Merge branch 'master' into feature/snphighlight

ProgrammingLife2016 · Jun 17, 2016 · d6a771e · d6a771e
2 parents 96268e8 + cfe5e68
commit d6a771e
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Showing 2 changed files with 30 additions and 25 deletions.
diff --git a/SE Deliverables/PL-3FinalReportDraft.pdf b/SE Deliverables/PL-3FinalReportDraft.pdf
diff --git a/src/main/java/gui/views/ribbon/RibbonView.java b/src/main/java/gui/views/ribbon/RibbonView.java
@@ -12,6 +12,10 @@
 import java.util.Queue;
 import java.util.Set;
 import java.util.stream.Collectors;
+import java.util.HashMap;
+import java.util.LinkedList;
+import java.util.List;
+import java.util.Queue;
 
 import javafx.scene.Group;
 import javafx.scene.paint.Paint;
@@ -74,6 +78,7 @@ public Group createNormalRibbons() {
 				Line line = new Line(xcoords.get(fromId - 1), ycoords.get(fromId - 1), 
 						xcoords.get(toId - 1), ycoords.get(toId - 1));
 				line.setStrokeWidth(calculateLineWidth(counts.get(fromId - 1).get(j)));
+
 				line.setStroke(colours.get(fromId - 1).get(j));
 		        res.getChildren().add(line);
 			}
@@ -233,6 +238,30 @@ public Group createInDels() {
 	 * @param genomes
 	 * @return
 	 */
+	public Paint getLineColor(int ff, int tt) {
+		Paint color = Paint.valueOf("0xff0000ff");
+		ArrayList<String> from = dbm.getDbReader().getGenomesThroughSegment(ff);
+		ArrayList<String> to = dbm.getDbReader().getGenomesThroughSegment(tt);
+		if (from.size() > to.size()) {
+			for (int i = 0; i < to.size(); i++) {
+				String genome = to.get(i);
+				if (lineages.containsKey(genome) && from.contains(genome) 
+						&& !genome.equals("MT_H37RV_BRD_V5.ref")) {
+					return NewickColourMatching.getLineageColour(lineages.get(genome));
+				}
+			}
+		} else {
+			for (int i = 0; i < from.size(); i++) {
+				String genome = from.get(i);
+				if (lineages.containsKey(genome) && to.contains(genome) 
+						&& !genome.equals("MT_H37RV_BRD_V5.ref")) {
+					return NewickColourMatching.getLineageColour(lineages.get(genome));
+				}
+			}
+		}
+		return color;
+	}
+
 	private ArrayList<ArrayList<Paint>> calculateColours(ArrayList<ArrayList<Integer>> linkIds, 
 			ArrayList<Integer> genomes) {
 		ArrayList<ArrayList<Paint>> colours = 
@@ -252,37 +281,14 @@ private ArrayList<ArrayList<Paint>> calculateColours(ArrayList<ArrayList<Integer
 				String genome = genomeNames.get(id - 1);
 				if (!genome.startsWith("M")) {
 					colour = getMajorityColor(dbm.getDbReader().getGenomeNames(genomeIds));
+
 				} 
 				colours.get(i).add(colour);
 			}
 		}
 		return colours;
 	}
 
-	public Paint getLineColor(int ff, int tt) {
-		Paint color = Paint.valueOf("0xff0000ff");
-		ArrayList<String> from = dbm.getDbReader().getGenomesThroughSegment(ff);
-		ArrayList<String> to = dbm.getDbReader().getGenomesThroughSegment(tt);
-		if (from.size() > to.size()) {
-			for (int i = 0; i < to.size(); i++) {
-				String genome = to.get(i);
-				if (lineages.containsKey(genome) && from.contains(genome) 
-						&& !genome.equals("MT_H37RV_BRD_V5.ref")) {
-					return NewickColourMatching.getLineageColour(lineages.get(genome));
-				}
-			}
-		} else {
-			for (int i = 0; i < from.size(); i++) {
-				String genome = from.get(i);
-				if (lineages.containsKey(genome) && to.contains(genome) 
-						&& !genome.equals("MT_H37RV_BRD_V5.ref")) {
-					return NewickColourMatching.getLineageColour(lineages.get(genome));
-				}
-			}
-		}
-		return color;
-	}
-
 	/**
 	 * Calculates the majority color that is present in all the genomes that are provided.
 	 * @param genomeNames
@@ -345,7 +351,6 @@ else if(fromId == links.size()/4 * 2) {
 			else if(fromId == links.size()/4 * 3) {
 				SplashController.progressNum.set(60);
 			}
-
 			List<Integer> edges = links.get(fromId - 1);
 
 			if (!bubbles.isEmpty() && fromId == bubbles.peek()[0]) {