2 package org.forester.evoinference.distance;
4 import java.text.DecimalFormat;
5 import java.util.ArrayList;
7 import java.util.Map.Entry;
9 import java.util.SortedMap;
10 import java.util.TreeMap;
12 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
13 import org.forester.evoinference.matrix.distance.DistanceMatrix;
15 public final class Sarray {
17 public final static int FACTOR = 1000000;
18 private final static boolean DEBUG = true;
19 private final List<SortedMap<Integer, int[]>> _data;
22 _data = new ArrayList<SortedMap<Integer, int[]>>();
25 final public void addPairing( final double key, final int value, final int j ) {
26 addPairing( ( int ) ( FACTOR * key ), value, getS( j ) );
29 final public void addPairing( final int key, final int value, final int j ) {
30 addPairing( key, value, getS( j ) );
33 final public SortedMap<Integer, int[]> getS( final int j ) {
34 return _data.get( j );
37 final public int[] getValues( final int key, final int j ) {
38 return getS( j ).get( key );
41 final public void initialize( final DistanceMatrix d ) {
42 for( int j = 0; j < d.getSize(); ++j ) {
43 final TreeMap<Integer, int[]> map = new TreeMap<Integer, int[]>();
45 for( int i = 0; i < j; ++i ) {
46 addPairing( ( int ) ( FACTOR * d.getValues()[ i ][ j ] ), i, map );
49 //System.out.println( toString() );
52 final public void initialize( final int size ) {
53 for( int j = 0; j < size; ++j ) {
54 final TreeMap<Integer, int[]> map = new TreeMap<Integer, int[]>();
59 final public void removePairing( final double key, final int value, final int j ) {
60 removePairing( ( int ) ( key * FACTOR ), value, j );
63 final public void removePairing( final int key, final int value, final int j ) {
64 final SortedMap<Integer, int[]> m = _data.get( j );
65 final int[] x = m.get( key );
69 .println( "________________________________________________________________________________________" );
70 System.out.println( toString() );
71 throw new IllegalArgumentException( "key " + key + " (->" + value + ") does not exist for row " + j );
73 if ( x.length == 1 ) {
77 final int[] xnew = new int[ x.length - 1 ];
79 for( int i = 0; ++i < x.length; ++i ) {
80 final int xv = x[ i ];
89 final public int size() {
93 // Slow, only for testing
94 @SuppressWarnings( "unchecked")
95 final public Set<Integer>[] toArray( final int j ) {
96 return _data.get( j ).values().toArray( new Set[ _data.get( j ).size() ] );
100 final public String toString() {
101 final DecimalFormat df = new DecimalFormat( "0.000000" );
102 final StringBuilder sb = new StringBuilder();
103 for( int j = 0; j < size(); ++j ) {
106 for( final Entry<Integer, int[]> entry : getSentrySet( j ) ) {
107 final double key = entry.getKey();
108 final int[] values = entry.getValue();
109 sb.append( df.format( key / FACTOR ) + "->" );
110 boolean first = true;
111 for( final int v : values ) {
122 return sb.toString();
125 final Set<Entry<Integer, int[]>> getSentrySet( final int j ) {
126 return getS( j ).entrySet();
129 final private static void addPairing( final int key, final int value, final SortedMap<Integer, int[]> m ) {
130 if ( !m.containsKey( key ) ) {
131 final int[] x = new int[ 1 ];
136 final int[] x = new int[ m.get( key ).length + 1 ];
137 for( int i = 0; i < ( x.length - 1 ); i++ ) {
138 x[ i ] = m.get( key )[ i ];
140 x[ x.length - 1 ] = value;