Replace Arrays by ArrayMatrix

src/main/java/org/mastodon/mamut/treesimilarity/ZhangUnorderedTreeEditDistance.java

@@ -137,9 +137,9 @@ public class ZhangUnorderedTreeEditDistance< T >
 
 	private final TreeDetails[] deleteCosts;
 
-	private final NodeMapping< T >[][] treeMappings;
+	private final ArrayMatrix< NodeMapping< T > > treeMappings;
 
-	private final NodeMapping< T >[][] forestMappings;
+	private final ArrayMatrix< NodeMapping< T > > forestMappings;
 
 	private final List< Tree< T > > subtrees1;
 
@@ -231,8 +231,8 @@ private ZhangUnorderedTreeEditDistance( final Tree< T > tree1, final Tree< T > t
 		insertCosts = new EditCosts<>( tree2, costFunction, subtrees2.size(), this::getTreeIndex2 ).costs;
 		deleteCosts = new EditCosts<>( tree1, costFunction, subtrees1.size(), this::getTreeIndex1 ).costs;
 
-		treeMappings = new NodeMapping[ subtrees1.size() ][ subtrees2.size() ];
-		forestMappings = new NodeMapping[ subtrees1.size() ][ subtrees2.size() ];
+		treeMappings = new ArrayMatrix<>( subtrees1.size(), subtrees2.size() );
+		forestMappings = new ArrayMatrix<>( subtrees1.size(), subtrees2.size() );
 	}
 
 	private int getTreeIndex1( Tree< T > tree1 )
@@ -286,7 +286,7 @@ private void log()
 			logger.trace( "forest insertion[{}] = {}", subtree, insertCosts[ getTreeIndex2( subtree ) ].forestCost );
 	}
 
-	private void logDistances( String prefix, NodeMapping< T >[][] nodeMappings )
+	private void logDistances( String prefix, ArrayMatrix< NodeMapping< T > > nodeMappings )
 	{
 		if ( !logger.isTraceEnabled() )
 			return;
@@ -296,7 +296,7 @@ private void logDistances( String prefix, NodeMapping< T >[][] nodeMappings )
 			StringJoiner stringJoiner = new StringJoiner( ", ", "[", "]" );
 			for ( Tree< T > t2 : subtrees2 )
 			{
-				NodeMapping< T > editOperation = nodeMappings[ getTreeIndex1( t1 ) ][ getTreeIndex2( t2 ) ];
+				NodeMapping< T > editOperation = nodeMappings.get( getTreeIndex1( t1 ), getTreeIndex2( t2 ) );
 				stringJoiner.add( editOperation == null ? "-" : Double.toString( editOperation.getCost() ) );
 			}
 			logger.trace( "{} distance[{}] = {}", prefix, t1, stringJoiner );
@@ -309,11 +309,11 @@ private void logDistances( String prefix, NodeMapping< T >[][] nodeMappings )
 	 */
 	private NodeMapping< T > treeMapping( Tree< T > tree1, Tree< T > tree2 )
 	{
-		NodeMapping< T > operation = treeMappings[ getTreeIndex1( tree1 ) ][ getTreeIndex2( tree2 ) ];
+		NodeMapping< T > operation = treeMappings.get( getTreeIndex1( tree1 ), getTreeIndex2( tree2 ) );
 		if ( operation == null )
 		{
 			operation = computeTreeMapping( tree1, tree2 );
-			treeMappings[ getTreeIndex1( tree1 ) ][ getTreeIndex2( tree2 ) ] = operation;
+			treeMappings.set( getTreeIndex1( tree1 ), getTreeIndex2( tree2 ), operation );
 		}
 		return operation;
 	}
@@ -348,11 +348,11 @@ private NodeMapping< T > computeTreeMapping( Tree< T > tree1, Tree< T > tree2 )
 	 */
 	private NodeMapping< T > forestMapping( final Tree< T > forest1, final Tree< T > forest2 )
 	{
-		NodeMapping< T > operation = forestMappings[ getTreeIndex1( forest1 ) ][ getTreeIndex2( forest2 ) ];
+		NodeMapping< T > operation = forestMappings.get( getTreeIndex1( forest1 ), getTreeIndex2( forest2 ) );
 		if ( operation == null )
 		{
 			operation = computeForestMapping( forest1, forest2 );
-			forestMappings[ getTreeIndex1( forest1 ) ][ getTreeIndex2( forest2 ) ] = operation;
+			forestMappings.set( getTreeIndex1( forest1 ), getTreeIndex2( forest2 ), operation );
 		}
 		return operation;
 	}
@@ -682,4 +682,31 @@ private TreeDetails( final double treeCost, final double forestCost )
 			this.forestCost = forestCost;
 		}
 	}
+
+	private static class ArrayMatrix< T >
+	{
+		private final ArrayList< ArrayList< T > > matrix;
+
+		private ArrayMatrix( int rows, int columns )
+		{
+			matrix = new ArrayList<>( rows );
+			for ( int i = 0; i < rows; i++ )
+			{
+				ArrayList< T > row = new ArrayList<>( columns );
+				for ( int j = 0; j < columns; j++ )
+					row.add( null );
+				matrix.add( row );
+			}
+		}
+
+		private T get( int i, int j )
+		{
+			return matrix.get( i ).get( j );
+		}
+
+		private void set( int i, int j, T value )
+		{
+			matrix.get( i ).set( j, value );
+		}
+	}
 }

src/main/java/org/mastodon/mamut/treesimilarity/util/ArrayMatrix.java

@@ -0,0 +1,13 @@
+package org.mastodon.mamut.treesimilarity.util;
+
+import java.util.List;
+
+public class ArrayMatrix< T >
+{
+	private final List< List< T > > matrix;
+
+	public ArrayMatrix( List< List< T > > matrix )
+	{
+		this.matrix = matrix;
+	}
+}