Merge pull request #42 from maartentbm/mutations

All sprint 7 progress.

Author: maartentbm

.gitignore

@@ -10,7 +10,9 @@
 *.nwk
 *.graph
 *.classpath
+resistanceCausingMutations.tsv
 resistanceCausingMutations.txt
+Gene_annotations.tsv
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*

SE deliverables/Sprint 7 (week 4.8)/Sprint 7 Reflection (w4.8).pdf

@@ -2,7 +2,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>ContextPL1</groupId>
   <artifactId>ContextPL1</artifactId>
-  <version>0.0.1-SNAPSHOT</version>
+  <version>7.1-SNAPSHOT</version>
   <name>Programming Life</name>
   <description>Context project of programming life</description>
   <dependencies>

SE deliverables/Sprint 8 (week 4.9)/Sprint 8 Plan (w4.9).pdf

@@ -1,5 +1,3 @@
-
-
 import javax.swing.SwingUtilities;
 
 import nl.tudelft.ti2806.pl1.gui.Window;
@@ -22,6 +20,7 @@ private Start() {
 	 */
 	public static void main(final String[] args) {
 		SwingUtilities.invokeLater(new Runnable() {
+			@Override
 			public void run() {
 				new Window();
 			}

pom.xml

@@ -1,49 +1,111 @@
 package nl.tudelft.ti2806.pl1.DGraph;
 
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Set;
+
+import nl.tudelft.ti2806.pl1.gui.contentpane.ViewArea;
+
 import org.graphstream.graph.Graph;
+import org.graphstream.graph.Node;
 import org.graphstream.graph.implementations.SingleGraph;
 
 /**
- * Converts a DGraph into a graphstream graph.
+ * Contains methods to create a visual graph from a data graph.
  * 
- * @author mark
+ * @author Mark, Maarten, Justin
  * 
+ * @see Graph
+ * @see DGraph
  */
 public final class ConvertDGraph {
 
 	/**
-	 * When this threshold is surpassed, the length instead of the label will be
-	 * shown.
+	 * When this threshold is surpassed, the length instead of the content of a
+	 * node will be displayed on or next to the node.
 	 */
 	private static final int LABEL_LENGTH_THRESHOLD = 10;
 
 	/**
-	 * Converts a DGraph into a graphstream graph.
+	 */
+	private ConvertDGraph() {
+	}
+
+	/**
+	 * Converts a data graph into a visual graph.
+	 * 
 	 * 
 	 * @param dgraph
-	 *            The dgraph to be converted
-	 * @return Graphstream graph
+	 *            The data graph to convert.
+	 * @return The visual graph containing all the nodes from the data graph.
 	 */
 	public static Graph convert(final DGraph dgraph) {
-		Graph graph = new SingleGraph("DNApp");
-		for (DNode n : dgraph.getNodes().values()) {
+		return convert(dgraph, new ViewArea(Integer.MIN_VALUE,
+				Integer.MAX_VALUE));
+	}
+
+	/**
+	 * Converts a part of a data graph into a visual graph.
+	 * 
+	 * @param dgraph
+	 *            The data graph to convert.
+	 * @param va
+	 *            The area of the graph to convert.
+	 * @return The visual graph containing the nodes positioned in the given
+	 *         view area of the data graph.
+	 */
+	public static Graph convert(final DGraph dgraph, final ViewArea va) {
+		Graph graph = new SingleGraph("");
+		Set<DEdge> edges = new HashSet<DEdge>();
+		for (DNode n : dgraph.getDNodes(va)) {
+			edges.addAll(n.getAllEdges());
 			String id = String.valueOf(n.getId());
-			graph.addNode(id);
-			graph.getNode(id).addAttribute("x", n.getX());
-			graph.getNode(id).addAttribute("y", n.getY());
-			graph.getNode(id).addAttribute("ui.label",
-					checkLabelLength(n.getContent()));
-			graph.getNode(id).addAttribute("ui.class", "common");
-			graph.getNode(id).addAttribute("ui.color", 1 - n.getPercUnknown());
+			Node gn = graph.addNode(id);
+			gn.addAttribute("x", n.getX());
+			gn.addAttribute("y", n.getY());
+			gn.addAttribute("ui.label", checkLabelLength(n.getContent()));
+			gn.addAttribute("ui.class", "common");
+			gn.addAttribute("ui.color", 1 - n.getPercUnknown());
+			gn.addAttribute("contentsize", n.getContent().length());
+			gn.addAttribute("collapsed",
+					new HashSet<Integer>(Arrays.asList(n.getId())));
 		}
-		for (DEdge edge : dgraph.getEdges()) {
-			String src = String.valueOf(edge.getStartNode().getId());
-			String target = String.valueOf(edge.getEndNode().getId());
-			graph.addEdge(src + target, src, target, true);
+		for (DEdge edge : edges) {
+			String from = String.valueOf(edge.getStartNode().getId());
+			String to = String.valueOf(edge.getEndNode().getId());
+			if (graph.getNode(from) == null) {
+				addNodeToGraph(graph, from, dgraph);
+			} else if (graph.getNode(to) == null) {
+				addNodeToGraph(graph, to, dgraph);
+			}
+			graph.addEdge(from + to, from, to, true);
 		}
 		return graph;
 	}
 
+	/**
+	 * Creates a visual node object, extracts the needed data from a data graph
+	 * and adds it to a visual graph.
+	 * 
+	 * @param g
+	 *            The graph to add the new node to.
+	 * @param id
+	 *            The id for the new node.
+	 * @param dg
+	 *            The data graph where the node is defined.
+	 * @return
+	 */
+	private static void addNodeToGraph(final Graph g, final String id,
+			final DGraph dg) {
+		Node gn = g.addNode(id);
+		DNode n = dg.getDNode(Integer.parseInt(id));
+		gn.addAttribute("x", n.getX());
+		gn.addAttribute("y", n.getY());
+		gn.addAttribute("ui.label", checkLabelLength(n.getContent()));
+		gn.addAttribute("ui.class", "common");
+		gn.addAttribute("ui.color", 1 - n.getPercUnknown());
+	}
+
 	/**
 	 * Compares the label with a threshold length and returns the label if it's
 	 * smaller than the threshold, otherwise it returns the length.

src/main/java/Start.java

@@ -111,4 +111,9 @@ public int hashCode() {
 		result += PRIME_37 * result + getEndNode().getId();
 		return result;
 	}
+
+	@Override
+	public String toString() {
+		return "<Edge[" + startNode + "->" + endNode + "]>";
+	}
 }

src/main/java/nl/tudelft/ti2806/pl1/DGraph/ConvertDGraph.java

@@ -6,33 +6,30 @@
 import java.util.Map;
 
 import nl.tudelft.ti2806.pl1.geneAnnotation.ReferenceGeneStorage;
+import nl.tudelft.ti2806.pl1.gui.contentpane.ViewArea;
+import nl.tudelft.ti2806.pl1.mutation.DeletionMutation;
+import nl.tudelft.ti2806.pl1.mutation.InsertionMutation;
+import nl.tudelft.ti2806.pl1.mutation.MutatedGraph;
+import nl.tudelft.ti2806.pl1.mutation.PointMutation;
 
 /**
  * The DGraph class for representing our data.
  * 
  * @author Mark
  *
  */
-public class DGraph {
+public class DGraph implements MutatedGraph, DynamicGraph {
 
-	/**
-	 * The nodes in the graph.
-	 */
+	/** The nodes in the graph. */
 	private final Map<Integer, DNode> nodes;
 
-	/**
-	 * A map storing a collection nodes per genome reference.
-	 */
+	/** A map storing a collection nodes per genome reference. */
 	private HashMap<String, Collection<DNode>> references;
 
-	/**
-	 * The edges in the graph.
-	 */
+	/** The edges in the graph. */
 	private Collection<DEdge> edges;
 
-	/**
-	 * The start node and end node of the graph.
-	 */
+	/** The start node and end node of the graph. */
 	private DNode start, end;
 
 	/** Storage of all the genes in the reference genome. */
@@ -45,6 +42,15 @@ public class DGraph {
 	// private static final String MUTATION_FILE =
 	// "resistanceCausingMutations.txt";
 
+	/** All the point mutations in the graph. */
+	private Collection<PointMutation> pointMutations;
+
+	/** All the deletion mutations in the graph. */
+	private Collection<DeletionMutation> delmutations;
+
+	/** All the insertion mutations in the graph. */
+	private Collection<InsertionMutation> insmutations;
+
 	/**
 	 * Creates a new DGraph.
 	 */
@@ -266,4 +272,77 @@ public final void setEnd(final DNode e) {
 		this.end = e;
 	}
 
+	/** {@inheritDoc} */
+	@Override
+	public Collection<PointMutation> getAllPointMutations() {
+		return pointMutations;
+	}
+
+	@Override
+	public Collection<PointMutation> getAllInDelMutations() {
+		return pointMutations;
+	}
+
+	/** {@inheritDoc} */
+	@Override
+	public Collection<DNode> getDNodes(final ViewArea va) {
+		ArrayList<DNode> ret = new ArrayList<DNode>();
+		for (DNode n : getNodes().values()) {
+			if (va.isContained(n)) {
+				ret.add(n);
+			}
+		}
+		return ret;
+	}
+
+	@Override
+	public String toString() {
+		return nodes + " " + edges;
+	}
+
+	/**
+	 * @param newPointMutations
+	 *            pointMutations to set.
+	 */
+	public void setPointMutations(
+			final Collection<PointMutation> newPointMutations) {
+		this.pointMutations = newPointMutations;
+	}
+
+	/**
+	 * @param deletionMutationsIn
+	 *            deletion mutations to set.
+	 */
+	public void setDeletionMutations(
+			final Collection<DeletionMutation> deletionMutationsIn) {
+		delmutations = deletionMutationsIn;
+	}
+
+	/** @return the deletion mutations. */
+	public Collection<DeletionMutation> getDelmutations() {
+		return delmutations;
+	}
+
+	/**
+	 * @return the insmutations
+	 */
+	public Collection<InsertionMutation> getInsmutations() {
+		return insmutations;
+	}
+
+	/**
+	 * @param insmutationsIn
+	 *            the insmutations to set
+	 */
+	public void setInsertionmutations(
+			final Collection<InsertionMutation> insmutationsIn) {
+		this.insmutations = insmutationsIn;
+	}
+
+	/**
+	 * @return the referenceGeneStorage
+	 */
+	public final ReferenceGeneStorage getReferenceGeneStorage() {
+		return referenceGeneStorage;
+	}
 }

src/main/java/nl/tudelft/ti2806/pl1/DGraph/DEdge.java

@@ -0,0 +1,13 @@
+/**
+ * 
+ */
+package nl.tudelft.ti2806.pl1.DGraph;
+
+/**
+ * @author Maarten, Justin
+ * @since 4-6-2015
+ *
+ */
+public interface DGraphInterface {
+
+}

src/main/java/nl/tudelft/ti2806/pl1/DGraph/DGraph.java

@@ -397,4 +397,9 @@ public final boolean equals(final Object o) {
 	public final int hashCode() {
 		return getId();
 	}
+
+	@Override
+	public String toString() {
+		return "<Node[" + id + "]>";
+	}
 }