Merge pull request #288 from ProgrammingLife2017/snp

Detect if children can be SNP'ed together

Author: MeAmAnUsername

ProgrammingLife.iml

@@ -12,11 +12,11 @@
     </content>
     <orderEntry type="inheritedJdk" />
     <orderEntry type="sourceFolder" forTests="false" />
-    <orderEntry type="library" name="Maven: com.github.uphy:javafx-console:ce9860eb36" level="project" />
     <orderEntry type="library" name="Maven: junit:junit:4.12" level="project" />
     <orderEntry type="library" name="Maven: org.hamcrest:hamcrest-core:1.3" level="project" />
     <orderEntry type="library" name="Maven: org.apache.commons:commons-lang3:3.5" level="project" />
     <orderEntry type="library" name="Maven: com.diffplug.durian:durian:3.4.0" level="project" />
+    <orderEntry type="library" name="Maven: com.github.uphy:javafx-console:ce9860eb36" level="project" />
     <orderEntry type="library" name="Maven: org.mapdb:mapdb:3.0.4" level="project" />
     <orderEntry type="library" name="Maven: org.jetbrains.kotlin:kotlin-stdlib:1.0.7" level="project" />
     <orderEntry type="library" name="Maven: org.jetbrains.kotlin:kotlin-runtime:1.0.7" level="project" />

src/main/java/programminglife/gui/controller/GraphController.java

@@ -15,7 +15,6 @@
 import java.util.LinkedList;
 
 /**
- * Created by Martijn van Meerten on 8-5-2017.
  * Controller for drawing the graph.
  */
 public class GraphController {
@@ -32,6 +31,7 @@ public class GraphController {
     private double zoomLevel = 1;
 
     private int centerNodeInt;
+    private boolean drawSNP = false;
 
     /**
      * Initialize controller object.
@@ -49,55 +49,45 @@ public int getCenterNodeInt() {
         return this.centerNodeInt;
     }
 
+    /**
+     * Utility function for benchmarking purposes.
+     * @param description the description to print
+     * @param r the {@link Runnable} to run/benchmark
+     */
+    private void time(String description, Runnable r) {
+        long start = System.nanoTime();
+        r.run();
+        Console.println(String.format("%s: %d ms", description, (System.nanoTime() - start) / 1000000));
+    }
+
     /**
      * Method to draw the subGraph decided by a center node and radius.
      * @param center the node of which the radius starts.
      * @param radius the amount of layers to be drawn.
      */
     public void draw(int center, int radius) {
-        long startTimeProgram = System.nanoTime();
-        GraphicsContext gc = canvas.getGraphicsContext2D();
-
-        long startTimeSubGraph = System.nanoTime();
-
-        DrawableSegment centerNode = new DrawableSegment(graph, center);
-        centerNodeInt = centerNode.getIdentifier();
-        subGraph = new SubGraph(centerNode, radius);
-
-        long finishTimeSubGraph = System.nanoTime();
-
-        long startLayoutTime = System.nanoTime();
-        subGraph.layout();
-        long finishTimeLayout = System.nanoTime();
-
-        long startTimeColorize = System.nanoTime();
-        colorize();
-        long finishTimeColorize = System.nanoTime();
-
-
-        long startTimeDrawing = System.nanoTime();
-        draw(gc);
-        long finishTimeDrawing = System.nanoTime();
-
-        highlightNode(center, Color.DARKORANGE);
-        centerOnNodeId(center);
-
-        long finishTime = System.nanoTime();
-        long differenceTimeProgram = finishTime - startTimeProgram;
-        long differenceTimeDrawing = finishTimeDrawing - startTimeDrawing;
-        long differenceTimeLayout = finishTimeLayout - startLayoutTime;
-        long differenceTimeSubGraph = finishTimeSubGraph - startTimeSubGraph;
-        long differenceTimeColorize = finishTimeColorize - startTimeColorize;
-        long msDifferenceTimeProgram = differenceTimeProgram / 1000000;
-        long millisecondTimeDrawing = differenceTimeDrawing / 1000000;
-        long msDifferenceTimeLayout = differenceTimeLayout / 1000000;
-        long msDifferenceTimeSubGraph = differenceTimeSubGraph / 1000000;
-        long msDifferenceTimeColorize = differenceTimeColorize / 1000000;
-        Console.println("time of SubGraph: " + msDifferenceTimeSubGraph);
-        Console.println("Time of layout:  " + msDifferenceTimeLayout);
-        Console.println("Time of Colorize:  " + msDifferenceTimeColorize);
-        Console.println("Time of Drawing:  " + millisecondTimeDrawing);
-        Console.println("Time of Total Program:  " + msDifferenceTimeProgram);
+        time("Total drawing", () -> {
+            DrawableSegment centerNode = new DrawableSegment(graph, center);
+            centerNodeInt = centerNode.getIdentifier();
+            GraphicsContext gc = canvas.getGraphicsContext2D();
+
+            time("Find subgraph", () -> subGraph = new SubGraph(centerNode, radius));
+
+            if (drawSNP) {
+                time("Replace SNPs", subGraph::replaceSNPs);
+            }
+            time("Layout subgraph", subGraph::layout);
+
+            time("Colorize", this::colorize);
+
+            time("Calculate genomes through edges", subGraph::calculateGenomes);
+            time("Drawing", () -> {
+                draw(gc);
+            });
+
+            centerOnNodeId(center);
+            highlightNode(center, Color.DARKORANGE);
+        });
     }
 
     /**
@@ -357,6 +347,13 @@ public void highlightByGenome(int genomeID) {
         highlightNodes(drawNodeList, Color.YELLOW);
     }
 
+    /**
+     * Sets if the glyph  snippets will be drawn or not.
+     */
+    void setSNP() {
+        drawSNP = !drawSNP;
+    }
+
     /**
      * Returns the node clicked on else returns null.
      * @param x position horizontally where clicked

src/main/java/programminglife/gui/controller/GuiController.java

@@ -20,6 +20,7 @@
 import javafx.stage.FileChooser;
 import javafx.stage.FileChooser.ExtensionFilter;
 import javafx.stage.Stage;
+import javafx.scene.canvas.Canvas;
 import jp.uphy.javafx.console.ConsoleView;
 import programminglife.ProgrammingLife;
 import programminglife.controller.MiniMapController;
@@ -65,8 +66,11 @@ public class GuiController implements Observer {
     @FXML private MenuItem btnInstructions;
     @FXML private Menu menuRecentGFA;
     @FXML private Menu menuRecentGFF;
-    @FXML private RadioMenuItem btnToggle;
+
+    @FXML private RadioMenuItem btnSNP;
+    @FXML private RadioMenuItem btnConsole;
     @FXML private RadioMenuItem btnMiniMap;
+
     @FXML private Button btnZoomReset;
     @FXML private Button btnTranslateReset;
     @FXML private Button btnDraw;
@@ -84,7 +88,7 @@ public class GuiController implements Observer {
     @FXML private AnchorPane anchorLeftControlPanel;
     @FXML private AnchorPane anchorGraphPanel;
     @FXML private AnchorPane anchorGraphInfo;
-    @FXML private javafx.scene.canvas.Canvas miniMap;
+    @FXML private Canvas miniMap;
 
     private double orgSceneX, orgSceneY;
 
@@ -276,18 +280,24 @@ private void fileChooser(ExtensionFilter filter, boolean isGFA) {
      */
     private void initMenuBar() {
         btnOpenGFA.setOnAction((ActionEvent event) -> fileChooser(extFilterGFA, true));
-        btnOpenGFF.setOnAction((ActionEvent event) -> fileChooser(extFilterGFF, false));
-
         btnOpenGFA.setAccelerator(new KeyCodeCombination(KeyCode.O, KeyCodeCombination.CONTROL_DOWN));
+        btnOpenGFF.setOnAction((ActionEvent event) -> fileChooser(extFilterGFF, false));
 
-        btnMiniMap.setOnAction(event -> miniMapController.toggleVisibility());
-        btnMiniMap.setAccelerator(new KeyCodeCombination(KeyCode.M, KeyCodeCombination.CONTROL_DOWN));
         btnQuit.setOnAction(event -> Alerts.quitAlert());
-        btnQuit.setAccelerator(new KeyCodeCombination(KeyCode.E, KeyCodeCombination.CONTROL_DOWN));
+        btnQuit.setAccelerator(new KeyCodeCombination(KeyCode.Q, KeyCodeCombination.CONTROL_DOWN));
+
         btnAbout.setOnAction(event -> Alerts.infoAboutAlert());
         btnAbout.setAccelerator(new KeyCodeCombination(KeyCode.I, KeyCodeCombination.CONTROL_DOWN));
         btnInstructions.setOnAction(event -> Alerts.infoInstructionAlert());
         btnInstructions.setAccelerator(new KeyCodeCombination(KeyCode.H, KeyCodeCombination.CONTROL_DOWN));
+
+        btnMiniMap.setOnAction(event -> miniMapController.toggleVisibility());
+        btnMiniMap.setAccelerator(new KeyCodeCombination(KeyCode.M, KeyCodeCombination.CONTROL_DOWN));
+        btnSNP.setOnAction(event -> {
+            graphController.setSNP();
+            Platform.runLater(this::draw);
+        });
+        btnSNP.setAccelerator(new KeyCodeCombination(KeyCode.G, KeyCodeCombination.CONTROL_DOWN));
     }
 
 
@@ -533,17 +543,17 @@ private void initConsole() {
         AnchorPane.setRightAnchor(console, 0.d);
         AnchorPane.setLeftAnchor(console, 0.d);
 
-        btnToggle.setOnAction(event -> {
-            if (btnToggle.isSelected()) {
+        btnConsole.setOnAction(event -> {
+            if (btnConsole.isSelected()) {
                 st.show();
             } else {
                 st.close();
             }
         });
 
         st.show();
-        btnToggle.setSelected(true);
-        root.visibleProperty().bind(btnToggle.selectedProperty());
+        btnConsole.setSelected(true);
+        root.visibleProperty().bind(btnConsole.selectedProperty());
 
         Console.setOut(console.getOut());
     }

src/main/java/programminglife/model/drawing/DrawableDummy.java

@@ -76,6 +76,11 @@ public String details() {
         return toString();
     }
 
+    @Override
+    public DrawableSNP createSNPIfPossible(SubGraph subGraph) {
+        return null;
+    }
+
     @Override
     public void colorize(SubGraph sg) {
         double genomeFraction = 0.d;
@@ -97,6 +102,7 @@ public void colorize(SubGraph sg) {
 
         this.setStrokeWidth(strokeWidth);
         this.setStrokeColor(strokeColor);
+
     }
 
     /**

src/main/java/programminglife/model/drawing/DrawableNode.java

@@ -50,6 +50,34 @@ public DrawableNode(GenomeGraph graph, int id) {
         }
     }
 
+
+    @Override
+    public final boolean equals(Object o) {
+        if (this == o) {
+            return true;
+        }
+
+        if (!this.getClass().equals(o.getClass())) {
+            return false;
+        }
+        return this.getIdentifier() == ((DrawableNode) o).getIdentifier();
+    }
+
+    @Override
+    public final int hashCode() {
+        int result = getGraph().hashCode();
+        result = 31 * result + getIdentifier();
+        return result;
+    }
+
+    /**
+     * Get the ID.
+     * @return the ID
+     */
+    public final int getIdentifier() {
+        return this.id;
+    }
+
     /**
      * Get the {@link GenomeGraph}.
      * @return the graph
@@ -110,6 +138,13 @@ private boolean isDrawDimensionsUpToDate() {
      */
     public abstract String details();
 
+    /**
+     * Checks if the children of this {@link DrawableNode} can be merged as a SNP.
+     * @param subGraph the {@link SubGraph} this {@link DrawableNode} is in
+     * @return null if children cannot be SNP'ed, SNP with (parent, child and mutation) otherwise
+     */
+    public abstract DrawableSNP createSNPIfPossible(SubGraph subGraph);
+
     /**
      * Color this according to contents.
      * @param subGraph {@link SubGraph} to colorize.
@@ -188,10 +223,6 @@ final XYCoordinate getRightBorderCenter() {
         return new XYCoordinate(location.getX() + getWidth(), location.getY() + 0.5 * getHeight());
     }
 
-    public final int getIdentifier() {
-        return id;
-    }
-
     public final XYCoordinate getLocation() {
         return location;
     }