj ][ otu1 ] + getDvalue( j, otu2 ) - d ) / 2; + _s.addPairing( new_d, mj, otu1 ); + _d_values[ mj ][ otu1 ] = new_d; } - 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; - } - _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 ) { + private double getDvalueUnmapped( final int i, final int j ) { if ( i < j ) { return _d_values[ i ][ j ]; } @@ -218,7 +213,7 @@ public final class NeighborJoiningR { } } - 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 ) { @@ -276,23 +271,20 @@ public final class NeighborJoiningR { 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 ); - } - } + _d_values = distances.getValues(); _s = new S(); _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() { @@ -335,37 +327,45 @@ public final class NeighborJoiningR { _min_i = -1; _min_j = -1; final int n_minus_2 = _n - 2; - printM(); + if ( _verbose ) { + printM(); + } 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 + ": " ); + if ( _verbose ) { + System.out.print( "j=" + j + " mj=" + m_j + ": " ); + } for( final Entry> 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 ); + //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 ); + // _d_min = getDvalueUnmapped( sorted_i, m_j ); min_m = m; _min_i = sorted_i; _min_j = j; } } } - System.out.println(); - for( final Entry> 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( " " ); + if ( _verbose ) { + System.out.println(); + for( final Entry> 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; } diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java index 621b42b..b510a61 100644 --- a/forester/java/src/org/forester/evoinference/distance/S.java +++ b/forester/java/src/org/forester/evoinference/distance/S.java @@ -23,7 +23,7 @@ public final class S { _data = new ArrayList>>(); } - final public void addPairing( final float key, final int value, final int j ) { + final public void addPairing( final double key, final int value, final int j ) { addPairing( ( int ) ( FACTOR * key ), value, getS( j ) ); } @@ -47,7 +47,7 @@ public final class S { addPairing( ( int ) ( FACTOR * d.getValues()[ i ][ j ] ), i, map ); } } - System.out.println( toString() ); + //System.out.println( toString() ); } final public void initialize( final int size ) { @@ -57,7 +57,7 @@ public final class S { } } - final public void removePairing( final float key, final int value, final int j ) { + final public void removePairing( final double key, final int value, final int j ) { removePairing( ( int ) ( key * FACTOR ), value, j ); }