From: cmzmasek@gmail.com Date: Thu, 6 Mar 2014 03:46:31 +0000 (+0000) Subject: inprogress X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=e628c857be63e8d8a8698f536b3a56b9ba61e1f9;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 e7eb3b1..4e53280 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -35,6 +35,7 @@ import java.util.List; import org.forester.evoinference.distance.NeighborJoining; import org.forester.evoinference.distance.NeighborJoiningF; +import org.forester.evoinference.distance.NeighborJoiningR; import org.forester.evoinference.distance.PairwiseDistanceCalculator; import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix; import org.forester.evoinference.matrix.character.CharacterStateMatrix; @@ -66,13 +67,21 @@ public class TestPhylogenyReconstruction { } public static void main( final String[] args ) { + System.out.println( "NJ" ); if ( testNeighborJoining() ) { - System.out.println( "OK." ); + System.out.println( " OK." ); } else { - System.out.println( "failed." ); + System.out.println( " failed." ); + } + System.out.println( "NJR" ); + if ( testNeighborJoiningR() ) { + System.out.println( " OK." ); } - timeNeighborJoining(); + else { + System.out.println( " failed." ); + } + //timeNeighborJoining(); } public static boolean test( final File test_dir ) { @@ -2217,6 +2226,40 @@ public class TestPhylogenyReconstruction { return true; } + private static boolean testNeighborJoiningR() { + try { + NeighborJoiningR nj = NeighborJoiningR.createInstance(); + final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 ); + m0.setIdentifier( 0, "A" ); + m0.setIdentifier( 1, "B" ); + m0.setIdentifier( 2, "C" ); + m0.setIdentifier( 3, "D" ); + m0.setRow( "5 ", 1 ); + m0.setRow( "3 6 ", 2 ); + m0.setRow( "7.5 10.5 5.5", 3 ); + final Phylogeny p0 = nj.execute( m0 ); + BasicSymmetricalDistanceMatrix m = new BasicSymmetricalDistanceMatrix( 6 ); + m.setRow( "5", 1 ); + m.setRow( "4 7", 2 ); + m.setRow( "7 10 7", 3 ); + m.setRow( "6 9 6 5", 4 ); + m.setRow( "8 11 8 9 8", 5 ); + m.setIdentifier( 0, "A" ); + m.setIdentifier( 1, "B" ); + m.setIdentifier( 2, "C" ); + m.setIdentifier( 3, "D" ); + m.setIdentifier( 4, "E" ); + m.setIdentifier( 5, "F" ); + nj = NeighborJoiningR.createInstance(); + final Phylogeny p1 = nj.execute( m ); + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testSymmetricalDistanceMatrixParser() { try { final String l = ForesterUtil.getLineSeparator(); diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java new file mode 100644 index 0000000..ee3b014 --- /dev/null +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -0,0 +1,293 @@ +// $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.SortedMap; +import java.util.SortedSet; +import java.util.TreeMap; +import java.util.TreeSet; + +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 NeighborJoiningR { + + 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 List>> _s; + + private NeighborJoiningR() { + _verbose = false; + _df = null; + } + + private NeighborJoiningR( 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 ) { + // Calculates the minimal distance. + // If more than one minimal distances, always the first found is used + updateM(); + final int otu1 = _min_i; + final int otu2 = _min_j; + // It is a condition that otu1 < otu2. + final PhylogenyNode node = new PhylogenyNode(); + 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 ) { + 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 = _d_values[ _mappings[ 0 ] ][ _mappings[ 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 ) { + 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 void calculateNetDivergences() { + for( int i = 0; i < _n; ++i ) { + _r[ i ] = calculateNetDivergence( i ); + } + } + + private double calculateNetDivergence( final int i ) { + double 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 ] ]; + } + } + } + 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 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(); + _s = new ArrayList>>(); + for( int j = 0; j < _n; ++j ) { + final TreeMap> map = new TreeMap>(); + for( int i = 0; i < j; ++i ) { + if ( !map.containsKey( _d_values[ i ][ j ] ) ) { + map.put( _d_values[ i ][ j ], new TreeSet() ); + } + map.get( _d_values[ i ][ j ] ).add( i ); + } + _s.add( map ); + } + initExternalNodes(); + printM(); + } + + final private void printM() { + for( int j = 1; j < _n; ++j ) { + for( int i = 0; i < _n; ++i ) { + System.out.print( _d_values[ i ][ j ] ); + System.out.print( " " ); + } + System.out.print( " " ); + for( final Entry> entry : _s.get( j ).entrySet() ) { + final double key = entry.getKey(); + final SortedSet value = entry.getValue(); + System.out.print( key + "=" ); + boolean first = true; + for( final Integer v : value ) { + if ( !first ) { + System.out.print( "," ); + } + first = false; + System.out.print( v ); + } + System.out.print( " " ); + } + System.out.println(); + } + } + + private final void updateM() { + calculateNetDivergences(); + Double min = Double.MAX_VALUE; + _min_i = -1; + _min_j = -1; + final int n_minus_2 = _n - 2; + for( int j = 1; j < _n; ++j ) { + final double r_j = _r[ j ]; + final int m_j = _mappings[ j ]; + for( int i = 0; i < j; ++i ) { + final double m = _d_values[ _mappings[ i ] ][ m_j ] - ( ( _r[ i ] + r_j ) / n_minus_2 ); + if ( m < min ) { + min = m; + _min_i = i; + _min_j = j; + } + } + } + } + + // 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 NeighborJoiningR createInstance() { + return new NeighborJoiningR(); + } + + public final static NeighborJoiningR createInstance( final boolean verbose, + final int maximum_fraction_digits_for_distances ) { + return new NeighborJoiningR( verbose, maximum_fraction_digits_for_distances ); + } +}