Python wrapper

fca/src/main/java/org/nmdp/ngs/fca/CompleteLattice.java

@@ -68,6 +68,15 @@ protected CompleteLattice(final Graph graph, PartiallyOrdered top) {
         size = 1;
     }
 
+    /**
+     * Create a CompleteLattice with a TinkerGraph instance. This is an experiment
+     * meant to avoid a fatal error in JPype implementation.
+     * @param top 
+     */
+    protected CompleteLattice(PartiallyOrdered top) {
+        this(new TinkerGraph(), top);
+    }
+
     public class Iterator<E extends PartiallyOrdered> implements java.util.Iterator<E> {
         private final java.util.Iterator<Vertex> vertices;
 
@@ -91,12 +100,24 @@ public void remove() {
         }
     }
 
-    protected boolean filter(final Vertex source, final Vertex target) {
+    public boolean filter(final Vertex source, final Vertex target) {
         E sourceConcept = source.getProperty(LABEL);
         E targetConcept = target.getProperty(LABEL);
         return filter(sourceConcept, targetConcept);
     }
 
+    public boolean up(final Vertex source, final Vertex target) {
+        E sourceLabel = source.getProperty(LABEL);
+        E targetLabel = target.getProperty(LABEL);
+        return sourceLabel.isLessOrEqualTo(targetLabel);
+    }
+
+    public boolean down(final Vertex source, final Vertex target) {
+        E sourceLabel = source.getProperty(LABEL);
+        E targetLabel = target.getProperty(LABEL);
+        return sourceLabel.isGreaterOrEqualTo(targetLabel);
+    }
+
     private boolean filter(final Vertex source, final E right) {
         if(source.getProperty(LABEL) == null) {
             return false;
@@ -142,12 +163,28 @@ protected final Vertex supremum(final E proposed, Vertex generator) {
         }
         return generator;
     }
+
+    public final Graph getGraph() {
+        return graph;
+    }
+
+    public final int getColor() {
+        return color;
+    }
+
+    public final void setColor(final int color) {
+        this.color = color;
+    }
 
     @Override
     public final E find(final E element) {
         return this.meet(element, this.top());
     }
 
+    public final Vertex findVertex(final E element) {
+        return this.meetVertex(element, this.top());
+    }
+
     @Override
     public final boolean contains(final E element) {
         return this.find(element).equals(element);
@@ -315,6 +352,10 @@ public final E bottom() {
         return bottom.getProperty(LABEL);
     }
 
+    public final Vertex bottomVertex() {
+        return bottom;
+    }
+
     /**
      * Find the greatest element.
      * @return the greatest lattice element
@@ -324,6 +365,10 @@ public final E top() {
         return top.getProperty(LABEL);
     }
 
+    public final Vertex topVertex() {
+        return top;
+    }
+
     @Override
     public E join(final E left, final E right) {
         return supremum((E) left.union(right), top).getProperty(LABEL);
@@ -334,6 +379,10 @@ public E meet(final E left, final E right) {
         return supremum((E) left.intersect(right), top).getProperty(LABEL);
     }
 
+    public Vertex meetVertex(final E left, final E right) {
+        return supremum((E) left.union(right), top);
+    }
+
     @Override
     public double measure(final E left, final E right) {
         return (double) join(left, right).measure() /

fca/src/main/java/org/nmdp/ngs/fca/ConceptLattice.java

@@ -47,6 +47,10 @@ public ConceptLattice(final Graph graph, long numBits) {
         super(graph, new Concept(new MutableBitSet(), ones(numBits)));
     }
 
+    public ConceptLattice(long numBits) {
+        super(new Concept(new MutableBitSet(), ones(numBits)));
+    }
+
     public Concept insert(final Concept concept) {
         Vertex added = super.addIntent(concept, top);
 

fca/src/main/java/org/nmdp/ngs/fca/IntervalLattice.java

@@ -23,12 +23,17 @@
 package org.nmdp.ngs.fca;
 
 import com.tinkerpop.blueprints.Graph;
+import com.tinkerpop.blueprints.impls.tg.TinkerGraph;
 
 public class IntervalLattice<C extends Comparable<?>> extends CompleteLattice<Interval<C>> {
 
     public IntervalLattice(final Graph graph) {
         super(graph, Interval.MAGIC);
     }
+
+    public IntervalLattice() {
+        super(new TinkerGraph(), Interval.MAGIC);
+    }
 
     public Interval<C> insert(final Interval<C> interval) {
         return super.addIntent(interval, top).getProperty(LABEL);

fca/src/test/java/org/nmdp/ngs/fca/ConceptLatticeTest.java

@@ -22,6 +22,7 @@
 */
 package org.nmdp.ngs.fca;
 
+import com.google.common.collect.ImmutableList;
 import static org.junit.Assert.assertEquals;
 
 import static org.nmdp.ngs.fca.TestUtil.list;
@@ -30,6 +31,7 @@
 import java.util.List;
 
 import com.tinkerpop.blueprints.impls.tg.TinkerGraph;
+import org.dishevelled.bitset.MutableBitSet;
 import static org.junit.Assert.assertFalse;
 import static org.junit.Assert.assertTrue;