From 083c646bffc9c910714880519a029ef8a38e4942 Mon Sep 17 00:00:00 2001 From: "cmzmasek@gmail.com" Date: Wed, 5 Mar 2014 04:28:38 +0000 Subject: [PATCH] inprogress --- .../archaeopteryx/tools/PhylogeneticInferrer.java | 4 +- .../evoinference/TestPhylogenyReconstruction.java | 191 +++++++++------- .../evoinference/distance/NeighborJoining.java | 24 -- .../evoinference/distance/NeighborJoiningF.java | 1 - .../evoinference/distance/NeighborJoiningX.java | 236 -------------------- .../distance/BasicSymmetricalDistanceMatrix.java | 40 ++-- .../org/forester/msa_compactor/MsaCompactor.java | 4 +- 7 files changed, 137 insertions(+), 363 deletions(-) delete mode 100644 forester/java/src/org/forester/evoinference/distance/NeighborJoiningX.java diff --git a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java index e6fe009..20da0c3 100644 --- a/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java +++ b/forester/java/src/org/forester/archaeopteryx/tools/PhylogeneticInferrer.java @@ -34,7 +34,7 @@ import java.util.List; import javax.swing.JOptionPane; import org.forester.archaeopteryx.MainFrameApplication; -import org.forester.evoinference.distance.NeighborJoining; +import org.forester.evoinference.distance.NeighborJoiningF; import org.forester.evoinference.distance.PairwiseDistanceCalculator; import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix; import org.forester.evoinference.tools.BootstrapResampler; @@ -142,7 +142,7 @@ public class PhylogeneticInferrer extends RunnableProcess { e.printStackTrace(); } } - final NeighborJoining nj = NeighborJoining.createInstance(); + final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 ); final Phylogeny phy = nj.execute( m ); PhylogenyMethods.extractFastaInformation( phy ); return phy; diff --git a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java index 98880ac..39e1a20 100644 --- a/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java +++ b/forester/java/src/org/forester/evoinference/TestPhylogenyReconstruction.java @@ -35,7 +35,6 @@ import java.util.List; import org.forester.evoinference.distance.NeighborJoining; import org.forester.evoinference.distance.NeighborJoiningF; -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; @@ -128,27 +127,6 @@ public class TestPhylogenyReconstruction { return true; } - private static boolean testDistanceCalculationMethods( final File test_dir ) { - try { - final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR - + "bcl.aln" ) ); - final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 ); - if ( pwd0.getSize() != 120 ) { - return false; - } - for( int i = 0; i < pwd0.getSize(); ++i ) { - if ( !isEqual( pwd0.getValue( i, i ), 0.0 ) ) { - return false; - } - } - } - catch ( final Exception e ) { - e.printStackTrace( System.out ); - return false; - } - return true; - } - private static boolean testBasicCharacterStateMatrix() { try { final CharacterStateMatrix matrix_0 = new BasicCharacterStateMatrix( 4, 8 ); @@ -424,6 +402,27 @@ public class TestPhylogenyReconstruction { return true; } + private static boolean testDistanceCalculationMethods( final File test_dir ) { + try { + final Msa msa0 = GeneralMsaParser.parse( new FileInputStream( test_dir + ForesterUtil.FILE_SEPARATOR + + "bcl.aln" ) ); + final BasicSymmetricalDistanceMatrix pwd0 = PairwiseDistanceCalculator.calcKimuraDistances( msa0 ); + if ( pwd0.getSize() != 120 ) { + return false; + } + for( int i = 0; i < pwd0.getSize(); ++i ) { + if ( !isEqual( pwd0.getValue( i, i ), 0.0 ) ) { + return false; + } + } + } + catch ( final Exception e ) { + e.printStackTrace( System.out ); + return false; + } + return true; + } + private static boolean testDolloParsimony() { try { final BinaryStates PRESENT = BinaryStates.PRESENT; @@ -1923,36 +1922,6 @@ public class TestPhylogenyReconstruction { private static boolean testNeighborJoining() { try { - final NeighborJoiningF njf = NeighborJoiningF.createInstance(); - final BasicSymmetricalDistanceMatrix m0f = new BasicSymmetricalDistanceMatrix( 4 ); - m0f.setIdentifier( 0, "A" ); - m0f.setIdentifier( 1, "B" ); - m0f.setIdentifier( 2, "C" ); - m0f.setIdentifier( 3, "D" ); - m0f.setRow( "5 ", 1 ); - m0f.setRow( "3 6 ", 2 ); - m0f.setRow( "7.5 10.5 5.5", 3 ); - final Phylogeny p0f = njf.execute( m0f ); - p0f.reRoot( p0f.getNode( "D" ) ); - if ( isUnequal( p0f.getNode( "A" ).getDistanceToParent(), 1 ) ) { - return false; - } - if ( isUnequal( p0f.getNode( "B" ).getDistanceToParent(), 4 ) ) { - return false; - } - if ( isUnequal( p0f.getNode( "C" ).getDistanceToParent(), 0.5 ) ) { - return false; - } - if ( isUnequal( p0f.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { - return false; - } - if ( isUnequal( p0f.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) { - return false; - } - if ( isUnequal( p0f.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) { - return false; - } - // NeighborJoining nj = NeighborJoining.createInstance(); final BasicSymmetricalDistanceMatrix m0 = new BasicSymmetricalDistanceMatrix( 4 ); m0.setIdentifier( 0, "A" ); @@ -2150,9 +2119,96 @@ public class TestPhylogenyReconstruction { if ( isUnequal( p3.getNode( "A" ).getParent().getParent().getDistanceToParent(), 0.05 ) ) { return false; } - //if ( TIME ) { - // timeNeighborJoining(); - //} + // + NeighborJoiningF njf = NeighborJoiningF.createInstance(); + final BasicSymmetricalDistanceMatrix m0f = new BasicSymmetricalDistanceMatrix( 4 ); + m0f.setIdentifier( 0, "A" ); + m0f.setIdentifier( 1, "B" ); + m0f.setIdentifier( 2, "C" ); + m0f.setIdentifier( 3, "D" ); + m0f.setRow( "5 ", 1 ); + m0f.setRow( "3 6 ", 2 ); + m0f.setRow( "7.5 10.5 5.5", 3 ); + final Phylogeny p0f = njf.execute( m0f ); + p0f.reRoot( p0f.getNode( "D" ) ); + if ( isUnequal( p0f.getNode( "A" ).getDistanceToParent(), 1 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "B" ).getDistanceToParent(), 4 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "C" ).getDistanceToParent(), 0.5 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "D" ).getDistanceToParent(), 2.5 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "A" ).getParent().getDistanceToParent(), 1.5 ) ) { + return false; + } + if ( isUnequal( p0f.getNode( "A" ).getParent().getParent().getDistanceToParent(), 2.5 ) ) { + return false; + } + // + m = new BasicSymmetricalDistanceMatrix( 7 ); + m.setIdentifier( 0, "Bovine" ); + m.setIdentifier( 1, "Mouse" ); + m.setIdentifier( 2, "Gibbon" ); + m.setIdentifier( 3, "Orang" ); + m.setIdentifier( 4, "Gorilla" ); + m.setIdentifier( 5, "Chimp" ); + m.setIdentifier( 6, "Human" ); + m.setRow( "0.00000 1.68660 1.71980 1.66060 1.52430 1.60430 1.59050", 0 ); + m.setRow( "1.68660 0.00000 1.52320 1.48410 1.44650 1.43890 1.46290", 1 ); + m.setRow( "1.71980 1.52320 0.00000 0.71150 0.59580 0.61790 0.55830", 2 ); + m.setRow( "1.66060 1.48410 0.71150 0.00000 0.46310 0.50610 0.47100", 3 ); + m.setRow( "1.52430 1.44650 0.59580 0.46310 0.00000 0.34840 0.30830", 4 ); + m.setRow( "1.60430 1.43890 0.61790 0.50610 0.34840 0.00000 0.26920", 5 ); + m.setRow( "1.59050 1.46290 0.55830 0.47100 0.30830 0.26920 0.00000", 6 ); + njf = NeighborJoiningF.createInstance( false, 5 ); + final Phylogeny p2f = njf.execute( m ); + p2f.reRoot( p2f.getNode( "Bovine" ) ); + if ( isUnequal( p2f.getNode( "Chimp" ).getDistanceToParent(), 0.15168 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Human" ).getDistanceToParent(), 0.11752 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Gorilla" ).getDistanceToParent(), 0.15393 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Orang" ).getDistanceToParent(), 0.28469 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Gibbon" ).getDistanceToParent(), 0.35793 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Mouse" ).getDistanceToParent(), 0.76891 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Bovine" ).getDistanceToParent(), 0.458845 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getDistanceToParent(), 0.03982 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Human" ).getParent().getDistanceToParent(), 0.03982 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getDistanceToParent(), 0.02696 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getDistanceToParent(), 0.04648 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent() + .getDistanceToParent(), 0.42027 ) ) { + return false; + } + if ( isUnequal( p2f.getNode( "Chimp" ).getParent().getParent().getParent().getParent().getParent() + .getDistanceToParent(), 0.458845 ) ) { + return false; + } } catch ( final Exception e ) { e.printStackTrace( System.out ); @@ -2523,43 +2579,22 @@ public class TestPhylogenyReconstruction { private static void timeNeighborJoining() { final NeighborJoiningF njf = NeighborJoiningF.createInstance(); - for( int n = 3; n <= 10; ++n ) { + for( int n = 3; n <= 8; ++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(); njf.execute( mt ); System.out.println( "Size: " + x + " -> " + ( new Date().getTime() - start_time ) + "ms" ); } final NeighborJoining nj = NeighborJoining.createInstance(); - for( int n = 3; n <= 10; ++n ) { + for( int n = 3; n <= 8; ++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(); 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 e3371c0..c0792a4 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoining.java @@ -201,30 +201,6 @@ public final class NeighborJoining { } } - 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 ); diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java index a098ff9..dd984ae 100644 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java +++ b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningF.java @@ -209,7 +209,6 @@ public final class NeighborJoiningF { } // 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; diff --git a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningX.java b/forester/java/src/org/forester/evoinference/distance/NeighborJoiningX.java deleted file mode 100644 index 8c4cc40..0000000 --- a/forester/java/src/org/forester/evoinference/distance/NeighborJoiningX.java +++ /dev/null @@ -1,236 +0,0 @@ -// $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 ); - } -} diff --git a/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java b/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java index fdf2ec4..14d7e97 100644 --- a/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java +++ b/forester/java/src/org/forester/evoinference/matrix/distance/BasicSymmetricalDistanceMatrix.java @@ -39,18 +39,14 @@ public final class BasicSymmetricalDistanceMatrix implements DistanceMatrix { // NumberFormat nf1 = NumberFormat.getInstance(); private final static NumberFormat PHYLIP_FORMATTER = new DecimalFormat( "0.000000" ); - final double[][] _values; final String[] _identifiers; + final double[][] _values; public BasicSymmetricalDistanceMatrix( final int size ) { _values = new double[ size ][ size ]; _identifiers = new String[ size ]; } - public final double[][] getValues() { - return _values; - } - @Override public final String getIdentifier( final int i ) { return _identifiers[ i ]; @@ -85,6 +81,10 @@ public final class BasicSymmetricalDistanceMatrix implements DistanceMatrix { return _values[ col ][ row ]; } + public final double[][] getValues() { + return _values; + } + public final void randomize( final long seed ) { final java.util.Random r = new java.util.Random( seed ); for( int j = 0; j < getSize(); ++j ) { @@ -122,6 +122,21 @@ public final class BasicSymmetricalDistanceMatrix implements DistanceMatrix { _values[ col ][ row ] = d; } + @Override + public final String toString() { + return toPhylip().toString(); + } + + @Override + public final StringBuffer toStringBuffer( final Format format ) { + switch ( format ) { + case PHYLIP: + return toPhylip(); + default: + throw new IllegalArgumentException( "Unknown format:" + format ); + } + } + public final void write( final Writer w ) throws IOException { w.write( " " ); w.write( getSize() + "" ); @@ -179,19 +194,4 @@ public final class BasicSymmetricalDistanceMatrix implements DistanceMatrix { } return sb; } - - @Override - public final String toString() { - return toPhylip().toString(); - } - - @Override - public final StringBuffer toStringBuffer( final Format format ) { - switch ( format ) { - case PHYLIP: - return toPhylip(); - default: - throw new IllegalArgumentException( "Unknown format:" + format ); - } - } } diff --git a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java index 35d524c..fb0d0fe 100644 --- a/forester/java/src/org/forester/msa_compactor/MsaCompactor.java +++ b/forester/java/src/org/forester/msa_compactor/MsaCompactor.java @@ -14,7 +14,7 @@ import java.util.SortedSet; import java.util.TreeSet; import org.forester.archaeopteryx.Archaeopteryx; -import org.forester.evoinference.distance.NeighborJoining; +import org.forester.evoinference.distance.NeighborJoiningF; import org.forester.evoinference.distance.PairwiseDistanceCalculator; import org.forester.evoinference.distance.PairwiseDistanceCalculator.PWD_DISTANCE_METHOD; import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix; @@ -258,7 +258,7 @@ public class MsaCompactor { e.printStackTrace(); } } - final NeighborJoining nj = NeighborJoining.createInstance(); + final NeighborJoiningF nj = NeighborJoiningF.createInstance( false, 5 ); final Phylogeny phy = nj.execute( m ); return phy; } -- 1.7.10.2