From 67eb6c24d137a9f045f58f08bba71f1999b9cb9c Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 12 Mar 2014 02:59:36 +0000 Subject: [PATCH] inprogress --- .../distance/CopyOfNeighborJoiningR.java | 353 ++++++++++++++++++++ .../evoinference/distance/NeighborJoiningR.java | 63 ++-- .../src/org/forester/evoinference/distance/S.java | 28 +- 3 files changed, 409 insertions(+), 35 deletions(-) create mode 100644 forester/java/src/org/forester/evoinference/distance/CopyOfNeighborJoiningR.java diff --git a/forester/java/src/org/forester/evoinference/distance/CopyOfNeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/CopyOfNeighborJoiningR.java new file mode 100644 index 0000000..692287e --- /dev/null +++ b/forester/java/src/org/forester/evoinference/distance/CopyOfNeighborJoiningR.java @@ -0,0 +1,353 @@ +// $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 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 ) { + 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> 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> 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 ); + } +} diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java index 6ebcbbf..bdc80be 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningR.java @@ -81,20 +81,22 @@ public final class NeighborJoiningR { 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 d = getDvalueUnmapped( 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 ); + _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, node ); @@ -141,30 +143,34 @@ public final class NeighborJoiningR { 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 ) ) { + if ( j == otu2 ) { continue; } - updateDvalue( otu1, otu2, j, d ); + if ( _mappings[ j ] > _mappings[ otu1 ] ) { + 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; + 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: " + getDvalue( otu1, j ) + ", " + otu1 + ", " + _mappings[ j ] ); - _s.removePairing( getDvalue( otu1, j ), _mappings[ otu1 ], _mappings[ j ] ); - System.out.println( "going to remove: " + getDvalue( j, otu2 ) + ", " + otu2 + ", " + _mappings[ j ] ); + System.out.println( "going to remove: " + getDvalueUnmapped( otu1, _mappings[ j ] ) + ", " + otu1 + ", " + + _mappings[ j ] ); + _s.removePairing( getDvalueUnmapped( otu1, _mappings[ j ] ), 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 ); + 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[ j ][ _mappings[ i ] ] = d; } private double getDvalue( final int i, final int j ) { @@ -218,7 +224,7 @@ public final class NeighborJoiningR { } private final void printProgress( final int otu1, final int otu2, final PhylogenyNode node ) { - System.out.println( "Node " + printProgressNodeToString( getExternalPhylogenyNode( otu1 ) ) + " joins " + System.out.println( "Node " + printProgressNodeToString( _external_nodes[ otu1 ] ) + " joins " + ( printProgressNodeToString( getExternalPhylogenyNode( otu2 ) ) ) + " [resulting in node " + ( printProgressNodeToString( node ) ) + "]" ); } @@ -258,6 +264,15 @@ public final class NeighborJoiningR { } 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" ); @@ -284,7 +299,7 @@ public final class NeighborJoiningR { private final double updateM() { 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; @@ -292,14 +307,15 @@ public final class NeighborJoiningR { 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 + ": " ); 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 = getDvalue( sorted_i, j ) - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 ); - if ( ( m < min ) && ( sorted_i != j ) ) { + final double m = getDvalueUnmapped( sorted_i, m_j ) - ( ( _r[ sorted_i ] + r_j ) / n_minus_2 ); + if ( ( m < min_m ) && ( sorted_i != j ) ) { _d_min = getDvalueUnmapped( sorted_i, m_j ); - min = m; + min_m = m; _min_i = sorted_i; _min_j = j; } @@ -318,13 +334,18 @@ public final class NeighborJoiningR { }*/ } 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 ] ); } } diff --git a/forester/java/src/org/forester/evoinference/distance/S.java b/forester/java/src/org/forester/evoinference/distance/S.java index fe70cd6..f1d94db 100644 --- a/forester/java/src/org/forester/evoinference/distance/S.java +++ b/forester/java/src/org/forester/evoinference/distance/S.java @@ -73,20 +73,20 @@ public final class S { throw new IllegalArgumentException( "key " + key + " (->" + value + ") does not exist for row " + j ); } } - if ( x.size() == 1 ) { - if ( DEBUG ) { - if ( !x.contains( value ) ) { - System.out.println(); - System.out - .println( "________________________________________________________________________________________" ); - System.out.println( toString() ); - throw new IllegalArgumentException( "pairing " + key + "->" + value + " does not exist for row " - + j ); - } - } - m.remove( key ); - } - else if ( x.size() > 1 ) { + // if ( x.size() == 1 ) { + // if ( DEBUG ) { + // if ( !x.contains( value ) ) { + // System.out.println(); + // System.out + // .println( "________________________________________________________________________________________" ); + // System.out.println( toString() ); + // throw new IllegalArgumentException( "pairing " + key + "->" + value + " does not exist for row " + // + j ); + // } + // } + // m.remove( key ); + // } + else if ( x.size() >= 1 ) { if ( DEBUG ) { if ( !x.remove( value ) ) { throw new IllegalArgumentException( "pairing " + key + "->" + value -- 1.7.10.2