Fix the scoring and show it in the pane.

gfokkema · gfokkema · commit 3946717ed6ba · 2015-06-20T15:16:23.000+02:00
Remove indepent mutation score.

Fix the zooming.
diff --git a/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/impl/command/AnalyzeCommand.java b/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/impl/command/AnalyzeCommand.java
@@ -1,9 +1,7 @@
 package nl.tudelft.dnainator.graph.impl.command;
 
-import java.util.Collections;
-import java.util.HashSet;
+import java.util.HashMap;
 import java.util.Map;
-import java.util.Set;
 
 import nl.tudelft.dnainator.graph.impl.NodeLabels;
 import nl.tudelft.dnainator.graph.impl.RelTypes;
@@ -80,7 +78,6 @@ public void execute(GraphDatabaseService service) {
 		) {
 			for (Node n : topologicalOrder(service, processed)) {
 				rankDest(n);
-				scoreIndependentMutation(n);
 			}
 			scoreDRMutations(service);
 			tx.success();
@@ -113,6 +110,7 @@ private void rankDest(Node n) {
 	 * @param service	the graph service
 	 */
 	private void scoreDRMutations(GraphDatabaseService service) {
+		Map<String, Object> params = new HashMap<>(1);
 		service.findNodes(NodeLabels.DRMUTATION).forEachRemaining(drannotations ->
 			drannotations.getRelationships(RelTypes.ANNOTATED).forEach(node -> {
 				// From the startref of the annotation
@@ -122,7 +120,7 @@ private void scoreDRMutations(GraphDatabaseService service) {
 					- (int) node.getStartNode().getProperty(SequenceProperties.STARTREF.name())
 					+ (int) node.getStartNode().getProperty(SequenceProperties.BASE_DIST.name());
 
-				Map<String, Object> params = Collections.singletonMap("dist", basedist);
+				params.put("dist", basedist);
 				ResourceIterator<Node> mutations = service.execute(GET_NODES_BASEDIST, params)
 									.columnAs(LABEL);
 				mutations.forEachRemaining(m -> {
@@ -132,18 +130,4 @@ private void scoreDRMutations(GraphDatabaseService service) {
 			})
 		);
 	}
-
-	/**
-	 * Scores the amount of independent mutations, using the phylogeny.
-	 * @param n the node representing the mutation.
-	 */
-	protected void scoreIndependentMutation(Node n) {
-		Set<Node> ancestors = new HashSet<>();
-		for (Relationship r : n.getRelationships(RelTypes.SOURCE)) {
-			r.getEndNode().getRelationships(RelTypes.ANCESTOR_OF, Direction.INCOMING).forEach(e ->
-				ancestors.add(e.getStartNode())
-			);
-		}
-		n.setProperty(Scores.INDEP_MUT.name(), ancestors.size());
-	}
 }
diff --git a/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/interestingness/InterestingnessStrategy.java b/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/interestingness/InterestingnessStrategy.java
@@ -5,6 +5,8 @@
  * is calculated.
  */
 public interface InterestingnessStrategy {
+	int RANGE_LOWER = 0;
+	int RANGE_UPPER = 1000;
 
 	/**
 	 * Compute the interestingness at the given location.
diff --git a/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/interestingness/ScoreContainer.java b/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/interestingness/ScoreContainer.java
@@ -9,7 +9,6 @@
  * Represents a location within the graph.
  */
 public interface ScoreContainer {
-
 	/**
 	 * @param id the identifier of the property, which is used to get the score of
 	 * a particular property.
diff --git a/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/interestingness/Scores.java b/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/interestingness/Scores.java
@@ -4,30 +4,26 @@
  * All of the supported scores.
  */
 public enum Scores implements ScoreIdentifier {
-	SEQ_LENGTH("seqLength") {
-		private static final int DENOMINATOR = 500;
+	SEQ_LENGTH("Sequence Length Score") {
 		private static final int SEQ_LENGTH_THRESHOLD = 5000;
 
 		@Override
 		public int applyImportanceModifier(int rawScore) {
 			if (rawScore < SEQ_LENGTH_THRESHOLD) {
-				return rawScore / DENOMINATOR;
+				return rawScore;
 			} else {
-				return (rawScore * rawScore) / DENOMINATOR;
+				return rawScore * rawScore;
 			}
 		}
 	},
-	INDEP_MUT("independentMutation") {
-		private static final int BASE = 8;
+	DR_MUT("Drug Resistance Mutation Score") {
+		private final int[] multipliers = { 0, 800, 1000 };
 		@Override
 		public int applyImportanceModifier(int rawScore) {
-			return (int) Math.pow(BASE, rawScore);
-		}
-	},
-	DR_MUT("drugResistanceMutation") {
-		@Override
-		public int applyImportanceModifier(int rawScore) {
-			return rawScore * 100;
+			if (rawScore >= multipliers.length) {
+				return multipliers[multipliers.length - 1];
+			}
+			return multipliers[rawScore];
 		}
 	};
 
diff --git a/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/interestingness/impl/SummingScoresStrategy.java b/dnainator-core/src/main/java/nl/tudelft/dnainator/graph/interestingness/impl/SummingScoresStrategy.java
@@ -10,9 +10,6 @@
  * {@link Scores} together.
  */
 public class SummingScoresStrategy implements InterestingnessStrategy {
-	private static final int RANGE_LOWER = 0;
-	private static final int RANGE_UPPER = 1000;
-
 	@Override
 	public int compute(ScoreContainer container) {
 		int sum = 0;
diff --git a/dnainator-core/src/test/java/nl/tudelft/dnainator/graph/impl/Neo4jGraphTest.java b/dnainator-core/src/test/java/nl/tudelft/dnainator/graph/impl/Neo4jGraphTest.java
@@ -9,7 +9,6 @@
 import nl.tudelft.dnainator.core.impl.SequenceNodeFactoryImpl;
 import nl.tudelft.dnainator.core.impl.SequenceNodeImpl;
 import nl.tudelft.dnainator.graph.impl.command.AnalyzeCommand;
-import nl.tudelft.dnainator.graph.interestingness.Scores;
 import nl.tudelft.dnainator.graph.query.GraphQueryDescription;
 import nl.tudelft.dnainator.parser.EdgeParser;
 import nl.tudelft.dnainator.parser.NodeParser;
@@ -284,19 +283,6 @@ public void testGetAnnotationsRangeInclusive() {
 		assertTrue(as.contains(last));
 	}
 
-	/**
-	 * Test the scoring of independent mutations.
-	 */
-	@Test
-	public void testIndependentMutationScore() {
-		EnrichedSequenceNode node11 = db.getNode("11");
-		EnrichedSequenceNode node2 = db.getNode("2");
-		EnrichedSequenceNode node9 = db.getNode("9");
-		assertEquals(node11.getScore(Scores.INDEP_MUT), 2);
-		assertEquals(node2.getScore(Scores.INDEP_MUT), 1);
-		assertEquals(node9.getScore(Scores.INDEP_MUT), 1);
-	}
-
 	private static void assertUnorderedIDEquals(Collection<String> expected,
 			Collection<EnrichedSequenceNode> actual) {
 		assertEquals(expected.stream().collect(Collectors.toSet()),
diff --git a/dnainator-core/src/test/java/nl/tudelft/dnainator/graph/interestingness/impl/SummingScoresStrategyTest.java b/dnainator-core/src/test/java/nl/tudelft/dnainator/graph/interestingness/impl/SummingScoresStrategyTest.java
@@ -13,7 +13,7 @@
  */
 public class SummingScoresStrategyTest {
 	private static final int TEST_SEQ_LENGTH = 5;
-	private static final int TEST_INDEP_MUT = 3;
+	private static final int TEST_DR_MUT = 1;
 	private SummingScoresStrategy strategy;
 	private ScoreContainer container;
 
@@ -25,17 +25,17 @@ public void setUp() {
 		this.strategy = new SummingScoresStrategy();
 		this.container = Mockito.mock(ScoreContainer.class);
 		Mockito.when(container.getScore(Scores.SEQ_LENGTH)).thenReturn(TEST_SEQ_LENGTH);
-		Mockito.when(container.getScore(Scores.INDEP_MUT)).thenReturn(TEST_INDEP_MUT);
+		Mockito.when(container.getScore(Scores.DR_MUT)).thenReturn(TEST_DR_MUT);
 	}
 
 	/**
 	 * Tests whether it returns the sum of all scores.
 	 */
 	@Test
 	public void testSum() {
-		assertEquals(strategy.compute(container),
-				Scores.SEQ_LENGTH.applyImportanceModifier(TEST_SEQ_LENGTH)
-				+ Scores.INDEP_MUT.applyImportanceModifier(TEST_INDEP_MUT));
+		int expected = Scores.SEQ_LENGTH.applyImportanceModifier(TEST_SEQ_LENGTH)
+				+ Scores.DR_MUT.applyImportanceModifier(TEST_DR_MUT);
+		assertEquals(expected, strategy.compute(container));
 	}
 
 }
diff --git a/dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/controllers/PropertyPaneController.java b/dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/controllers/PropertyPaneController.java
@@ -19,7 +19,7 @@ public class PropertyPaneController {
 	private SlidingAnimation animation;
 	private static final int WIDTH = 300;
 	private static final int ANIM_DURATION = 250;
-	private static final int MAX_PROPERTY_SIZE = 750;
+	private static final int MAX_PROPERTY_SIZE = 500;
 
 	@SuppressWarnings("unused") @FXML private VBox propertyPane;
 
@@ -50,7 +50,7 @@ private void addLabel(PropertyType type, String value) {
 		if (value != null && value.length() > MAX_PROPERTY_SIZE) {
 			ScrollPane sp = new ScrollPane(label);
 			sp.setFitToWidth(true);
-			sp.setPrefHeight(WIDTH);
+			sp.setPrefHeight(WIDTH / 2);
 			label = sp;
 		}
 		propertyPane.getChildren().add(new VBox(description, label));
diff --git a/dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/drawables/Thresholds.java b/dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/drawables/Thresholds.java
@@ -5,7 +5,7 @@
  * The amount corresponds to the level of scaling.
  */
 public enum Thresholds {
-	GRAPH(1.7),
+	GRAPH(2.0),
 	CLUSTER(4.0);
 	
 	private final double threshold;
diff --git a/dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/drawables/strains/ClusterDrawable.java b/dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/drawables/strains/ClusterDrawable.java
@@ -4,7 +4,6 @@
 import nl.tudelft.dnainator.core.PropertyType;
 import nl.tudelft.dnainator.core.SequenceNode;
 import nl.tudelft.dnainator.core.impl.Cluster;
-import nl.tudelft.dnainator.graph.interestingness.Scores;
 import nl.tudelft.dnainator.javafx.ColorServer;
 import nl.tudelft.dnainator.javafx.drawables.Drawable;
 import nl.tudelft.dnainator.javafx.views.AbstractView;
@@ -32,7 +31,8 @@ enum ClusterPropertyTypes implements PropertyType {
 	ENDREF("End base on ref. strain"),
 	SOURCES("Sources"),
 	STARTRANK("Start rank"),
-	BASEDIST("Start base");
+	BASEDIST("Start base"),
+	SCORE("Total interestingness score");
 
 	private String description;
 	private ClusterPropertyTypes(String description) {
@@ -105,8 +105,10 @@ private void initSingletonProperties() {
 		properties.put(ClusterPropertyTypes.BASEDIST, Integer.toString(sn.getBaseDistance()));
 		properties.put(ClusterPropertyTypes.STARTREF, Integer.toString(sn.getStartRef()));
 		properties.put(ClusterPropertyTypes.ENDREF, Integer.toString(sn.getEndRef()));
-		properties.put(Scores.SEQ_LENGTH, Integer.toString(sn.getScore(Scores.SEQ_LENGTH)));
 		properties.put(ClusterPropertyTypes.SEQUENCE, sn.getSequence());
+
+		properties.put(ClusterPropertyTypes.SCORE, Integer.toString(sn.getInterestingnessScore()));
+		sn.getScores().forEach((k, v) -> properties.put(k, Integer.toString(v)));
 	}
 
 	private void draw(ColorServer colorServer) {
diff --git a/dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/drawables/strains/Strain.java b/dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/drawables/strains/Strain.java
@@ -31,7 +31,8 @@ public class Strain extends SemanticDrawable {
 	private static final int OFFSET = 10;
 	private static final double ANNOTATION_HEIGHT = 50;
 	private static final int RANK_WIDTH = 10;
-	private static final int CLUSTER_DIVIDER = 100;
+	private static final int ZOOM_MIN = 200;
+	private static final int ZOOM_MAX = 800;
 
 	private ColorServer colorServer;
 	private Graph graph;
@@ -79,13 +80,15 @@ protected void loadContent(Bounds bounds) {
 	@Override
 	public void loadChildren(Bounds bounds) {
 		Range ranks = getRange(bounds);
+		int interestingness = Math.max(0, Math.min((int) bounds.getWidth() - ZOOM_MIN, ZOOM_MAX));
+		System.out.println("load iteration: " + ranks.getX() + " -> " + ranks.getY()
+					+ " zoom: " + interestingness);
 
-		System.out.println("load iteration: " + ranks.getX() + " -> " + ranks.getY());
 		List<String> roots = graph.getRank(ranks.getX()).stream()
 				.map(SequenceNode::getId).collect(Collectors.toList());
 		List<Annotation> annotations = getSortedAnnotations(ranks);
 		Map<Integer, List<Cluster>> result = graph.getAllClusters(roots, ranks.getY(),
-				(int) (bounds.getWidth() / CLUSTER_DIVIDER));
+				interestingness);
 		clusters.clear();
 		childContent.getChildren().clear();
 
diff --git a/dnainator-javafx/src/test/java/nl/tudelft/dnainator/javafx/drawables/strains/StrainTest.java b/dnainator-javafx/src/test/java/nl/tudelft/dnainator/javafx/drawables/strains/StrainTest.java
@@ -103,7 +103,7 @@ public void testUpdate() {
 		assertTrue(content.isVisible());
 		verify(graph, never()).getRank(anyInt());
 
-		strain.update(new Rectangle(5000, 2500).getBoundsInLocal(), 1.7);
+		strain.update(new Rectangle(5000, 2500).getBoundsInLocal(), 2.0);
 		assertFalse(content.isVisible());
 		verify(graph, Mockito.atLeastOnce()).getRank(anyInt());
 
