Fix the scoring of TKK_REF, heighten the score for seq length, fix jump to node.

Author: gfokkema

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

@@ -7,6 +7,7 @@
 import nl.tudelft.dnainator.graph.impl.RelTypes;
 import nl.tudelft.dnainator.graph.impl.properties.AnnotationProperties;
 import nl.tudelft.dnainator.graph.impl.properties.SequenceProperties;
+import nl.tudelft.dnainator.graph.impl.properties.SourceProperties;
 import nl.tudelft.dnainator.graph.interestingness.Scores;
 
 import org.neo4j.collection.primitive.Primitive;
@@ -32,8 +33,10 @@ public class AnalyzeCommand implements Command {
 	private static final int INIT_CAP = 4096;
 	private static final String LABEL = "n";
 	private static final String GET_NODES_BASEDIST =
-			"MATCH (n:" + NodeLabels.NODE.name() + ") "
-			+ "WHERE {dist} >= n." + SequenceProperties.BASE_DIST.name()
+			"MATCH (n:" + NodeLabels.NODE.name() + ")-[:" + RelTypes.SOURCE.name() + "]-s, "
+			+ "    (t {" + SourceProperties.SOURCE.name() + ": \"TKK_REF\"})"
+			+ "WHERE NOT (n-->t)"
+			+ " AND {dist} >= n." + SequenceProperties.BASE_DIST.name()
 			+ " AND {dist} < n." + SequenceProperties.BASE_DIST.name()
 			+ " + n." + Scores.SEQ_LENGTH.name() + " RETURN n AS " + LABEL;
 	private ResourceIterator<Node> roots;

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

@@ -5,15 +5,12 @@
  */
 public enum Scores implements ScoreIdentifier {
 	SEQ_LENGTH("Sequence Length Score") {
-		private static final int SEQ_LENGTH_THRESHOLD = 5000;
+		private static final int SEQ_LENGTH_THRESHOLD = 799;
+		private static final int SEQ_LENGTH_MULTIPLIER = 3;
 
 		@Override
 		public int applyImportanceModifier(int rawScore) {
-			if (rawScore < SEQ_LENGTH_THRESHOLD) {
-				return rawScore;
-			} else {
-				return rawScore * rawScore;
-			}
+			return Math.min(SEQ_LENGTH_THRESHOLD, rawScore * SEQ_LENGTH_MULTIPLIER);
 		}
 	},
 	DR_MUT("Drug Resistance Mutation Score") {

dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/drawables/strains/ClusterDrawable.java

@@ -56,7 +56,7 @@ public class ClusterDrawable extends Group implements Drawable, Propertyable {
 	protected static final double MEDIUM_RADIUS = 5;
 	protected static final double LARGE_RADIUS = 6;
 	protected static final int PIETHRESHOLD = 20;
-	private static final int INTERESTINGNESS_THRESHOLD = 600;
+	private static final int INTERESTINGNESS_THRESHOLD = 800;
 	private Cluster cluster;
 	private Set<String> sources;
 	private Pie pie;

dnainator-javafx/src/main/java/nl/tudelft/dnainator/javafx/views/StrainView.java

@@ -111,7 +111,7 @@ public void gotoNode(String id) {
 			// This has to be done separately to first pan to where the sequence node should be
 			// in order for it to get loaded and drawn with a cluster drawable.
 			if (cluster != null) {
-					setPan(0, cluster.getTranslateY() * strain.getRankWidth());
+				translate.setY(-cluster.getTranslateY());
 			}
 		}
 	}