3 // FORESTER -- software libraries and applications
4 // for evolutionary biology research and applications.
6 // Copyright (C) 2008-2009 Christian M. Zmasek
7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
10 // This library is free software; you can redistribute it and/or
11 // modify it under the terms of the GNU Lesser General Public
12 // License as published by the Free Software Foundation; either
13 // version 2.1 of the License, or (at your option) any later version.
15 // This library is distributed in the hope that it will be useful,
16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
18 // Lesser General Public License for more details.
20 // You should have received a copy of the GNU Lesser General Public
21 // License along with this library; if not, write to the Free Software
22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
24 // Contact: phylosoft @ gmail . com
25 // WWW: www.phylosoft.org/forester
27 package org.forester.evoinference.matrix.distance;
29 import java.io.IOException;
30 import java.io.Writer;
31 import java.text.DecimalFormat;
32 import java.text.NumberFormat;
33 import java.util.StringTokenizer;
35 import org.forester.util.ForesterUtil;
36 import org.forester.util.IllegalFormatUseException;
38 public class BasicSymmetricalDistanceMatrix implements DistanceMatrix {
40 NumberFormat nf1 = NumberFormat.getInstance();
41 private final static NumberFormat PHYLIP_FORMATTER = new DecimalFormat( "0.000000" );
42 final double[][] _values;
43 final String[] _identifiers;
45 public BasicSymmetricalDistanceMatrix( final int size ) {
46 _values = new double[ size ][ size ];
47 _identifiers = new String[ size ];
50 public String getIdentifier( final int i ) {
51 return _identifiers[ i ];
54 public int getIndex( final String identifier ) {
55 for( int i = 0; i < _identifiers.length; i++ ) {
56 if ( getIdentifier( i ).equals( identifier ) ) {
60 throw new IllegalArgumentException( "identifier [" + identifier + "] not found in distance matrix" );
63 public int getSize() {
64 return _values.length;
67 public double getValue( final int col, final int row ) {
69 if ( col >= getSize() ) {
70 throw new IndexOutOfBoundsException( "" );
74 else if ( col > row ) {
75 return _values[ row ][ col ];
77 return _values[ col ][ row ];
80 public void randomize( final long seed ) {
81 final java.util.Random r = new java.util.Random( seed );
82 for( int j = 0; j < getSize(); ++j ) {
83 for( int i = 0; i < j; ++i ) {
84 setValue( i, j, r.nextDouble() );
89 public void setIdentifier( final int i, final String identifier ) {
90 _identifiers[ i ] = identifier;
93 public void setRow( final String s, final int row ) {
94 final StringTokenizer tk = new StringTokenizer( s );
96 while ( tk.hasMoreElements() ) {
97 setValue( i, row, new Double( tk.nextToken() ).doubleValue() );
102 public void setValue( final int col, final int row, final double d ) {
103 if ( ( col == row ) && ( d != 0.0 ) ) {
104 throw new IllegalArgumentException( "attempt to set a non-zero value on the diagonal of a symmetrical distance matrix" );
106 else if ( col > row ) {
107 _values[ row ][ col ] = d;
109 _values[ col ][ row ] = d;
112 public void write( final Writer w ) throws IOException {
114 w.write( getSize() + "" );
115 w.write( ForesterUtil.LINE_SEPARATOR );
116 for( int row = 0; row < getSize(); ++row ) {
117 if ( !ForesterUtil.isEmpty( getIdentifier( row ) ) ) {
118 w.write( ForesterUtil.pad( getIdentifier( row ), 10, ' ', false ).toString() );
123 throw new IllegalFormatUseException( "Phylip format does not allow empty identifiers" );
125 for( int col = 0; col < getSize(); ++col ) {
126 w.write( PHYLIP_FORMATTER.format( getValue( col, row ) ) );
127 if ( col < getSize() - 1 ) {
132 if ( row < getSize() - 1 ) {
133 w.write( ForesterUtil.LINE_SEPARATOR );
138 private StringBuffer toPhylip() {
139 final StringBuffer sb = new StringBuffer();
144 sb.append( getSize() );
145 sb.append( ForesterUtil.LINE_SEPARATOR );
146 for( int row = 0; row < getSize(); ++row ) {
147 if ( !ForesterUtil.isEmpty( getIdentifier( row ) ) ) {
148 sb.append( ForesterUtil.pad( getIdentifier( row ), 10, ' ', false ) );
153 throw new IllegalFormatUseException( "Phylip format does not allow empty identifiers" );
156 for( int col = 0; col < getSize(); ++col ) {
157 sb.append( PHYLIP_FORMATTER.format( getValue( col, row ) ) );
158 if ( col < getSize() - 1 ) {
163 if ( row < getSize() - 1 ) {
164 sb.append( ForesterUtil.LINE_SEPARATOR );
171 public String toString() {
172 return toPhylip().toString();
175 public StringBuffer toStringBuffer( final Format format ) {
180 throw new IllegalArgumentException( "Unknown format:" + format );