[WIP] Implement scoring for independent mutations.

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

@@ -79,14 +79,22 @@ public void execute(GraphDatabaseService service) {
 			// It is automatically closed after the try block, which frees the allocated memory.
 			PrimitiveLongSet processed = Primitive.offHeapLongSet(INIT_CAP)
 		) {
+			System.out.println("executing");
+			long start = System.nanoTime();
 			for (Node n : topologicalOrder(service, processed)) {
 				rankDest(n);
+				scoreIndependentMutation(service, n);
 			}
+			System.out.println((System.nanoTime() - start) * 1e-6 + " ms");
 			scoreDRMutations(service);
 			tx.success();
 		}
 	}
 
+	private void scoreIndependentMutation(GraphDatabaseService service, Node n) {
+		new MutationFinderCommand(n).execute(service);
+	}
+
 	/**
 	 * Rank the destination nodes of the outgoing edges of the given node.
 	 * @param n the source node of the destination nodes to be ranked.

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

@@ -0,0 +1,44 @@
+package nl.tudelft.dnainator.graph.impl.command;
+
+import nl.tudelft.dnainator.graph.impl.RelTypes;
+import nl.tudelft.dnainator.graph.interestingness.Scores;
+
+import org.neo4j.graphdb.Direction;
+import org.neo4j.graphdb.GraphDatabaseService;
+import org.neo4j.graphdb.Node;
+import org.neo4j.graphdb.Path;
+import org.neo4j.graphdb.Transaction;
+
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Map;
+import java.util.Set;
+
+public class MutationFinderCommand implements Command {
+	private Map<Node, Set<Node>> sources;
+	private Node mutation;
+
+	public MutationFinderCommand(Node mutation) {
+		this.mutation = mutation;
+		this.sources = new HashMap<>();
+
+	}
+
+	@Override
+	public void execute(GraphDatabaseService service) {
+		Set<Node> commonancestors = new HashSet<>();
+		try (Transaction tx = service.beginTx()) {
+			for (Path p : service.traversalDescription()
+				.breadthFirst()
+				.relationships(RelTypes.SOURCE, Direction.OUTGOING)
+				.relationships(RelTypes.ANCESTOR_OF, Direction.INCOMING)
+				.evaluator(new PhyloEvaluator())
+				.traverse(mutation)
+			) {
+				commonancestors.add(p.endNode());
+			}
+			mutation.setProperty(Scores.INDEP_MUT.name(), commonancestors.size());
+			tx.success();
+		}
+	}
+}

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

@@ -0,0 +1,39 @@
+package nl.tudelft.dnainator.graph.impl.command;
+
+import nl.tudelft.dnainator.graph.impl.NodeLabels;
+import nl.tudelft.dnainator.graph.impl.RelTypes;
+
+import org.neo4j.graphdb.Direction;
+import org.neo4j.graphdb.Node;
+import org.neo4j.graphdb.Path;
+import org.neo4j.graphdb.Relationship;
+import org.neo4j.graphdb.traversal.Evaluation;
+import org.neo4j.graphdb.traversal.Evaluator;
+
+import java.util.HashSet;
+import java.util.Set;
+
+public class PhyloEvaluator implements Evaluator {
+	private Set<Node> clusters = new HashSet<>();
+
+	@Override
+	public Evaluation evaluate(Path path) {
+		if (path.endNode().hasLabel(NodeLabels.NODE)) {
+			return Evaluation.EXCLUDE_AND_CONTINUE;
+		} else if (path.endNode().hasLabel(NodeLabels.SOURCE)) {
+			clusters.add(path.endNode());
+			return Evaluation.EXCLUDE_AND_CONTINUE;
+		}
+
+		for (Relationship rel : path.endNode().getRelationships(Direction.OUTGOING,
+									RelTypes.ANCESTOR_OF)) {
+			if (!clusters.contains(rel.getEndNode())) {
+				return Evaluation.INCLUDE_AND_PRUNE;
+			}
+		}
+
+		clusters.add(path.endNode());
+		return Evaluation.EXCLUDE_AND_CONTINUE;
+	}
+
+}

dnainator-core/src/main/java/nl/tudelft/dnainator/graph/interestingness/Scores.java

@@ -22,6 +22,12 @@ public int applyImportanceModifier(int rawScore) {
 			}
 			return multipliers[rawScore];
 		}
+	},
+	INDEP_MUT("independentMutation") {
+		@Override
+		public int applyImportanceModifier(int rawScore) {
+			return rawScore * 100;
+		}
 	};
 
 	private String name;

dnainator-core/src/test/java/nl/tudelft/dnainator/graph/impl/Neo4jGraphTest.java

@@ -40,7 +40,6 @@
 import java.util.stream.Collectors;
 
 import static nl.tudelft.dnainator.graph.impl.properties.SequenceProperties.ID;
-
 import static org.hamcrest.Matchers.lessThan;
 import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertFalse;
@@ -111,9 +110,10 @@ private static File getTreeFile() throws URISyntaxException {
 	@Test
 	public void testNodeLookup() {
 		// CHECKSTYLE.OFF: MagicNumber
-		SequenceNode node1 = new SequenceNodeImpl("2", Arrays.asList("ASDF", "ASD"), 1, 5, "TATA");
-		SequenceNode node2 = new SequenceNodeImpl("3", Arrays.asList("ASDF"), 5, 9, "TATA");
-		SequenceNode node3 = new SequenceNodeImpl("5", Arrays.asList("ASDF"), 4, 8, "TATA");
+		SequenceNode node1 = new SequenceNodeImpl("2", Arrays.asList("TKK_001",
+										"TKK_002"), 1, 5, "TATA");
+		SequenceNode node2 = new SequenceNodeImpl("3", Arrays.asList("TKK_001"), 5, 9, "TATA");
+		SequenceNode node3 = new SequenceNodeImpl("5", Arrays.asList("TKK_001"), 4, 8, "TATA");
 		assertEquals(node1, db.getNode("2"));
 		assertEquals(node2, db.getNode("3"));
 		assertEquals(node3, db.getNode("5"));
@@ -126,7 +126,7 @@ public void testNodeLookup() {
 	@Test
 	public void testRootLookup() {
 		// CHECKSTYLE.OFF: MagicNumber
-		SequenceNode root = new SequenceNodeImpl("5", Arrays.asList("ASDF"), 4, 8, "TATA");
+		SequenceNode root = new SequenceNodeImpl("5", Arrays.asList("TKK_001"), 4, 8, "TATA");
 		assertEquals(root, db.getRootNode());
 		// CHECKSTYLE.ON: MagicNumber
 	}
@@ -239,13 +239,13 @@ public void testQueryFilter() {
 	@Test
 	public void testQuerySources() {
 		GraphQueryDescription qd = new GraphQueryDescription()
-			.containsSource("ASDF");
+			.containsSource("TKK_001");
 		Set<String> expect = new HashSet<>();
 		Collections.addAll(expect, "2", "5", "3", "7", "8", "11");
 		assertUnorderedIDEquals(expect, db.queryNodes(qd));
 
 		// Also test for multiple sources (reusing the old one)
-		qd = qd.containsSource("ASD");
+		qd = qd.containsSource("TKK_002");
 		Collections.addAll(expect, "9", "10");
 		assertUnorderedIDEquals(expect, db.queryNodes(qd));
 

dnainator-core/src/test/java/nl/tudelft/dnainator/graph/impl/command/MutationFinderCommandTest.java

@@ -0,0 +1,114 @@
+package nl.tudelft.dnainator.graph.impl.command;
+
+import nl.tudelft.dnainator.annotation.impl.AnnotationCollectionImpl;
+import nl.tudelft.dnainator.annotation.impl.AnnotationImpl;
+import nl.tudelft.dnainator.core.EnrichedSequenceNode;
+import nl.tudelft.dnainator.core.impl.SequenceNodeFactoryImpl;
+import nl.tudelft.dnainator.graph.impl.Neo4jBatchBuilder;
+import nl.tudelft.dnainator.graph.impl.Neo4jGraph;
+import nl.tudelft.dnainator.graph.impl.NodeLabels;
+import nl.tudelft.dnainator.graph.impl.command.MutationFinderCommand;
+import nl.tudelft.dnainator.graph.impl.properties.SequenceProperties;
+import nl.tudelft.dnainator.parser.EdgeParser;
+import nl.tudelft.dnainator.parser.NodeParser;
+import nl.tudelft.dnainator.parser.TreeParser;
+import nl.tudelft.dnainator.parser.exceptions.ParseException;
+import nl.tudelft.dnainator.parser.impl.EdgeParserImpl;
+import nl.tudelft.dnainator.parser.impl.NodeParserImpl;
+import nl.tudelft.dnainator.tree.TreeNode;
+
+import org.junit.AfterClass;
+import org.junit.BeforeClass;
+import org.junit.Test;
+import org.neo4j.graphdb.Node;
+import org.neo4j.io.fs.FileUtils;
+
+import java.io.BufferedReader;
+import java.io.File;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.net.URISyntaxException;
+import java.util.Collection;
+import java.util.stream.Collectors;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.fail;
+
+public class MutationFinderCommandTest {
+	private static final String DB_PATH = "target/neo4j-tree-junit";
+	private static Neo4jGraph db;
+	private static InputStream nodeFile;
+	private static InputStream edgeFile;
+	private static AnnotationImpl first;
+	private static AnnotationImpl middle;
+	private static AnnotationImpl last;
+
+	/**
+	 * Setup the database and construct the graph.
+	 * @throws URISyntaxException 
+	 */
+	@BeforeClass
+	public static void setUp() throws URISyntaxException {
+		try {
+			FileUtils.deleteRecursively(new File(DB_PATH));
+			nodeFile = getNodeFile();
+			edgeFile = getEdgeFile();
+			NodeParser np = new NodeParserImpl(new SequenceNodeFactoryImpl(),
+					new BufferedReader(new InputStreamReader(nodeFile, "UTF-8")));
+			EdgeParser ep = new EdgeParserImpl(new BufferedReader(
+							new InputStreamReader(edgeFile, "UTF-8")));
+			TreeNode phylo = new TreeParser(getTreeFile()).parse();
+			db = (Neo4jGraph) new Neo4jBatchBuilder(DB_PATH, new AnnotationCollectionImpl(), phylo)
+				.constructGraph(np, ep)
+				.build();
+		} catch (IOException e) {
+			fail("Couldn't initialize DB");
+		} catch (ParseException e) {
+			fail("Couldn't parse file: " + e.getMessage());
+		}
+		//CHECKSTYLE.OFF: MagicNumber
+		first = new AnnotationImpl("first", 0, 10, true);
+		middle = new AnnotationImpl("middle", 5, 25, true);
+		last = new AnnotationImpl("last", 20, 30, true);
+		//CHECKSTYLE.ON: MagicNumber
+		db.addAnnotation(first);
+		db.addAnnotation(middle);
+		db.addAnnotation(last);
+	}
+
+	private static InputStream getNodeFile() {
+		return MutationFinderCommandTest.class.getResourceAsStream("/strains/advancedtopo.node.graph");
+	}
+
+	private static InputStream getEdgeFile() {
+		return MutationFinderCommandTest.class.getResourceAsStream("/strains/advancedtopo.edge.graph");
+	}
+
+	private static File getTreeFile() throws URISyntaxException {
+		return new File(MutationFinderCommandTest.class.getResource("/strains/advancedtopo.nwk")
+				.toURI());
+	}
+
+	/**
+	 * Test returning a source set.
+	 * @param expected
+	 * @param actual
+	 */
+	@Test
+	public void testIndependentMutations() {
+		db.execute(e -> {
+			Node node = e.findNode(NodeLabels.NODE, SequenceProperties.ID.name(), "6");
+			new MutationFinderCommand(node).execute(e);
+		});
+	}
+
+	/**
+	 * Clean up after ourselves.
+	 * @throws IOException when the database could not be deleted
+	 */
+	@AfterClass
+	public static void cleanUp() throws IOException {
+		db.shutdown();
+	}
+}

dnainator-core/src/test/resources/strains/advancedtopo.edge.graph

@@ -0,0 +1,6 @@
+1 2
+2 3
+3 4
+5 6
+6 7
+7 8

dnainator-core/src/test/resources/strains/advancedtopo.node.graph

@@ -0,0 +1,16 @@
+> 1 | TKK_001 | 1 | 5
+TATA
+> 2 | TKK_001,TKK_002 | 2 | 6
+TATA
+> 3 | TKK_001,TKK_002,TKK_003 | 3 | 7
+TATA
+> 4 | TKK_003,TKK_004,TKK_005,TKK_006 | 4 | 8
+TATA
+> 5 | TKK_006 | 5 | 9
+TATA
+> 6 | TKK_001,TKK_003,TKK_005 | 6 | 10
+TATA
+> 7 | TKK_004,TKK_002,TKK_003 | 7 | 11
+TATA
+> 8 | TKK_001,TKK_002,TKK_003,TKK_004,TKK_005,TKK_006 | 8 | 12
+TATA

dnainator-core/src/test/resources/strains/advancedtopo.nwk

@@ -0,0 +1 @@
+((TKK_001:0.1,TKK_002:0.2),(TKK_003:0.3,((TKK_004:0.4,TKK_005:0.5),TKK_005:0.6)))

dnainator-core/src/test/resources/strains/topo.node.graph

@@ -1,16 +1,16 @@
-> 2 | ASDF,ASD | 1 | 5
+> 2 | TKK_001,TKK_002 | 1 | 5
 TATA
-> 9 | ASD | 2 | 6
+> 9 | TKK_002 | 2 | 6
 TATA
-> 10 | ASD | 3 | 7
+> 10 | TKK_002 | 3 | 7
 TATA
-> 5 | ASDF | 4 | 8
+> 5 | TKK_001 | 4 | 8
 TATA
-> 3 | ASDF | 5 | 9
+> 3 | TKK_001 | 5 | 9
 TATA
-> 7 | ASDF | 6 | 10
+> 7 | TKK_001,TKK_004 | 6 | 10
 TATA
-> 11 | ASD,FDSA,ASDF | 7 | 11
+> 11 | TKK_001,TKK_002,TKK_003 | 7 | 11
 TATA
-> 8 | ASDF | 8 | 12
+> 8 | TKK_001,TKK_002 | 8 | 12
 TATA

dnainator-core/src/test/resources/strains/topo.nwk

@@ -1 +1 @@
-(FDSA:0.1,(ASDF:0.2,ASD:0.3))
+((TKK_001:0.1,TKK_002:0.2),(TKK_003:0.3,TKK_004:0.4))