Merge pull request #32 from maartentbm/mavenExecutable

Maven executable

Author: Keraito

.gitignore

@@ -10,7 +10,6 @@
 *.nwk
 *.graph
 *.classpath
-*.project
 
 # virtual machine crash logs, see http://www.java.com/en/download/help/error_hotspot.xml
 hs_err_pid*

.project

@@ -0,0 +1,35 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<projectDescription>
+	<name>ContextPL1</name>
+	<comment></comment>
+	<projects>
+	</projects>
+	<buildSpec>
+		<buildCommand>
+			<name>org.eclipse.jdt.core.javabuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>edu.umd.cs.findbugs.plugin.eclipse.findbugsBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>net.sf.eclipsecs.core.CheckstyleBuilder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+		<buildCommand>
+			<name>org.eclipse.m2e.core.maven2Builder</name>
+			<arguments>
+			</arguments>
+		</buildCommand>
+	</buildSpec>
+	<natures>
+		<nature>org.eclipse.m2e.core.maven2Nature</nature>
+		<nature>org.eclipse.jdt.core.javanature</nature>
+		<nature>edu.umd.cs.findbugs.plugin.eclipse.findbugsNature</nature>
+		<nature>net.sf.eclipsecs.core.CheckstyleNature</nature>
+	</natures>
+</projectDescription>

.settings/org.eclipse.core.resources.prefs

@@ -35,9 +35,27 @@
       <plugin>
         <artifactId>maven-compiler-plugin</artifactId>
         <version>3.1</version>
+      </plugin>
+  	  <plugin>
+        <artifactId>maven-assembly-plugin</artifactId>
+        <executions>
+          <execution>
+            <phase>package</phase>
+            <goals>
+              <goal>single</goal>
+            </goals>
+          </execution>
+        </executions>
         <configuration>
-          <source/>
-          <target/>
+          <descriptorRefs>
+            <descriptorRef>jar-with-dependencies</descriptorRef>
+          </descriptorRefs>
+          <archive>
+        		<manifest>
+          			<addClasspath>true</addClasspath>
+          			<mainClass>Start</mainClass>
+        		</manifest>
+      		</archive>
         </configuration>
       </plugin>
     </plugins>

pom.xml

@@ -179,8 +179,7 @@ public final boolean loadGraph(final File nodes, final File edges)
 		} catch (UnsupportedEncodingException e) {
 			e.printStackTrace();
 		}
-		graph.addAttribute("ui.stylesheet",
-				"url('src/main/resources/stylesheet.css')");
+		graph.addAttribute("ui.stylesheet", "url('stylesheet.css')");
 		// System.setProperty("org.graphstream.ui.renderer",
 		// "org.graphstream.ui.j2dviewer.J2DGraphRenderer");
 		Viewer viewer = new Viewer(graph,
@@ -269,6 +268,7 @@ private void notifyObservers(final DNode selectedNodeIn) {
 	/**
 	 * {@inheritDoc} Changes to the graph graphics based on the selected node.
 	 */
+	@Override
 	public final void update(final DNode newSelectedNode) {
 		text.setText(newSelectedNode.getContent());
 		// TODO change strings to constants (still have to decide in which class
@@ -363,6 +363,7 @@ class Scrolling implements MouseWheelListener {
 		 * @param e
 		 *            MouseWheelEvent for which is being handled.
 		 */
+		@Override
 		public void mouseWheelMoved(final MouseWheelEvent e) {
 			int rotation = -1 * e.getWheelRotation();
 			if (count > NEWLEVEL) {
@@ -472,23 +473,25 @@ private ScrollListener(final JScrollBar scrollBar) {
 		}
 
 		/** {@inheritDoc} */
+		@Override
 		public void adjustmentValueChanged(final AdjustmentEvent e) {
-			int type = e.getAdjustmentType();
-			if (type == AdjustmentEvent.BLOCK_DECREMENT) {
-				System.out.println("Scroll block decr");
-			} else if (type == AdjustmentEvent.BLOCK_INCREMENT) {
-				System.out.println("Scroll block incr");
-			} else if (type == AdjustmentEvent.UNIT_DECREMENT) {
-				System.out.println("Scroll unit incr");
-			} else if (type == AdjustmentEvent.UNIT_INCREMENT) {
-				System.out.println("Scroll unit incr");
-			} else if (type == AdjustmentEvent.TRACK) {
-				System.out.println("Scroll track");
-				System.out.println("e.getValue() == " + e.getValue());
-				// TODO (use this for genome location plotting?)
-				// seems to always have this adjustment event type :$
-				// http://examples.javacodegeeks.com/desktop-java/awt/event/adjustmentlistener-example
-			}
+			// int type = e.getAdjustmentType();
+			// if (type == AdjustmentEvent.BLOCK_DECREMENT) {
+			// System.out.println("Scroll block decr");
+			// } else if (type == AdjustmentEvent.BLOCK_INCREMENT) {
+			// System.out.println("Scroll block incr");
+			// } else if (type == AdjustmentEvent.UNIT_DECREMENT) {
+			// System.out.println("Scroll unit incr");
+			// } else if (type == AdjustmentEvent.UNIT_INCREMENT) {
+			// System.out.println("Scroll unit incr");
+			// } else if (type == AdjustmentEvent.TRACK) {
+			// System.out.println("Scroll track");
+			// System.out.println("e.getValue() == " + e.getValue());
+			// // TODO (use this for genome location plotting?)
+			// // seems to always have this adjustment event type :$
+			// //
+			// http://examples.javacodegeeks.com/desktop-java/awt/event/adjustmentlistener-example
+			// }
 		}
 
 	}
@@ -511,6 +514,7 @@ public GenomeHighlight() {
 		}
 
 		/** {@inheritDoc} */
+		@Override
 		public void update(final GenomeRow genomeRow,
 				final boolean genomeFilterChanged,
 				final boolean genomeHighlightChanged) {
@@ -541,22 +545,25 @@ class NodeClickListener implements ViewerListener {
 		/**
 		 * {@inheritDoc}
 		 */
+		@Override
 		public void viewClosed(final String viewName) {
 		}
 
 		/**
 		 * {@inheritDoc}
 		 */
+		@Override
 		public void buttonReleased(final String id) {
 			Event.statusBarMid("Selected node: " + id);
+			selectNode(graph.getNode(id));
 			notifyObservers(dgraph.getDNode(Integer.valueOf(id)));
 		}
 
 		/**
 		 * {@inheritDoc}
 		 */
+		@Override
 		public void buttonPushed(final String id) {
-			selectNode(graph.getNode(id));
 		}
 	}
 
@@ -575,24 +582,29 @@ public void buttonPushed(final String id) {
 	class ViewMouseListener implements MouseListener {
 
 		/** {@inheritDoc} */
+		@Override
 		public void mouseReleased(final MouseEvent e) {
 			vp.pump();
 		}
 
 		/** {@inheritDoc} */
+		@Override
 		public void mousePressed(final MouseEvent e) {
 			vp.pump();
 		}
 
 		/** {@inheritDoc} */
+		@Override
 		public void mouseExited(final MouseEvent e) {
 		}
 
 		/** {@inheritDoc} */
+		@Override
 		public void mouseEntered(final MouseEvent e) {
 		}
 
 		/** {@inheritDoc} */
+		@Override
 		public void mouseClicked(final MouseEvent e) {
 		}