package org.forester.evoinference.distance;
+import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.List;
import java.util.Map.Entry;
import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
-public class S {
+public final class S {
- private final List<SortedMap<Double, SortedSet<Integer>>> _data;
+ public final static int FACTOR = 1000000;
+ private final static boolean DEBUG = true;
+ private final List<SortedMap<Integer, SortedSet<Integer>>> _data;
- S() {
- _data = new ArrayList<SortedMap<Double, SortedSet<Integer>>>();
+ public S() {
+ _data = new ArrayList<SortedMap<Integer, SortedSet<Integer>>>();
}
- void addPairing( final double key, final int value, final int j ) {
- final SortedMap<Double, SortedSet<Integer>> m = _data.get( j );
- addPairing( key, value, m );
+ final public void addPairing( final double key, final int value, final int j ) {
+ addPairing( ( int ) ( FACTOR * key ), value, getS( j ) );
}
- SortedMap<Double, SortedSet<Integer>> getS( final int j ) {
+ final public void addPairing( final int key, final int value, final int j ) {
+ addPairing( key, value, getS( j ) );
+ }
+
+ final public SortedMap<Integer, SortedSet<Integer>> getS( final int j ) {
return _data.get( j );
}
- Set<Entry<Double, SortedSet<Integer>>> getSentrySet( final int j ) {
- return _data.get( j ).entrySet();
+ final public SortedSet<Integer> getValues( final int key, final int j ) {
+ return getS( j ).get( key );
}
- void initialize( final BasicSymmetricalDistanceMatrix d ) {
+ final public void initialize( final BasicSymmetricalDistanceMatrix d ) {
for( int j = 0; j < d.getSize(); ++j ) {
- final TreeMap<Double, SortedSet<Integer>> map = new TreeMap<Double, SortedSet<Integer>>();
+ final TreeMap<Integer, SortedSet<Integer>> map = new TreeMap<Integer, SortedSet<Integer>>();
_data.add( map );
for( int i = 0; i < j; ++i ) {
- addPairing( d.getValues()[ i ][ j ], i, map );
+ addPairing( ( int ) ( FACTOR * d.getValues()[ i ][ j ] ), i, map );
}
}
+ System.out.println( toString() );
+ }
+
+ final public void initialize( final int size ) {
+ for( int j = 0; j < size; ++j ) {
+ final TreeMap<Integer, SortedSet<Integer>> map = new TreeMap<Integer, SortedSet<Integer>>();
+ _data.add( map );
+ }
}
- void removePairing( final double key, final int value, final int j ) {
- final SortedMap<Double, SortedSet<Integer>> m = _data.get( j );
+ final public void removePairing( final double key, final int value, final int j ) {
+ removePairing( ( int ) ( key * FACTOR ), value, j );
+ }
+
+ final public void removePairing( final int key, final int value, final int j ) {
+ final SortedMap<Integer, SortedSet<Integer>> m = _data.get( j );
final SortedSet<Integer> x = m.get( key );
+ if ( DEBUG ) {
+ if ( x == null ) {
+ System.out.println( toString() );
+ throw new IllegalArgumentException( "key " + key + " (->" + value + ") does not exist for row " + j );
+ }
+ }
if ( x.size() == 1 ) {
- if ( !x.contains( value ) ) {
- //TODO remove me later
- throw new IllegalStateException( "!x.contains( value )" );
+ if ( DEBUG ) {
+ if ( !x.contains( value ) ) {
+ throw new IllegalArgumentException( "pairing " + key + "->" + value + " does not exist for row "
+ + j );
+ }
}
m.remove( key );
}
else if ( x.size() > 1 ) {
- final boolean removed = x.remove( value );
- if ( !removed ) {
- //TODO remove me later
- throw new IllegalStateException( value + " not found" );
+ if ( DEBUG ) {
+ if ( !x.remove( value ) ) {
+ throw new IllegalArgumentException( "pairing " + key + "->" + value
+ + " does not exist (could not be removed) for row " + j );
+ }
+ }
+ else {
+ x.remove( value );
}
}
- else {
- //TODO remove me later
- throw new IllegalStateException( "empty" );
+ else if ( DEBUG ) {
+ throw new IllegalStateException();
}
}
- private static void addPairing( final double key, final int value, final SortedMap<Double, SortedSet<Integer>> m ) {
+ final public int size() {
+ return _data.size();
+ }
+
+ // Slow, only for testing
+ @SuppressWarnings( "unchecked")
+ final public SortedSet<Integer>[] toArray( final int j ) {
+ return _data.get( j ).values().toArray( new SortedSet[ _data.get( j ).size() ] );
+ }
+
+ @Override
+ final public String toString() {
+ final DecimalFormat df = new DecimalFormat( "0.00" );
+ final StringBuilder sb = new StringBuilder();
+ for( int j = 0; j < size(); ++j ) {
+ for( final Entry<Integer, SortedSet<Integer>> entry : getSentrySet( j ) ) {
+ final double key = entry.getKey();
+ final SortedSet<Integer> values = entry.getValue();
+ sb.append( df.format( key / FACTOR ) + "->" );
+ boolean first = true;
+ for( final int v : values ) {
+ if ( !first ) {
+ sb.append( "," );
+ }
+ first = false;
+ sb.append( v );
+ }
+ sb.append( " " );
+ }
+ sb.append( "\n" );
+ }
+ return sb.toString();
+ }
+
+ final Set<Entry<Integer, SortedSet<Integer>>> getSentrySet( final int j ) {
+ return getS( j ).entrySet();
+ }
+
+ final private static void addPairing( final int key, final int value, final SortedMap<Integer, SortedSet<Integer>> m ) {
if ( !m.containsKey( key ) ) {
final TreeSet<Integer> x = new TreeSet<Integer>();
x.add( value );
m.put( key, x );
}
else {
- if ( m.get( key ).contains( value ) ) {
- //TODO remove me later
- throw new IllegalStateException( "pairing " + key + " -> " + value + " already exists" );
+ if ( DEBUG ) {
+ if ( m.get( key ).contains( value ) ) {
+ throw new IllegalArgumentException( "pairing " + key + "->" + value + " already exists" );
+ }
}
m.get( key ).add( value );
}
git://source.jalview.org / jalview.git / blobdiff