Fruitless attempts to select a tab in CyBrowser

Some copyright headers updated

src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/CyUtilities.java

+/*******************************************************************************
+ * Copyright (C) 2018 Philipp Spohr
+ * 
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ * 
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
+
+package de.hhu.ba.yoshikoWrapper.cytoUtil;
+
+
+import java.awt.Component;
+
+import org.cytoscape.application.swing.CytoPanel;
+import org.cytoscape.application.swing.CytoPanelComponent;
+import org.cytoscape.application.swing.CytoPanelName;
+
+import de.hhu.ba.yoshikoWrapper.core.CyCore;
+
+/**
+ * Helper functions that simplify the Cytoscape API that haven't found a home in any other class
+ *
+ */
+public class CyUtilities {
+
+	/**
+	 * Selects the tab containing the CyBrowser in the result panel if such a tab exists
+	 */
+	public static void highlightCyBrowser() {
+		//We retrieve the result panel
+		CytoPanel resultPanel = CyCore.swing.getCytoPanel(CytoPanelName.EAST);
+		for (int i= 0; i< resultPanel.getCytoPanelComponentCount(); i++) {
+			Component component = resultPanel.getComponentAt(i);
+			if (component instanceof CytoPanelComponent) {
+				CytoPanelComponent cmp = (CytoPanelComponent) component;
+				if (cmp.getTitle().equals("CyBrowser")) {
+					resultPanel.setSelectedIndex(i);
+					return;
+				}
+			}
+			
+		}
+//		int index = resultPanel.indexOfComponent("edu.ucsf.rbvi.cyBrowser.internal.view.ResultsPanelBrowser");
+//		if (index != -1) {
+//			resultPanel.setSelectedIndex(index);
+//		}
+//		else {
+//			//TODO: Output something?
+//			System.err.println("Failed to identify CyBrowser tab");
+//		}
+	}
+
+}

src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/NodeMap.java

 /*******************************************************************************
- * Copyright (C) 2017 Philipp Spohr
+ * Copyright (C) 2018 Philipp Spohr
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

src/main/java/de/hhu/ba/yoshikoWrapper/cytoUtil/StyleManager.java

+/*******************************************************************************
+ * Copyright (C) 2017 Philipp Spohr
+ * 
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ * 
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ * 
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.cytoUtil;
 
 import java.util.List;

src/main/java/de/hhu/ba/yoshikoWrapper/help/HelpLinks.java

 /*******************************************************************************
- * Copyright (C) 2017 Philipp Spohr
+ * Copyright (C) 2018 Philipp Spohr
  *
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -22,10 +22,11 @@
 package de.hhu.ba.yoshikoWrapper.help;
 
 import java.util.HashMap;
+import java.util.Map;
 
 public final class HelpLinks {
 
-	public static final HashMap<String,Object> mainInfo = new HashMap<String,Object>();
+	public static final Map<String, Object> mainInfo = new HashMap<String,Object>();
 	static {
 		mainInfo.put("url", "file:///home/philipp/workspace/cs/cytoscape-tutorials/presentations/yoshiko.html");
 		//mainInfo.put("url", "https://spqrph.github.io/cytoscape-tutorials/presentations/yoshiko.html#/title");

src/main/java/de/hhu/ba/yoshikoWrapper/swing/components/HelpButton.java

+/*******************************************************************************
+ * Copyright (C) 2018 Philipp Spohr
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 package de.hhu.ba.yoshikoWrapper.swing.components;
 
 import java.awt.event.ActionEvent;
@@ -12,6 +33,7 @@ import javax.swing.JButton;
 
 import de.hhu.ba.yoshikoWrapper.core.LocalizationManager;
 import de.hhu.ba.yoshikoWrapper.cytoUtil.CommandExecutor;
+import de.hhu.ba.yoshikoWrapper.cytoUtil.CyUtilities;
 import de.hhu.ba.yoshikoWrapper.help.HelpLinks;
 import de.hhu.ba.yoshikoWrapper.swing.GraphicsLoader;
 
@@ -34,7 +56,9 @@ public class HelpButton extends JButton{
 	private static final ImageIcon hlIcon = GraphicsLoader.getInfoIconHL(SIZE);
 
 
-
+	/**
+	 * Default Constructor, creates a JButton that opens the help section in CyBrowser
+	 */
 	public HelpButton() {
 
 		super(defaultIcon);
@@ -48,8 +72,9 @@ public class HelpButton extends JButton{
 			new ActionListener() {
 				@Override
 				public void actionPerformed(ActionEvent e) {
-
 					CommandExecutor.executeCommand("cybrowser", "show",HelpLinks.mainInfo , null);
+					//Workaround to instantly select/highlight the CyBrowser tab
+					CyUtilities.highlightCyBrowser();
 				}
 			}
 		);

src/main/java/de/hhu/ba/yoshikoWrapper/tasks/AlgorithmTask.java

@@ -293,7 +293,7 @@ public class AlgorithmTask extends AbstractTask implements ObservableTask, Tunab
 	public void cancel() {
 		//Free C++ resources
 		if (c_algorithm != null) {
-			System.out.println("Deleting CoreAlgorithm instance!");
+			//System.out.println("Deleting CoreAlgorithm instance!");
 			c_algorithm.cancel();
 			c_algorithm.delete();
 		}