From: cmzmasek@gmail.com Date: Wed, 5 Mar 2014 03:30:35 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=88fadb6580a37c8c55e7062cc6dab09ee583a6fd;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 c2c2d89..a526e76 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -34,6 +34,7 @@ import java.util.Date; import java.util.List; import org.forester.evoinference.distance.NeighborJoining; +import org.forester.evoinference.distance.NeighborJoiningX; import org.forester.evoinference.distance.PairwiseDistanceCalculator; import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix; import org.forester.evoinference.matrix.character.CharacterStateMatrix; @@ -71,7 +72,7 @@ public class TestPhylogenyReconstruction { else { System.out.println( "failed." ); } - //timeNeighborJoining(); + timeNeighborJoining(); } public static boolean test( final File test_dir ) { @@ -2503,5 +2504,18 @@ public class TestPhylogenyReconstruction { nj.execute( mt ); System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } + final NeighborJoiningX njx = NeighborJoiningX.createInstance(); + for( int n = 3; n <= 10; ++n ) { + final int x = ( int ) Math.pow( 2, n ); + final BasicSymmetricalDistanceMatrix mt = new BasicSymmetricalDistanceMatrix( x ); + mt.randomize( new Date().getTime() ); + // for( int i = 0; i < mt.getSize(); i++ ) { + // mt.setIdentifier( i, i + "i" ); + // } + // System.out.println( mt.toStringBuffer( Format.PHYLIP ) ); + final long start_time = new Date().getTime(); + njx.execute( mt ); + System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); + } } } diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java index b92d367..3cd0d28 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java @@ -39,13 +39,13 @@ public final class NeighborJoining { private BasicSymmetricalDistanceMatrix _d; private double[][] _d_values; - private double[][] _m_values; - private double[] _r; - private int _n; + private final DecimalFormat _df; private PhylogenyNode[] _external_nodes; + private double[][] _m_values; private int[] _mappings; + private int _n; + private double[] _r; private final boolean _verbose; - private final DecimalFormat _df; private NeighborJoining() { _verbose = false; @@ -63,65 +63,6 @@ public final class NeighborJoining { _df.setRoundingMode( RoundingMode.HALF_UP ); } - private final void printM() { - System.out.println( "M:" ); - for( final double[] _m_value : _m_values ) { - for( int j = 0; j < _m_values.length; j++ ) { - System.out.print( _m_value[ j ] ); - System.out.print( " " ); - } - System.out.println(); - } - System.out.println(); - } - - private final void printD() { - System.out.println( "D:" ); - for( final double[] _d_value : _d_values ) { - for( int j = 0; j < _d_values.length; j++ ) { - System.out.print( _d_value[ j ] ); - System.out.print( " " ); - } - System.out.println(); - } - System.out.println(); - } - - private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) { - // final int otu1_m = _mappings[ otu1 ]; - // final int otu2_m = _mappings[ otu2 ]; - // int i_m; - for( int i = 0; i < _n; ++i ) { - if ( ( i == otu1 ) || ( i == otu2 ) ) { - continue; - } - if ( otu1 < i ) { - _d_values[ _mappings[ otu1 ] ][ _mappings[ i ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2; - } - else { - _d_values[ _mappings[ i ] ][ _mappings[ otu1 ] ] = ( 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; - } - } - - private final void calculateNetDivergences() { - double d; - // int i_m; - for( int i = 0; i < _n; ++i ) { - d = 0; - //i_m = _mappings[ i ]; - for( int n = 0; n < _n; ++n ) { - //d += _d_values[ i_m ][ _mappings[ n ] ]; - if ( i != n ) { - d += getValueFromD( i, n ); - } - } - _r[ i ] = d; - } - } - public final Phylogeny execute( final BasicSymmetricalDistanceMatrix distance ) { reset( distance ); final Phylogeny phylogeny = new Phylogeny(); @@ -144,7 +85,7 @@ public final class NeighborJoining { } // It is a condition that otu1 < otu2. final PhylogenyNode node = new PhylogenyNode(); - final double d = getValueFromD( otu1, otu2 ); + final double d = _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ]; final double d1 = ( d / 2 ) + ( ( _r[ otu1 ] - _r[ otu2 ] ) / ( 2 * ( _n - 2 ) ) ); final double d2 = d - d1; if ( _df == null ) { @@ -166,7 +107,7 @@ public final class NeighborJoining { updateMappings( otu2 ); --_n; } - final double d = getValueFromD( 0, 1 ) / 2; + final double d = _d_values[ _mappings[ 0 ] ][ _mappings[ 1 ] ] / 2; if ( _df == null ) { getExternalPhylogenyNode( 0 ).setDistanceToParent( d ); getExternalPhylogenyNode( 1 ).setDistanceToParent( d ); @@ -195,15 +136,54 @@ public final class NeighborJoining { return pl; } - private final PhylogenyNode getExternalPhylogenyNode( final int i ) { - return _external_nodes[ _mappings[ i ] ]; + private final void calculateDistancesFromNewNode( final int otu1, final int otu2, final double d ) { + final int m_otu1 = _mappings[ otu1 ]; + final int m_otu2 = _mappings[ otu2 ]; + for( int i = 0; i < _n; ++i ) { + if ( ( i == otu1 ) || ( i == otu2 ) ) { + continue; + } + final int m_i = _mappings[ i ]; + if ( otu1 < i ) { + if ( otu2 > i ) { + _d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2; + } + else { + _d_values[ m_otu1 ][ m_i ] = ( _d_values[ m_otu1 ][ m_i ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2; + } + } + else { + if ( otu2 > i ) { + _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_i ][ m_otu2 ] - d ) / 2; + } + else { + _d_values[ m_i ][ m_otu1 ] = ( _d_values[ m_i ][ m_otu1 ] + _d_values[ m_otu2 ][ m_i ] - d ) / 2; + } + } + } } - private final double getValueFromD( final int otu1, final int otu2 ) { - if ( otu1 > otu2 ) { - return _d_values[ _mappings[ otu2 ] ][ _mappings[ otu1 ] ]; + private final void calculateNetDivergences() { + double d; + for( int i = 0; i < _n; ++i ) { + d = 0; + final int m_i = _mappings[ i ]; + for( int n = 0; n < _n; ++n ) { + if ( i != n ) { + if ( i > n ) { + d += _d_values[ _mappings[ n ] ][ m_i ]; + } + else { + d += _d_values[ m_i ][ _mappings[ n ] ]; + } + } + } + _r[ i ] = d; } - return _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ]; + } + + private final PhylogenyNode getExternalPhylogenyNode( final int i ) { + return _external_nodes[ _mappings[ i ] ]; } private final void initExternalNodes() { @@ -216,12 +196,36 @@ public final class NeighborJoining { _external_nodes[ i ].setName( id ); } else { - _external_nodes[ i ].setName( "" + i ); + _external_nodes[ i ].setName( Integer.toString( i ) ); } _mappings[ i ] = i; } } + private final void printD() { + System.out.println( "D:" ); + for( final double[] _d_value : _d_values ) { + for( int j = 0; j < _d_values.length; j++ ) { + System.out.print( _d_value[ j ] ); + System.out.print( " " ); + } + System.out.println(); + } + System.out.println(); + } + + private final void printM() { + System.out.println( "M:" ); + for( final double[] _m_value : _m_values ) { + for( int j = 0; j < _m_values.length; j++ ) { + System.out.print( _m_value[ j ] ); + System.out.print( " " ); + } + System.out.println(); + } + System.out.println(); + } + private final void printProgress( final int otu1, final int otu2 ) { final PhylogenyNode n1 = getExternalPhylogenyNode( otu1 ); final PhylogenyNode n2 = getExternalPhylogenyNode( otu2 ); @@ -243,15 +247,12 @@ public final class NeighborJoining { private final void updateM() { calculateNetDivergences(); - final double r_j; - final int j_m; - final int _n_2 = _n - 2; + final int n_minus_2 = _n - 2; for( int j = 1; j < _n; ++j ) { - //r_j = _r[ j ]; - // j_m = _mappings[ j ]; + final double r_j = _r[ j ]; + final int m_j = _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 ] ][ m_j ] - ( ( _r[ i ] + r_j ) / n_minus_2 ); } } } diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningX.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningX.java new file mode 100644 index 0000000..8c4cc40 --- /dev/null +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningX.java @@ -0,0 +1,236 @@ +// $Id: +// FORESTER -- software libraries and applications +// for evolutionary biology research and applications. +// +// Copyright (C) 2008-2009 Christian M. Zmasek +// Copyright (C) 2008-2009 Burnham Institute for Medical Research +// 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 org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix; +import org.forester.phylogeny.Phylogeny; +import org.forester.phylogeny.PhylogenyNode; +import org.forester.util.ForesterUtil; + +public final class NeighborJoiningX { + + private BasicSymmetricalDistanceMatrix _d; + private double[][] _d_values; + private final DecimalFormat _df; + private PhylogenyNode[] _external_nodes; + private double[][] _m_values; + private int[] _mappings; + private int _n; + private double[] _r; + private final boolean _verbose; + + private NeighborJoiningX() { + _verbose = false; + _df = null; + } + + private NeighborJoiningX( 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 ) { + updateM(); + // Calculates the minimal distance. + // If more than one minimal distances, always the first found is used + // could randomize this, so that any would be returned in a randomized fashion... + double minimum = _m_values[ 0 ][ 1 ]; + int otu1 = 0; + int otu2 = 1; + for( int j = 1; j < _n; ++j ) { + for( int i = 0; i < j; ++i ) { + if ( _m_values[ i ][ j ] < minimum ) { + minimum = _m_values[ i ][ j ]; + otu1 = i; + otu2 = j; + } + } + } + // It is a condition that otu1 < otu2. + final PhylogenyNode node = new PhylogenyNode(); + final double d = getValueFromD( 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 ); + } + calculateDistancesFromNewNode( otu1, otu2, d ); + _external_nodes[ _mappings[ otu1 ] ] = node; + updateMappings( otu2 ); + --_n; + } + final double d = getValueFromD( 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 ); + } + phylogeny.setRoot( root ); + phylogeny.setRooted( false ); + return phylogeny; + } + + public final List execute( final List distances_list ) { + final List pl = new ArrayList(); + 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 ) { + for( int i = 0; i < _n; ++i ) { + if ( ( i == otu1 ) || ( i == otu2 ) ) { + continue; + } + if ( otu1 < i ) { + _d_values[ _mappings[ otu1 ] ][ _mappings[ i ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2; + } + else { + _d_values[ _mappings[ i ] ][ _mappings[ otu1 ] ] = ( getValueFromD( otu1, i ) + getValueFromD( i, otu2 ) - d ) / 2; + } + } + } + + private final void calculateNetDivergences() { + double d; + for( int i = 0; i < _n; ++i ) { + d = 0; + for( int n = 0; n < _n; ++n ) { + if ( i != n ) { + d += getValueFromD( i, n ); + } + } + _r[ i ] = d; + } + } + + private final PhylogenyNode getExternalPhylogenyNode( final int i ) { + return _external_nodes[ _mappings[ i ] ]; + } + + private final double getValueFromD( final int otu1, final int otu2 ) { + if ( otu1 > otu2 ) { + return _d_values[ _mappings[ otu2 ] ][ _mappings[ otu1 ] ]; + } + return _d_values[ _mappings[ otu1 ] ][ _mappings[ otu2 ] ]; + } + + 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( "" + i ); + } + _mappings[ i ] = i; + } + } + + private final void printProgress( final int otu1, final int otu2 ) { + final PhylogenyNode n1 = getExternalPhylogenyNode( otu1 ); + final PhylogenyNode n2 = getExternalPhylogenyNode( otu2 ); + System.out.println( "Node " + ( ForesterUtil.isEmpty( n1.getName() ) ? n1.getId() : n1.getName() ) + " joins " + + ( ForesterUtil.isEmpty( n2.getName() ) ? n2.getId() : n2.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(); + _m_values = new double[ _n ][ _n ]; + initExternalNodes(); + } + + private final void updateM() { + calculateNetDivergences(); + for( int j = 1; j < _n; ++j ) { + for( int i = 0; i < j; ++i ) { + _m_values[ i ][ j ] = getValueFromD( i, j ) - ( ( _r[ i ] + _r[ j ] ) / ( _n - 2 ) ); + } + } + } + + // 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 NeighborJoiningX createInstance() { + return new NeighborJoiningX(); + } + + public final static NeighborJoiningX createInstance( final boolean verbose, + final int maximum_fraction_digits_for_distances ) { + return new NeighborJoiningX( verbose, maximum_fraction_digits_for_distances ); + } +}