Change graph interfaces to accommodate larger graphs.

The number of links is now a long value. Instead of returning a
collection of links, we now return an iterable (since collections have 
integer-valued sizes).

Author: pbloem

nodes/pom.xml

@@ -102,7 +102,7 @@
     <dependency>
      	<groupId>com.github.pbloem</groupId>
      	<artifactId>kit</artifactId>
-     	<version>v0.1.8</version>
+     	<version>v0.1.9</version>
     </dependency>   
 <!--     <dependency> -->
 <!--   	  <groupId>peterbloem.nl</groupId> -->

nodes/src/main/java/org/nodes/DGraph.java

@@ -21,7 +21,7 @@ public interface DGraph<L> extends Graph<L>
 	@Override
 	public DNode<L> get(int i);
 
-	public Collection<? extends DLink<L>> links();
+	public Iterable<? extends DLink<L>> links();
 
 	/**
 	 * Adds a new node with the given label 

nodes/src/main/java/org/nodes/DTGraph.java

@@ -30,15 +30,13 @@ public interface DTGraph<L, T> extends DGraph<L>, TGraph<L, T>
 	@Override
 	public DTNode<L, T> get(int i);
 
-	public Collection<? extends DTLink<L, T>> links();	
+	public Iterable<? extends DTLink<L, T>> links();	
 
 	/**
 	 * Adds a new node with the given label 
 	 */
 	public DTNode<L, T> add(L label);
-	
-	public int numLinks();
-	
+		
 	/**
 	 * Returns the node labels
 	 * @return

nodes/src/main/java/org/nodes/DiskDGraph.java

@@ -73,7 +73,7 @@ public class DiskDGraph implements DGraph<String>, FastWalkable<String, DNode<St
 	private List<List<Integer>> in;
 	private List<List<Integer>> out;
 
-	private int numLinks = 0;
+	private long numLinks = 0;
 	private long modCount = 0;
 
 	// * changes for any edit which causes the node indices to change 
@@ -85,7 +85,7 @@ public class DiskDGraph implements DGraph<String>, FastWalkable<String, DNode<St
 	private Long hashMod = null;
 
 	private boolean sorted = false;
-	
+		
 	public DiskDGraph(File dir)
 	{
 		this(dir, false);
@@ -94,7 +94,7 @@ public DiskDGraph(File dir)
 	/**
 	 * 
 	 * @param dbFile The file containing the graph structure. If the file doesn't exist, 
-	 *   it will be created. IF it does exist, the graph it contains will be loaded.
+	 *   it will be created. If it does exist, the graph it contains will be loaded.
 	 * @param nullLabels If true, all labels will be null (saving some space). 
 	 *    Adding a node with a nonnull label will result in an exception.
 	 */
@@ -126,7 +126,7 @@ public int size()
 	}
 
 	@Override
-	public int numLinks()
+	public long numLinks()
 	{
 		return numLinks;
 	}
@@ -827,14 +827,22 @@ public List<? extends DNode<String>> nodes()
 		return new NodeList(Series.series(size()));
 	}
 
+	/**
+	 * NOTE: If hasLongNumLinks is true and the graph has more links than 
+	 * Integer.MAX_VALUE, the {size()} of the returned collection
+	 * will be -1.
+	 * 
+	 * @return
+	 */
 	@Override
-	public Collection<? extends DLink<String>> links()
+	public Iterable<? extends DLink<String>> links()
 	{
 		return new LinkCollection();
 	}
 
 	/**
 	 * A collection of all links in this graph.
+	 * The iterator it returns can be safely used.
 	 * 
 	 * @author Peter
 	 *
@@ -850,7 +858,7 @@ public Iterator<DLink<String>> iterator()
 		@Override
 		public int size()
 		{
-			return numLinks;
+			return (int)numLinks();
 		}
 
 		private class LLIterator implements Iterator<DLink<String>>
@@ -1265,7 +1273,8 @@ public static DiskDGraph fromFile(File file, File tmpDir, File dbFile)
 
 	public void close()
 	{
-		db.atomicInteger("numLinks").createOrOpen().set(numLinks);
+		db.atomicLong("numLinks").createOrOpen().set(numLinks);
+		
 		db.close();
 	}
 

nodes/src/main/java/org/nodes/Graph.java

@@ -20,10 +20,6 @@
  * API level.</li>
  * </ul>
  * 
- * TODO: Create a separate UGraph & UTGraph. Undirected graphs behave differently than 
- * directed graphs. Letting Graph be the interface for undirected graphs violates
- * LSP.
- * 
  * <h2>A note on equality and inheritance</h2>
  * <p>
  * Our choice to use inheritance in the definition of graphs presents a problem
@@ -42,7 +38,7 @@
  * graphs to be equal, their level must match.
  * </p>
  *        
- * 
+ * TODO: Make numLinks() return a long, and make {links()} return an iterable.
  * 
  * 
  * @param <L>
@@ -67,7 +63,7 @@ public interface Graph<L>
 	 * behavior.
 	 * @return
 	 */
-	public Collection<? extends Link<L>> links();
+	public Iterable<? extends Link<L>> links();
 
 	/**
 	 * @return The graph's size in nodes.
@@ -79,7 +75,7 @@ public interface Graph<L>
 	 */
 	public Node<L> add(L label);
 
-	public int numLinks();
+	public long numLinks();
 
 	/**
 	 * Returns the node labels

nodes/src/main/java/org/nodes/LightDGraph.java

@@ -46,7 +46,7 @@ public class LightDGraph<L> implements DGraph<L>, FastWalkable<L, DNode<L>>
 	private List<List<Integer>> out;
 	private List<List<Integer>> in;	
 
-	private int numLinks = 0;
+	private long numLinks = 0;
 	private long modCount = 0;
 
 	// * changes for any edit which causes the node indices to change 
@@ -79,7 +79,7 @@ public int size()
 	}
 
 	@Override
-	public int numLinks()
+	public long numLinks()
 	{
 		return numLinks;
 	}
@@ -712,7 +712,7 @@ public List<? extends DNode<L>> nodes()
 	}
 
 	@Override
-	public Collection<? extends DLink<L>> links()
+	public Iterable<? extends DLink<L>> links()
 	{
 		return new LinkCollection();
 	}
@@ -734,7 +734,7 @@ public Iterator<DLink<L>> iterator()
 		@Override
 		public int size()
 		{
-			return numLinks;
+			return (int)numLinks;
 		}
 
 		private class LLIterator implements Iterator<DLink<L>>

nodes/src/main/java/org/nodes/LightDTGraph.java

@@ -31,7 +31,7 @@ public class LightDTGraph<L,T> implements DTGraph<L, T> {
 	private List<List<T>> outTags;
 	private List<List<T>> inTags;
 
-	private int numLinks = 0;
+	private long numLinks = 0;
 	private long modCount = 0;
 
 	// * changes for any edit which causes the node indices to change 
@@ -121,7 +121,7 @@ public DTNode<L, T> get(int i) {
 	}
 
 	@Override
-	public Collection<? extends DTLink<L, T>> links() {
+	public Iterable<? extends DTLink<L, T>> links() {
 		return new LinkCollection();
 	}
 
@@ -140,7 +140,7 @@ public DTNode<L, T> add(L label) {
 	}
 
 	@Override
-	public int numLinks() {
+	public long numLinks() {
 		return numLinks;
 	}
 
@@ -960,7 +960,7 @@ public Iterator<DTLink<L,T>> iterator()
 		@Override
 		public int size()
 		{
-			return numLinks;
+			return (int)numLinks;
 		}
 
 		private class LLIterator implements Iterator<DTLink<L,T>>

nodes/src/main/java/org/nodes/LightUGraph.java

@@ -49,7 +49,7 @@ public class LightUGraph<L> implements UGraph<L>, FastWalkable<L, UNode<L>>
 
 	List<List<Integer>> neighbors;
 
-	private int numLinks = 0;
+	private long numLinks = 0;
 	private long modCount = 0;
 
 	// * changes for any edit which causes the node indices to change 
@@ -81,7 +81,7 @@ public int size()
 	}
 
 	@Override
-	public int numLinks()
+	public long numLinks()
 	{
 		return numLinks;
 	}
@@ -529,7 +529,7 @@ public List<? extends UNode<L>> nodes()
 	}
 
 	@Override
-	public Collection<? extends ULink<L>> links()
+	public Iterable<? extends ULink<L>> links()
 	{
 		return new LinkCollection();
 	}
@@ -551,7 +551,7 @@ public Iterator<ULink<L>> iterator()
 		@Override
 		public int size()
 		{
-			return numLinks;
+			return (int)numLinks;
 		}
 
 		private class LLIterator implements Iterator<ULink<L>>

nodes/src/main/java/org/nodes/MapDTGraph.java

@@ -54,7 +54,7 @@ public class MapDTGraph<L, T> implements DTGraph<L, T>, HasPersistentNodes, HasP
 	protected List<MapDTNode> nodeList = new ArrayList<MapDTNode>();
 	protected Map<L, Set<MapDTNode>> nodes = new LinkedHashMap<L, Set<MapDTNode>>();
 
-	protected int numEdges = 0;
+	protected long numLinks = 0;
 	protected long modCount = 0;
 
 	protected int hash;
@@ -242,7 +242,7 @@ public MapDTLink connect(TNode<L, T> other, T tag)
 			neighborsTo.add(mdtOther);
 			mdtOther.neighborsFrom.add(this);
 
-			numEdges++;
+			numLinks++;
 			modCount++;
 
 			return link;
@@ -790,7 +790,7 @@ public void remove()
 
 			dead = true;
 
-			numEdges--;
+			numLinks--;
 			modCount++;
 		}
 
@@ -937,9 +937,9 @@ public Set<L> labels()
 	}
 
 	@Override
-	public int numLinks()
+	public long numLinks()
 	{
-		return numEdges;
+		return numLinks;
 	}
 
 	@Override
@@ -955,7 +955,7 @@ public List<? extends DTNode<L, T>> nodes()
 	}
 
 	@Override
-	public Collection<MapDTLink> links()
+	public Iterable<MapDTLink> links()
 	{
 		return new LinkCollection();
 	}
@@ -971,7 +971,7 @@ public Iterator<MapDTLink> iterator()
 		@Override
 		public int size()
 		{
-			return numLinks();
+			return (int)numLinks();
 		}
 
 		private class LCIterator implements Iterator<MapDTLink>

nodes/src/main/java/org/nodes/MapUTGraph.java

@@ -54,7 +54,7 @@ public class MapUTGraph<L, T> implements UTGraph<L, T>, HasPersistentNodes, HasP
 	protected Map<L, Set<MapUTNode>> nodes = new LinkedHashMap<L, Set<MapUTNode>>();
 	protected Set<T> tags = new LinkedHashSet<T>();
 
-	protected int numEdges = 0;
+	protected long numLinks = 0;
 	protected long modCount = 0;
 
 	protected int hash;
@@ -222,7 +222,7 @@ public MapUTLink connect(TNode<L, T> other, T tag)
 			neighbors.add(mutOther);
 			mutOther.neighbors.add(this);
 
-			numEdges++;
+			numLinks++;
 			modCount++;
 
 			return link;
@@ -571,7 +571,7 @@ public void remove()
 
 			dead = true;
 
-			numEdges --;
+			numLinks --;
 			modCount++;
 		}
 
@@ -712,9 +712,9 @@ public Set<L> labels()
 	}
 
 	@Override
-	public int numLinks()
+	public long numLinks()
 	{
-		return numEdges;
+		return numLinks;
 	}
 
 	@Override
@@ -730,7 +730,7 @@ public List<? extends UTNode<L, T>> nodes()
 	}
 
 	@Override
-	public Collection<MapUTLink> links()
+	public Iterable<MapUTLink> links()
 	{
 		return new LinkCollection();
 	}
@@ -747,7 +747,7 @@ public Iterator<MapUTLink> iterator()
 		@Override
 		public int size()
 		{
-			return numLinks();
+			return (int)numLinks();
 		}
 
 		private class LCIterator implements Iterator<MapUTLink>