Merge pull request #83 from ProgrammingLife3/fix/edgeWeight

Fix/edge weight

Author: Delfil

src/main/java/tudelft/ti2806/pl3/data/filter/Filter.java

@@ -13,6 +13,8 @@
  *            the element type to filter
  */
 public interface Filter<T> {
-	
+
+	List<String> getGenomes();
+
 	void filter(List<T> list);
 }

src/main/java/tudelft/ti2806/pl3/data/filter/GenomeFilter.java

@@ -21,6 +21,11 @@ public GenomeFilter(List<String> genomes) {
 		this.genomes = genomes;
 	}
 
+	@Override
+	public List<String> getGenomes() {
+		return genomes;
+	}
+
 	/**
 	 * Filter that removes all nodes that are not in the genome list.
 	 * It also removes the genomes from the node that should be filtered out.
@@ -44,4 +49,27 @@ public void filter(List<DataNode> nodes) {
 		}
 		nodes.removeAll(remove);
 	}
+
+	@Override
+	public boolean equals(Object o) {
+		if (this == o) {
+			return true;
+		}
+		if (o == null || getClass() != o.getClass()) {
+			return false;
+		}
+
+		GenomeFilter that = (GenomeFilter) o;
+
+		if (genomes != null ? !genomes.equals(that.genomes) : that.genomes != null) {
+			return false;
+		}
+
+		return true;
+	}
+
+	@Override
+	public int hashCode() {
+		return genomes != null ? genomes.hashCode() : 0;
+	}
 }

src/main/java/tudelft/ti2806/pl3/util/CollectionUtil.java

@@ -0,0 +1,45 @@
+package tudelft.ti2806.pl3.util;
+
+import java.util.Collection;
+import java.util.List;
+import java.util.Set;
+import java.util.stream.Collectors;
+
+/**
+ * Created by Boris Mattijssen on 17-06-15.
+ */
+public class CollectionUtil {
+
+	private CollectionUtil() {}
+
+
+	/**
+	 * Calculates the intersection between two collections.
+	 *
+	 * @param collection1
+	 * 		collection 1
+	 * @param collection2
+	 * 		collection 2
+	 * @param <T>
+	 * 		type of both collections
+	 * @return the intersection between the two collections
+	 */
+	public static <T> Collection<T> intersection(Collection<T> collection1, Collection<T> collection2) {
+		return collection1.stream().filter(t -> collection2.contains(t)).collect(Collectors.toList());
+	}
+
+	/**
+	 * Calculates the intersection between two collections.
+	 *
+	 * @param collection1
+	 * 		collection 1
+	 * @param collection2
+	 * 		collection 2
+	 * @param <T>
+	 * 		type of both collections
+	 * @return the intersection between the two collections
+	 */
+	public static <T> Set<T> intersectionListSet(List<T> collection1, Set<T> collection2) {
+		return collection1.stream().filter(t -> collection2.contains(t)).collect(Collectors.toSet());
+	}
+}

src/main/java/tudelft/ti2806/pl3/util/EdgeUtil.java

@@ -120,33 +120,12 @@ public static void setEdgeWeight(List<WrapperClone> wrapperClones) {
 			Set<Genome> genomes = new HashSet<>(wrapperClone.getGenome());
 			Collections.sort(wrapperClone.getOutgoing());
 			for (Wrapper outgoing : wrapperClone.getOutgoing()) {
-				Collection<Genome> intersection = intersection(outgoing.getGenome(), genomes);
+				Collection<Genome> intersection = CollectionUtil.intersection(
+						outgoing.getGenome(), genomes);
 				wrapperClone.getOutgoingWeight().add(intersection.size());
 				genomes.removeAll(intersection);
 			}
 		}
 	}
 
-	/**
-	 * Calculates the intersection between two collections.
-	 *
-	 * @param collection1
-	 * 		collection 1
-	 * @param collection2
-	 * 		collection 2
-	 * @param <T>
-	 * 		type of both collections
-	 * @return the intersection between the two collections
-	 */
-	public static <T> Collection<T> intersection(Collection<T> collection1, Collection<T> collection2) {
-		Collection<T> list = new ArrayList<T>();
-
-		for (T t : collection1) {
-			if (collection2.contains(t)) {
-				list.add(t);
-			}
-		}
-
-		return list;
-	}
 }

src/main/java/tudelft/ti2806/pl3/visualization/FilteredGraphModel.java

@@ -2,8 +2,6 @@
 
 import tudelft.ti2806.pl3.ScreenSize;
 import tudelft.ti2806.pl3.data.Genome;
-import tudelft.ti2806.pl3.util.observable.LoadingObservable;
-import tudelft.ti2806.pl3.util.observers.LoadingObserver;
 import tudelft.ti2806.pl3.data.filter.Filter;
 import tudelft.ti2806.pl3.data.graph.DataNode;
 import tudelft.ti2806.pl3.data.graph.Edge;
@@ -16,12 +14,18 @@
 import tudelft.ti2806.pl3.data.wrapper.operation.yposition.PositionNodeYOnGenomeSpace;
 import tudelft.ti2806.pl3.data.wrapper.util.WrapUtil;
 import tudelft.ti2806.pl3.util.CollectInterest;
+import tudelft.ti2806.pl3.util.CollectionUtil;
 import tudelft.ti2806.pl3.util.EdgeUtil;
+import tudelft.ti2806.pl3.util.observable.LoadingObservable;
+import tudelft.ti2806.pl3.util.observers.LoadingObserver;
 
 import java.util.ArrayList;
-import java.util.Collection;
+import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
+import java.util.Map;
 import java.util.Observable;
+import java.util.Set;
 
 /**
  * This model filters the original graph data, based on the filter selections.
@@ -40,7 +44,7 @@ public class FilteredGraphModel extends Observable implements LoadingObservable,
 
 	protected GraphDataRepository originalGraphData;
 	private Wrapper collapsedNode;
-	private Collection<Filter<DataNode>> filters;
+	private List<Filter<DataNode>> filters;
 	private PositionNodeYOnGenomeSpace positionNodeYOnGenomeSpace;
 
 	private ArrayList<LoadingObserver> loadingObservers = new ArrayList<>();
@@ -49,6 +53,8 @@ public class FilteredGraphModel extends Observable implements LoadingObservable,
 	private CollectInterest collectInterest;
 	private List<Genome> genomes;
 
+	private Map<List<Filter<DataNode>>, Integer> filtersToGenomesCountMap;
+
 	/**
 	 * Construct the model containing the filtered data.<br>
 	 * The model gets the original graph data and filters this data. Then it informs its listeners, to give them the
@@ -61,11 +67,12 @@ public FilteredGraphModel(GraphDataRepository originalGraphData) {
 		this.originalGraphData = originalGraphData;
 		filters = new ArrayList<>();
 		genomes = new ArrayList<>();
+		filtersToGenomesCountMap = new HashMap<>();
 		positionNodeYOnGenomeSpace = new PositionNodeYOnGenomeSpace();
 		calculateCollapse = new CalculateCollapseOnSpace();
 	}
 
-	public void setFilters(Collection<Filter<DataNode>> filters) {
+	public void setFilters(List<Filter<DataNode>> filters) {
 		this.filters = filters;
 	}
 
@@ -186,4 +193,32 @@ public void graphParsed() {
 	public List<Genome> getGenomes() {
 		return genomes;
 	}
+
+	/**
+	 * Count the genomes in the filtered data.
+	 * @return
+	 *      returns the amount of genomes in the original data set when no filters are applied,
+	 *      otherwise it calculates the amount of genomes in the filtered data and returns it.
+	 */
+	public int getGenomesCount() {
+		if (filters.size() > 0) {
+			if (filtersToGenomesCountMap.get(filters) == null) {
+				if (filters.size() == 1) {
+					filtersToGenomesCountMap.put(filters,
+							filters.iterator().next().getGenomes().size());
+				} else if (filters.size() > 1) {
+					Set<String> filteredGenomes = new HashSet<>(
+							filters.iterator().next().getGenomes());
+					for (Filter<DataNode> filter : filters) {
+						filteredGenomes = CollectionUtil.intersectionListSet(
+								filter.getGenomes(), filteredGenomes);
+					}
+					filtersToGenomesCountMap.put(filters, filteredGenomes.size());
+				}
+			}
+			return filtersToGenomesCountMap.get(filters);
+		} else {
+			return genomes.size();
+		}
+	}
 }

src/main/java/tudelft/ti2806/pl3/visualization/GraphController.java

@@ -101,7 +101,7 @@ public void parseGraph(File nodeFile, File edgeFile) throws FileNotFoundExceptio
 	 */
 	public void addFilter(String name, Filter<DataNode> filter) {
 		filters.put(name, filter);
-		filteredGraphModel.setFilters(filters.values());
+		filteredGraphModel.setFilters(new ArrayList<>(filters.values()));
 		filteredGraphModel.produceWrappedGraphData();
 		graphMoved();
 	}

src/main/java/tudelft/ti2806/pl3/visualization/GraphView.java

@@ -8,15 +8,16 @@
 import org.graphstream.ui.swingViewer.View;
 import org.graphstream.ui.swingViewer.Viewer;
 import org.graphstream.ui.swingViewer.util.DefaultShortcutManager;
-import tudelft.ti2806.pl3.util.observable.LoadingObservable;
-import tudelft.ti2806.pl3.util.observers.LoadingObserver;
-import tudelft.ti2806.pl3.controls.MouseManager;
+
 import tudelft.ti2806.pl3.ScreenSize;
+import tudelft.ti2806.pl3.controls.MouseManager;
 import tudelft.ti2806.pl3.data.graph.DataNode;
 import tudelft.ti2806.pl3.data.wrapper.Wrapper;
 import tudelft.ti2806.pl3.data.wrapper.WrapperClone;
 import tudelft.ti2806.pl3.exception.EdgeZeroWeightException;
 import tudelft.ti2806.pl3.exception.NodeNotFoundException;
+import tudelft.ti2806.pl3.util.observable.LoadingObservable;
+import tudelft.ti2806.pl3.util.observers.LoadingObserver;
 
 import java.awt.Component;
 import java.awt.event.ComponentAdapter;
@@ -36,7 +37,9 @@
  */
 public class GraphView
 		implements Observer, tudelft.ti2806.pl3.View, ViewInterface, LoadingObservable {
-	/**
+	private static final float EDGE_THICKNESS_SCALE = 10f;
+
+    /**
 	 * The zoomLevel used to draw the graph.<br>
 	 * A zoom level of 1.0 shows the graph 1:1, so that every base pair should
 	 * be readable, each with  pixels to draw its
@@ -125,7 +128,7 @@ public Graph generateGraph() throws EdgeZeroWeightException {
 		graph.clear();
 		setGraphPropertys();
 		final double someSize = panel.getBounds().height
-				/ ((double) panel.getBounds().width * zoomLevel / zoomedGraphModel
+				/ (panel.getBounds().width * zoomLevel / zoomedGraphModel
 				.getWrappedCollapsedNode().getWidth())
 				/ zoomedGraphModel.getWrappedCollapsedNode().getGenome().size();
 		graphData.forEach(node -> {
@@ -169,13 +172,14 @@ private void addNormalEdge(Graph graph, Wrapper from, Wrapper to, int i) throws
 		Edge edge = graph.addEdge(from.getId() + "-" + to.getId(),
 				Integer.toString(from.getId()), Integer.toString(to.getId()), true);
 		int weight = from.getOutgoingWeight().get(i);
-		float percent = ((float) weight) / ((float) zoomedGraphModel.getGenomes().size());
+		float percent = ((float) weight) / ((float) zoomedGraphModel.getGenomesCount());
+
 		if (weight == 0) {
 			edge.addAttribute("ui.label", "fix me!");
 			throw new EdgeZeroWeightException(
 					"The weight of the edge from " + from + " to " + to + " cannot be 0.");
 		} else {
-			edge.addAttribute("ui.style", "size: " + (percent * 5f) + "px;");
+			edge.addAttribute("ui.style", "size: " + (percent * EDGE_THICKNESS_SCALE) + "px;");
 		}
 	}
 
@@ -226,7 +230,7 @@ public double getViewPercent() {
 	 */
 	public void setOffsetToCenter() {
 		Point3 point3 = viewer.getDefaultView().getCamera()
-				.transformPxToGu(0, (double) ScreenSize.getInstance().getHeight() / 2d);
+				.transformPxToGu(0, ScreenSize.getInstance().getHeight() / 2d);
 		offsetToCenter = (float) point3.x * -1;
 	}
 

src/main/java/tudelft/ti2806/pl3/visualization/ZoomedGraphModel.java

@@ -142,4 +142,8 @@ public void notifyLoadingObservers(Object arguments) {
 			loadingObserver.update(this, arguments);
 		}
 	}
+
+	public int getGenomesCount() {
+		return filteredGraphModel.getGenomesCount();
+	}
 }