Merge branch 'dev'

Author: albert-smit

.gitignore

@@ -72,3 +72,8 @@ hs_err_pid*
 
 # pmd config file
 .eclipse-pmd
+.pmd
+.pmdruleset.xml
+
+#
+*.log.1

SE-Deliverables/Sprintplan8.pdf

@@ -0,0 +1,12 @@
+<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+	xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
+	<modelVersion>4.0.0</modelVersion>
+	<artifactId>lifetiles-core</artifactId>
+	<parent>
+		<groupId>nl.tudelft.lifetiles</groupId>
+		<artifactId>lifetiles-parent</artifactId>
+		<version>1.7-SNAPSHOT</version>
+		<relativePath>../</relativePath>
+	</parent>
+	<name>lifetiles-core</name>
+</project>

SE-Deliverables/Sprintreflection7.pdf

@@ -5,7 +5,6 @@
 import java.util.List;
 import java.util.Map;
 import java.util.concurrent.CopyOnWriteArrayList;
-import java.util.function.BiConsumer;
 import java.util.logging.Level;
 
 import javafx.fxml.Initializable;
@@ -28,7 +27,7 @@ public abstract class AbstractController implements Initializable {
     /**
      * The listeners for messages.
      */
-    private final Map<Message, List<BiConsumer<AbstractController, Object[]>>> listeners;
+    private final Map<Message, List<ShoutCallback>> listeners;
 
     /**
      * Create a new controller and register it.
@@ -43,16 +42,18 @@ public AbstractController() {
      *
      * @param message
      *            the message
+     * @param subject
+     *            The subject of this message.
      * @param args
      *            the arguments of the message
      */
-    protected final void shout(final Message message, final Object... args) {
+    protected final void shout(final Message message, final String subject,
+            final Object... args) {
         for (AbstractController c : controllers) {
-            List<BiConsumer<AbstractController, Object[]>> listenersOther = c
-                    .getListeners(message);
+            List<ShoutCallback> listenersOther = c.getListeners(message);
             if (listenersOther != null) {
                 listenersOther.stream().forEach(
-                        listener -> listener.accept(this, args));
+                        listener -> listener.accept(this, subject, args));
             }
         }
 
@@ -68,11 +69,11 @@ protected final void shout(final Message message, final Object... args) {
      *            the action to perform when recieving the message
      */
     protected final void listen(final Message message,
-            final BiConsumer<AbstractController, Object[]> action) {
+            final ShoutCallback action) {
         if (listeners.containsKey(message)) {
             listeners.get(message).add(action);
         } else {
-            List<BiConsumer<AbstractController, Object[]>> newListeners;
+            List<ShoutCallback> newListeners;
             newListeners = new ArrayList<>();
             newListeners.add(action);
             listeners.put(message, newListeners);
@@ -86,8 +87,7 @@ protected final void listen(final Message message,
      *            the message
      * @return a map of listeners for messages
      */
-    private List<BiConsumer<AbstractController, Object[]>> getListeners(
-            final Message message) {
+    private List<ShoutCallback> getListeners(final Message message) {
         return listeners.get(message);
     }
 

lifetiles-core/pom.xml

@@ -38,7 +38,7 @@ public final void initialize(final URL location,
 
         repaint(true);
 
-        listen(Message.OPENED, (controller, args) -> {
+        listen(Message.OPENED, (controller, subject, args) -> {
             repaint(false);
         });
     }

…/core/controller/AbstractController.java …/core/controller/AbstractController.javasrc/main/java/nl/tudelft/lifetiles/core/controller/AbstractController.java renamed to lifetiles-core/src/main/java/nl/tudelft/lifetiles/core/controller/AbstractController.java src/main/java/nl/tudelft/lifetiles/core/controller/AbstractController.java renamed to lifetiles-core/src/main/java/nl/tudelft/lifetiles/core/controller/AbstractController.java

@@ -3,13 +3,7 @@
 import java.io.File;
 import java.io.IOException;
 import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
 import java.util.ResourceBundle;
-import java.util.Set;
 
 import javafx.event.ActionEvent;
 import javafx.fxml.FXML;
@@ -21,12 +15,9 @@
 import javafx.stage.Window;
 import nl.tudelft.lifetiles.core.util.FileUtils;
 import nl.tudelft.lifetiles.core.util.Message;
-import nl.tudelft.lifetiles.graph.controller.GraphController;
-import nl.tudelft.lifetiles.graph.model.Graph;
 import nl.tudelft.lifetiles.notification.controller.NotificationController;
 import nl.tudelft.lifetiles.notification.model.AbstractNotification;
 import nl.tudelft.lifetiles.notification.model.NotificationFactory;
-import nl.tudelft.lifetiles.sequence.model.Sequence;
 
 /**
  * The controller of the menu bar.
@@ -40,6 +31,22 @@ public class MenuController extends AbstractController {
      * Constant annotation extension, currently as defined by client: '.txt'.
      */
     private static final String ANNOTATION_EXTENSION = ".txt";
+    /**
+     * Extension of the node file.
+     */
+    private static final String NODE_EXTENSION = ".node.graph";
+    /**
+     * Extension of the edge file.
+     */
+    private static final String EDGE_EXTENSION = ".edge.graph";
+    /**
+     * Extension of the tree file.
+     */
+    private static final String TREE_EXTENSION = ".nwk";
+    /**
+     * Extension of the sequence meta data file.
+     */
+    private static final String META_EXTENSION = ".meta";
 
     /**
      * The initial x-coordinate of the window.
@@ -62,11 +69,6 @@ public class MenuController extends AbstractController {
      */
     private NotificationFactory nf;
 
-    /**
-     * all sequences, to reset the filters.
-     */
-    private Set<Sequence> sequences;
-
     /**
      * Handle action related to "Open" menu item.
      *
@@ -79,7 +81,7 @@ private void openAction(final ActionEvent event) {
             loadDataFiles();
         } catch (IOException e) {
             AbstractNotification notification = nf.getNotification(e);
-            shout(NotificationController.NOTIFY, notification);
+            shout(NotificationController.NOTIFY, "", notification);
         }
     }
 
@@ -91,9 +93,7 @@ private void openAction(final ActionEvent event) {
      */
     @FXML
     private void resetAction(final ActionEvent event) {
-        if (sequences != null) {
-            shout(Message.FILTERED, sequences);
-        }
+        shout(Message.RESET, "");
     }
 
     /**
@@ -113,31 +113,95 @@ private void loadDataFiles() throws IOException {
         if (directory == null) {
             return;
         }
+        loadGraph(directory);
+        loadTree(directory);
+        loadAnnotations(directory);
+        loadMetaData(directory);
+    }
 
-        List<File> dataFiles = new ArrayList<>();
-        List<File> annotations = FileUtils.findByExtension(directory,
-                ANNOTATION_EXTENSION);
+    /**
+     * Loads the graph from files in the specified directory.
+     *
+     * @param directory
+     *            The directory in which to locate the files.
+     * @throws IOException
+     *             When the directory does not contain exactly one graph file
+     *             and one node file.
+     */
+    private void loadGraph(final File directory) throws IOException {
+        File nodeFile = FileUtils.getSingleFileByExtension(directory,
+                NODE_EXTENSION);
+        File edgeFile = FileUtils.getSingleFileByExtension(directory,
+                EDGE_EXTENSION);
+        shout(Message.OPENED, "graph", nodeFile, edgeFile);
+    }
 
-        List<String> exts = Arrays.asList(".node.graph", ".edge.graph", ".nwk");
-        for (String ext : exts) {
-            List<File> hits = FileUtils.findByExtension(directory, ext);
-            if (hits.size() != 1) {
-                throw new IOException("Expected 1 " + ext + " file intead of "
-                        + hits.size());
-            }
+    /**
+     * Loads the sequence meta-data file in the specified directory.
+     *
+     * @param directory
+     *            The directory in which to locate the files.
+     * @throws IOException
+     *             When the directory does not contain exactly one graph file
+     *             and one node file.
+     */
+    private void loadMetaData(final File directory) throws IOException {
+        File metaDataFile = loadOrWarn(directory, META_EXTENSION);
+        if (metaDataFile != null) {
+            shout(Message.OPENED, "meta", metaDataFile);
+        }
+    }
+
+    /**
+     * Loads the annotations from a file in the specified directory.
+     *
+     * @param directory
+     *            The directory from which to load annotations.
+     */
+    private void loadAnnotations(final File directory) {
+        File annotationFile = loadOrWarn(directory, ANNOTATION_EXTENSION);
+        if (annotationFile != null) {
+            shout(Message.OPENED, "annotations", annotationFile);
+        }
+    }
 
-            dataFiles.add(hits.get(0));
+    /**
+     * Loads the tree from a file in the specified directory.
+     *
+     * @param directory
+     *            The directory in which to search for the tree file.
+     */
+    private void loadTree(final File directory) {
+        File treeFile = loadOrWarn(directory, TREE_EXTENSION);
+        if (treeFile != null) {
+            shout(Message.OPENED, "tree", treeFile);
         }
+    }
 
-        shout(Message.OPENED, dataFiles.get(0), dataFiles.get(1),
-                dataFiles.get(2));
-        if (annotations == null || annotations.isEmpty()) {
-            shout(NotificationController.NOTIFY, nf.getNotification(
-                    "Annotation file (" + ANNOTATION_EXTENSION
-                            + ") can't be found", NotificationFactory.WARNING));
-        } else {
-            shout(GraphController.ANNOTATIONS, annotations.get(0));
+    /**
+     * Loads a file from the specified directory, with the specified extension,
+     * and give a warning.
+     *
+     * @param directory
+     *            The directory in which to search for the file.
+     * @param extension
+     *            The extension to search for.
+     * @return The found file.
+     */
+    private File loadOrWarn(final File directory, final String extension) {
+        try {
+            File file = FileUtils
+                    .getSingleFileByExtension(directory, extension);
+            return file;
+        } catch (IOException e) {
+            shout(NotificationController.NOTIFY,
+                    "",
+                    nf.getNotification(
+                            extension
+                                    + " file could not be found or multiple files found ",
+                            NotificationFactory.WARNING));
         }
+        return null;
     }
 
     /**
@@ -152,7 +216,7 @@ private void insertAnnotationsAction(final ActionEvent event) {
             loadAnnotationsFile();
         } catch (IOException e) {
             AbstractNotification notification = nf.getNotification(e);
-            shout(NotificationController.NOTIFY, notification);
+            shout(NotificationController.NOTIFY, "", notification);
         }
     }
 
@@ -175,7 +239,7 @@ private void loadAnnotationsFile() throws IOException {
             return;
         }
 
-        shout(GraphController.ANNOTATIONS, file);
+        shout(Message.OPENED, "annotations", file);
     }
 
     /**
@@ -210,15 +274,5 @@ public final void initialize(final URL location,
             final ResourceBundle resources) {
         addDraggableNode(menuBar);
         nf = new NotificationFactory();
-        // listen to loaded to get the sequence list
-        listen(Message.LOADED,
-                (controller, args) -> {
-                    if (controller instanceof GraphController) {
-                        assert args[0] instanceof Graph;
-                        assert (args[1] instanceof Map<?, ?>);
-                        Map<String, Sequence> sequenceMap = (Map<String, Sequence>) args[1];
-                        sequences = new HashSet<Sequence>(sequenceMap.values());
-                    }
-                });
     }
 }

…iles/core/controller/MainController.java …iles/core/controller/MainController.javasrc/main/java/nl/tudelft/lifetiles/core/controller/MainController.java renamed to lifetiles-core/src/main/java/nl/tudelft/lifetiles/core/controller/MainController.java src/main/java/nl/tudelft/lifetiles/core/controller/MainController.java renamed to lifetiles-core/src/main/java/nl/tudelft/lifetiles/core/controller/MainController.java

@@ -0,0 +1,20 @@
+package nl.tudelft.lifetiles.core.controller;
+
+/**
+ * Function interface for shouts.
+ *
+ * @author Rutger van den Berg
+ *
+ */
+@FunctionalInterface
+public interface ShoutCallback {
+    /**
+     * @param sender
+     *            The sending controller.
+     * @param subject
+     *            The subject of the message.
+     * @param args
+     *            The optional arguments.
+     */
+    void accept(AbstractController sender, String subject, Object[] args);
+}