Merge branch 'backupplan'

src/main/java/coordinates/CoordinateDetermination.java

@@ -78,10 +78,15 @@ public Coordinate[] calcCoords() {
 			int alreadyDrawn = 0;
 			int leftToDraw = countGenomesInSeg(i);
 			Coordinate coords = coordinates[i - 1];
-
 			ArrayList<Integer> outgoingedges = links.get(i - 1);
 
 			for (int j = 0; j < outgoingedges.size(); j++) {
+
+				if (outgoingedges.get(j) < 5) {
+					System.out.println(i);
+					System.out.println(j);
+					System.out.println(outgoingedges.get(j));
+				}
 				leftToDraw = leftToDraw - countGenomesInLink(i, outgoingedges.get(j));
 				int xc = coords.getX() + 100;
 				int yc = coords.getY() - 50 * leftToDraw + 50 * alreadyDrawn;

src/main/java/db/DatabaseProcessor.java

@@ -19,7 +19,6 @@
 public class DatabaseProcessor {
 	private Statement db;
 	private DatabaseReader dbr;
-	private int noOfSegments;
 
 	public DatabaseProcessor(Statement db, DatabaseReader dbr) {
 		this.db = db;
@@ -34,6 +33,8 @@ public void updateCoordinates() {
 		Coordinate[] coordinates = coorddet.calcCoords();
 		SplashController.progressString.set("Saving segment coordinates");
 		for (int i = 1; i <= coordinates.length; i++) {
+			System.out.println(i);
+			System.out.println(coordinates[i - 1]);
 			if ( (i % coordinates.length) / 10 == 0) {
 				SplashController.progressString
 					.set((i * 100 / coordinates.length) + "% Stored");
@@ -58,17 +59,23 @@ public void locateBubbles() {
 
 		ArrayList<ArrayList<Integer>> links = dbr.getLinks();
 		for (int segmentId = 1; segmentId <= links.size(); segmentId++) {
+			System.out.println(segmentId);
 			ArrayList<Integer> outgoingEdges = links.get(segmentId - 1);
-
+			System.out.println("a");
 			if (outgoingEdges.size() > 1) {
+				System.out.println("b");
 				int firstChildId = outgoingEdges.get(0);
+				System.out.println("c");
 				int secondChildId = outgoingEdges.get(1);
+				System.out.println("d");
 				ArrayList<Integer> firstChildEdges = links.get(firstChildId - 1);
+				System.out.println("e");
 				ArrayList<Integer> secondChildEdges = links.get(secondChildId - 1);
-
+				System.out.println("f");
 				int firstChildEdge;
 				int secondChildEdge;
 				try {
+					System.out.println("g");
 					firstChildEdge = firstChildEdges.get(0);
 					secondChildEdge = secondChildEdges.get(0);
 				} catch (IndexOutOfBoundsException e) {
@@ -77,8 +84,16 @@ public void locateBubbles() {
 				}
 				if (secondChildEdge == firstChildEdge) {
 					try {
-						this.db.executeUpdate(new BubbleTuple(segmentId, firstChildEdge)
-								.getInsertQuery());
+						System.out.println("h");
+						ArrayList<Integer> genomeIds = dbr.getGenomesInBubble(segmentId, 
+								firstChildEdge, firstChildId, secondChildId);
+						System.out.println("i");
+						for (int i = 0; i < genomeIds.size(); i++) {
+							System.out.println("i: " + i);
+							this.db.executeUpdate(new BubbleTuple(segmentId, 
+									firstChildEdge, genomeIds.get(i))
+									.getInsertQuery());
+						}
 					} catch (SQLException e) {
 						e.printStackTrace();
 					}
@@ -112,35 +127,34 @@ public void updateDblinkcount(int fromId, int toId, int count ) {
 	 */
 
 	public void calculateLinkCounts() {
-		HashMap<Integer, Integer> hashmap = new HashMap<Integer, Integer>();
 		ArrayList<Integer> from = dbr.getAllFromId();
 		ArrayList<Integer> to = dbr.getAllToId();
-		noOfSegments = to.get(to.size() - 1);
-		SplashController.progressString.set("Retrieving link data");
-		for (int i = 0; i < from.size(); i++) {
-			if ( ((i + 1) % from.size()) / 10 == 0) {
-				SplashController.progressString
-					.set((i * 100 / from.size() + 1) + "% Retrieved");
-			}
-			hashmap.put(noOfSegments * (from.get(i) - 1) + to.get(i) - 1, 0);
-		}
+		int noOfSegments = to.get(to.size() - 1);
+
+		ArrayList<ArrayList<Integer>> allLinks = new ArrayList<ArrayList<Integer>>();
+
 		SplashController.progressString.set("Starting to analyze genomes");
+
 		for (int i = 1; i <= dbr.countGenomes(); i++) {
-			hashmap = analyzeGenome(hashmap, i);
+			ArrayList<ArrayList<Integer>> links = analyzeGenome(i);
+			allLinks.addAll(links);
 			SplashController.progressString.set(i + "genome(s) analyzed");
 		}
+
 		SplashController.progressString.set("Storing link data");
+
 		try {
 			this.db.executeUpdate("DELETE FROM LINKS");
 		} catch (SQLException e) {
 			e.printStackTrace();
 		}
-		for (int i = 0; i < from.size(); i++) {
+
+		for (int i = 0; i < allLinks.size(); i++) {
 			if ( ((i + 1) % from.size()) / 10 == 0) {
 				SplashController.progressString.set((i * 100 / from.size() + 1) + "% Stored");
 			}
-			updateDblinkcount(from.get(i), to.get(i), 
-					hashmap.get(noOfSegments * (from.get(i) - 1) + to.get(i) - 1));
+			ArrayList<Integer> link = allLinks.get(i);
+			updateDblinkcount(link.get(0), link.get(1), link.get(2));
 		}
 	}
 
@@ -151,25 +165,29 @@ public void calculateLinkCounts() {
 	 * @param genomeID The ID of the genome we're analyzing
 	 * @return An updated HashMap where data about the genome we analyzed is also stored
 	 */
-	public HashMap<Integer, Integer> analyzeGenome(HashMap<Integer, Integer> map, int genomeId) {
+	public ArrayList<ArrayList<Integer>> analyzeGenome(int genomeId) {
 		String query = "SELECT * "
 				+ "FROM GENOMESEGMENTLINK WHERE GENOMEID = " + genomeId;
+		ArrayList<ArrayList<Integer>> links = new ArrayList<ArrayList<Integer>>();
 		try (ResultSet rs = this.db.executeQuery(query)) {
 			if (rs.next()) {
 				int first = rs.getInt(1);
 				int second;
 				while (rs.next()) {
+					ArrayList<Integer> link = new ArrayList<Integer>();
 					second = rs.getInt(1);
-					int currentcount = map.remove(noOfSegments * (first - 1) + second - 1);
-					map.put(noOfSegments * (first - 1) + second - 1, currentcount + 1);
+					link.add(first);
+					link.add(second);
+					link.add(genomeId);
+					links.add(link);
 					first = second;
 				}
-				return map;
+				return links;
 			}
 			return null;
 		} catch (SQLException e) {
 			e.printStackTrace();
-			return map;
+			return null;
 		}
 	}