Remove assignIndices method from ZhangUnorderedTreeEditDistance

Instead, introduce a new class Node that can be implemented by CachedTree
This allows that TreeUtils.getAllAttributes() can be reused in the constructor for ZhangUnorderedTreeEditDistance

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

@@ -28,6 +28,7 @@
  */
 package org.mastodon.mamut.treesimilarity;
 
+import org.mastodon.mamut.treesimilarity.tree.Node;
 import org.mastodon.mamut.treesimilarity.tree.Tree;
 import org.mastodon.mamut.treesimilarity.tree.TreeUtils;
 import org.mastodon.mamut.treesimilarity.util.FlowNetwork;
@@ -200,7 +201,7 @@ private NodeMapping< T > treeMapping()
  private static < T > double distanceTreeToNull( Tree< T > tree2, ToDoubleBiFunction< T, T > costFunction )
  {
  double distance = 0;
- for ( Tree< T > subtree : TreeUtils.listOfSubtrees( tree2 ) )
+ for ( Tree< T > subtree : TreeUtils.getAllChildren( tree2 ) )
  distance += costFunction.applyAsDouble( null, subtree.getAttribute() );
  return distance;
  }
@@ -212,8 +213,10 @@ private ZhangUnorderedTreeEditDistance( final Tree< T > tree1, final Tree< T > t
 
  root1 = new CachedTree<>( tree1 );
  root2 = new CachedTree<>( tree2 );
- subtrees1 = assignIndices( root1 );
- subtrees2 = assignIndices( root2 );
+ subtrees1 = TreeUtils.getAllChildren( root1 );
+ subtrees2 = TreeUtils.getAllChildren( root2 );
+ subtrees1.forEach( cachedTree -> cachedTree.index = subtrees1.indexOf( cachedTree ) );
+ subtrees2.forEach( cachedTree -> cachedTree.index = subtrees2.indexOf( cachedTree ) );
 
  costMatrix = new double[ subtrees1.size() ][ subtrees2.size() ];
  for ( CachedTree< T > subtree1 : subtrees1 )
@@ -269,21 +272,6 @@ private void computeChangeCosts( CachedTree< T > tree, ToDoubleBiFunction< T, T
  tree.forestCost = forestCosts;
  }
 
- private List< CachedTree< T > > assignIndices( CachedTree< T > cachedTree )
- {
- List< CachedTree< T > > list = new ArrayList<>();
- assignIndex( list, cachedTree );
- return list;
- }
-
- private void assignIndex( List< CachedTree< T > > list, CachedTree< T > cachedTree )
- {
- list.add( cachedTree );
- cachedTree.index = list.size() - 1;
- for ( CachedTree< T > child : cachedTree.children )
- assignIndex( list, child );
- }
-
  /**
  * Calculate the Zhang edit distance between two (labeled) unordered trees.
  *
@@ -648,7 +636,7 @@ private static < T > NodeMapping< T > findBestMapping( final NodeMapping< T > a,
  return c;
  }
 
- private static class CachedTree< T >
+ private static class CachedTree< T > implements Node< CachedTree< T > >
  {
  private int index;
 
@@ -679,7 +667,7 @@ private boolean isLeaf()
  return isLeaf;
  }
 
- private List< CachedTree< T > > getChildren()
+ public List< CachedTree< T > > getChildren()
  {
  return children;
  }

src/main/java/org/mastodon/mamut/treesimilarity/tree/Node.java

@@ -0,0 +1,13 @@
+package org.mastodon.mamut.treesimilarity.tree;
+
+import java.util.Collection;
+
+public interface Node< T >
+{
+ /**
+ * Get the children of this {@link Tree}.
+ *
+ * @return The list of child {@link Tree} objects.
+ */
+ Collection< T > getChildren();
+}

src/main/java/org/mastodon/mamut/treesimilarity/tree/Tree.java

@@ -28,21 +28,13 @@
  */
 package org.mastodon.mamut.treesimilarity.tree;
 
-import java.util.Collection;
-
 /**
  * A tree data structure.
  *
  * @param <T> the type of the attribute of the tree nodes.
  */
-public interface Tree< T >
+public interface Tree< T > extends Node< Tree< T > >
 {
- /**
- * Get the children of this {@link Tree}.
- *
- * @return The list of child {@link Tree} objects.
- */
- Collection< Tree< T > > getChildren();
 
  /**
  * Get the attribute of this {@link Tree}.

src/main/java/org/mastodon/mamut/treesimilarity/tree/TreeUtils.java

@@ -29,6 +29,7 @@
 package org.mastodon.mamut.treesimilarity.tree;
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Collections;
 import java.util.List;
 import java.util.concurrent.atomic.AtomicInteger;
@@ -40,22 +41,6 @@ private TreeUtils()
  // prevent from instantiation
  }
 
- /**
- * Returns a complete list of all descendant subtrees of the given {@code Tree}, including itself.
- *
- * @return The list of subtrees.
- */
- public static < T > List< Tree< T > > listOfSubtrees( final Tree< T > tree )
- {
- if ( tree == null )
- return Collections.emptyList();
- List< Tree< T > > list = new ArrayList<>();
- list.add( tree );
- for ( Tree< T > child : tree.getChildren() )
- list.addAll( listOfSubtrees( child ) );
- return list;
- }
-
  /**
  * Gets the number of descendant subtrees of this {@link Tree}, including itself.
  * @return the number
@@ -64,7 +49,7 @@ public static < T > int size( final Tree< T > tree )
  {
  if ( tree == null )
  return 0;
- return listOfSubtrees( tree ).size();
+ return getAllChildren( tree ).size();
  }
 
  /**
@@ -76,10 +61,40 @@ public static < T > int size( final Tree< T > tree )
  public static < T > List< T > getAllAttributes( final Tree< T > tree )
  {
  List< T > attributes = new ArrayList<>();
- listOfSubtrees( tree ).forEach( subtree -> attributes.add( subtree.getAttribute() ) );
+ getAllChildren( tree ).forEach( subtree -> attributes.add( subtree.getAttribute() ) );
  return attributes;
  }
 
+ /**
+ * Recursively collects all children of the given node, including the node itself.
+ *
+ * @param node The root node.
+ * @param <T> The type of the node.
+ * @return A list of all children nodes.
+ */
+ public static < T extends Node< T > > List< T > getAllChildren( T node )
+ {
+ if ( node == null )
+ return Collections.emptyList();
+ List< T > result = new ArrayList<>();
+ result.add( node );
+ getAllChildrenRecursive( node, result );
+ return result;
+ }
+
+ private static < T extends Node< T > > void getAllChildrenRecursive( T node, List< T > result )
+ {
+ Collection< T > children = node.getChildren();
+ if ( children != null )
+ {
+ for ( T child : children )
+ {
+ result.add( child );
+ getAllChildrenRecursive( child, result );
+ }
+ }
+ }
+
  /**
  * Creates a String of the given tree as a Java code snippet that can be used to create the tree.
  * @param tree The tree to print.

src/test/java/org/mastodon/mamut/treesimilarity/tree/TreeUtilsTest.java

@@ -40,7 +40,7 @@ class TreeUtilsTest
 {
 
  @Test
- void testListOfSubtrees()
+ void testGetAllChildren()
  {
  Tree< Double > emptyTree = SimpleTreeExamples.emptyTree();
 
@@ -49,8 +49,8 @@ void testListOfSubtrees()
  subtrees1.add( tree1 );
  subtrees1.addAll( tree1.getChildren() );
 
- assertEquals( Collections.singletonList( emptyTree ), TreeUtils.listOfSubtrees( emptyTree ) );
- assertEquals( subtrees1, TreeUtils.listOfSubtrees( tree1 ) );
+ assertEquals( Collections.singletonList( emptyTree ), TreeUtils.getAllChildren( emptyTree ) );
+ assertEquals( subtrees1, TreeUtils.getAllChildren( tree1 ) );
  }
 
  @Test

src/test/java/org/mastodon/mamut/treesimilarity/util/NodeMappingTest.java

@@ -163,10 +163,10 @@ private double computeCosts( Tree< Double > tree1, Tree< Double > tree2, Map< Tr
  Set< Tree< Double > > keys = mapping.keySet();
  Set< Tree< Double > > values = new HashSet<>( mapping.values() );
  double costs = 0;
- for ( Tree< Double > subtree : TreeUtils.listOfSubtrees( tree1 ) )
+ for ( Tree< Double > subtree : TreeUtils.getAllChildren( tree1 ) )
  if ( !keys.contains( subtree ) )
  costs += DEFAULT_COSTS.applyAsDouble( subtree.getAttribute(), null );
- for ( Tree< Double > subtree : TreeUtils.listOfSubtrees( tree2 ) )
+ for ( Tree< Double > subtree : TreeUtils.getAllChildren( tree2 ) )
  if ( !values.contains( subtree ) )
  costs += DEFAULT_COSTS.applyAsDouble( subtree.getAttribute(), null );
  for ( Map.Entry< Tree< Double >, Tree< Double > > entry : mapping.entrySet() )