Add back propagateSourceIDs, and also store the propagatedSources for clustering

Author: Balletie

dnainator-core/src/main/java/nl/tudelft/dnainator/graph/impl/command/TopologicalPathExpander.java

@@ -2,6 +2,7 @@
 
 import nl.tudelft.dnainator.graph.impl.NodeLabels;
 import nl.tudelft.dnainator.graph.impl.RelTypes;
+import nl.tudelft.dnainator.graph.impl.properties.BubbleProperties;
 import nl.tudelft.dnainator.graph.impl.properties.SequenceProperties;
 
 import org.neo4j.graphdb.Direction;
@@ -65,7 +66,7 @@ public Iterable<Relationship> expand(Path path,
 
 		// Encode the unclosed propagated bubbles on the edges.
 		from.getRelationships(RelTypes.NEXT, Direction.OUTGOING)
-			.forEach(out -> relIDtoSourceIDs.put(out.getId(), toPropagate));
+			.forEach(out -> propagateSourceIDs(toPropagate, out));
 
 		// Process all outgoing edges.
 		List<Relationship> expand = new LinkedList<>();
@@ -119,6 +120,12 @@ private void createBubbleSource(Node n, Set<Long> toPropagate) {
 		}
 	}
 
+	private void propagateSourceIDs(Set<Long> propagatedUnique, Relationship out) {
+		out.setProperty(BubbleProperties.BUBBLE_SOURCE_IDS.name(),
+				propagatedUnique.stream().mapToLong(l -> l).toArray());
+		relIDtoSourceIDs.put(out.getId(), propagatedUnique);
+	}
+
 	private void createBubbleSink(Node n) {
 		int degree = n.getDegree(RelTypes.NEXT, Direction.INCOMING);
 		if (degree >= 2) {

dnainator-core/src/main/java/nl/tudelft/dnainator/graph/impl/properties/BubbleProperties.java

@@ -0,0 +1,8 @@
+package nl.tudelft.dnainator.graph.impl.properties;
+
+/**
+ * Properties of nodes within bubbles.
+ */
+public enum BubbleProperties {
+	BUBBLE_SOURCE_IDS
+}