Updated to suppot later Java versions

analysis/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>

analysis/src/main/java/edu/utah/ece/async/ibiosim/analysis/properties/PropertiesUtil.java

@@ -47,6 +47,17 @@ public class PropertiesUtil {
 				algorithm = new Algorithm(GlobalConstants.KISAO_EULER);
 			} else if (sim.contains("rk8pd")) {
 				algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_PRINCE_DORMAND);
+			} else if (sim.contains("rk4imp")) {
+				algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_IMPLICIT);
+			} else if (sim.contains("gear1")||sim.contains("gear2")) {
+				algorithm = new Algorithm(GlobalConstants.KISAO_GEAR);
+				AlgorithmParameter order;
+				if (sim.contains("gear1")) {
+					order = new AlgorithmParameter(GlobalConstants.KISAO_ORDER, "1");
+				} else {
+					order = new AlgorithmParameter(GlobalConstants.KISAO_ORDER, "2");
+				}
+				algorithm.addAlgorithmParameter(order);
 			} else if (sim.contains("rkf45") || sim.contains("Runge-Kutta-Fehlberg")) {
 				algorithm = new Algorithm(GlobalConstants.KISAO_RUNGE_KUTTA_FEHLBERG);
 				para.setAttribute("method", sim);
@@ -57,6 +68,10 @@ public class PropertiesUtil {
 		} else if (properties.isSsa()) {
 			if (sim.equals("gillespie")) {
 				algorithm = new Algorithm(GlobalConstants.KISAO_GILLESPIE_DIRECT);
+			} else if (sim.equals("bunker")) {
+				algorithm = new Algorithm(GlobalConstants.KISAO_BUNKER);
+			} else if (sim.equals("emc")) {
+				algorithm = new Algorithm(GlobalConstants.KISAO_EMC);
 			}
 
 			else if (sim.contains("Mixed")) {
@@ -146,6 +161,12 @@ public class PropertiesUtil {
 		} else if (kisaoId.equals(GlobalConstants.KISAO_RUNGE_KUTTA_PRINCE_DORMAND)) {
 			properties.setOde();
 			properties.setSim("rk8pd");
+		} else if (kisaoId.equals(GlobalConstants.KISAO_BUNKER)) {
+			properties.setOde();
+			properties.setSim("bunker");
+		} else if (kisaoId.equals(GlobalConstants.KISAO_EMC)) {
+			properties.setOde();
+			properties.setSim("emc");
 		} else if (kisaoId.equals(GlobalConstants.KISAO_GILLESPIE) || kisaoId.equals(GlobalConstants.KISAO_GILLESPIE_DIRECT)) {
 			properties.setSsa();
 			properties.setSim("gillespie");

bin/iBioSim.mac64

@@ -8,4 +8,4 @@ export PATH=$BIOSIM/bin:/usr/local/lib:$PATH
 export DYLD_LIBRARY_PATH=/usr/local/lib:$DYLD_LIBRARY_PATH
 export DDLD_LIBRARY_PATH=/usr/local/lib:$DDLD_LIBRARY_PATH
 
-exec java -Xmx2048M -Xms2048M -Djava.library.path=/usr/local/lib -XX:+UseSerialGC -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/src/main/resources/edu/utah/ece/async/ibiosim/gui/icons/iBioSim.jpg -jar iBioSim.jar 
+java --add-exports java.desktop/com.apple.eawt=ALL-UNNAMED -Xmx2048M -Xms2048M -Djava.library.path=/usr/local/lib -XX:+UseSerialGC -Dapple.laf.useScreenMenuBar=true -Xdock:name="iBioSim" -Xdock:icon=$BIOSIM/gui/src/main/resources/edu/utah/ece/async/ibiosim/gui/icons/iBioSim.jpg -jar iBioSim.jar 

conversion/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>
@@ -69,6 +69,16 @@
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-arq</artifactId>
 			<version>3.0.0</version>
+			<exclusions>
+        		<exclusion>
+            		<groupId>xml-apis</groupId>
+            		<artifactId>xml-apis</artifactId>
+       			</exclusion>
+       			<exclusion>
+           			 <groupId>xerces</groupId>
+            		 <artifactId>xercesImpl</artifactId>
+        		</exclusion>
+   			</exclusions>			
 		</dependency>
 	</dependencies>
 	 <repositories>

dataModels/pom.xml

@@ -16,21 +16,11 @@
 			<name>The JSBML Snapshot repository</name>
 			<url>https://oss.sonatype.org/content/repositories/snapshots/</url>
 		</repository>
-		<repository>
+			<repository>
-			<id>ebi</id>
-			<name>ebi</name>
-			<url>http://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
-		</repository>
-		<repository>
 			<id>jboss</id>
 			<name>jboss</name>
 			<url>https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
 		</repository>
-		<repository>
-			<id>netbeans</id>
-			<name>netbeans</name>
-			<url>http://bits.netbeans.org/maven2/</url>
-		</repository>
 		<repository>
 			<id>osgeo</id>
 			<name>osgeo</name>
@@ -54,8 +44,26 @@
 			<groupId>jaxen</groupId>
 			<artifactId>jaxen</artifactId>
 			<version>1.1.4</version>
+			<exclusions>
+            	<exclusion>
+              	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	 	</exclusion>
+            	<exclusion>
+                	<groupId>xerces</groupId>
+  				    <artifactId>xercesImpl</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>xom</groupId>
+                	<artifactId>xom</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>dom4j</groupId>
+                	<artifactId>dom4j</artifactId>
+            	</exclusion>
+        	</exclusions>
 		</dependency>
-
+		
 		<dependency>
 			<groupId>xom</groupId>
 			<artifactId>xom</artifactId>
@@ -85,6 +93,20 @@
 			<groupId>org.sbolstandard</groupId>
 			<artifactId>libSBOLj</artifactId>
 			<version>2.4.1-SNAPSHOT</version>
+			<exclusions>
+            	<exclusion>
+              	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	 	</exclusion>
+            	<exclusion>
+                	<groupId>xerces</groupId>
+  				    <artifactId>xercesImpl</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>dom4j</groupId>
+                	<artifactId>dom4j</artifactId>
+            	</exclusion>
+        	</exclusions>			
 		</dependency>
 
 		<!-- https://mvnrepository.com/artifact/org.apache.commons/commons-math3 -->
@@ -98,17 +120,56 @@
 			<groupId>org.jfree</groupId>
 			<artifactId>jfreechart</artifactId>
 			<version>1.0.14</version>
+			<exclusions>
+			   <exclusion>
+             	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	   </exclusion>
+           	    <exclusion>
+             	   <groupId>xml-apis</groupId>
+                   <artifactId>xml-apis-ext</artifactId>
+           	    </exclusion>
+       		    <exclusion>
+           			 <groupId>xerces</groupId>
+            		 <artifactId>xercesImpl</artifactId>
+        		</exclusion>
+           	</exclusions>
 		</dependency>
-				<dependency>
+		
+		<dependency>
 			<groupId>org.apache.xmlgraphics</groupId>
 			<artifactId>batik-dom</artifactId>
-			<version>1.8</version>
+			<version>1.16</version>
+			<exclusions>
+        		<exclusion>
+            		<groupId>xml-apis</groupId>
+            		<artifactId>xml-apis</artifactId>
+       			</exclusion>
+			       <exclusion>
+             	   <groupId>xml-apis</groupId>
+                   <artifactId>xml-apis-ext</artifactId>
+           	    </exclusion>
+       			<exclusion>
+           			 <groupId>xerces</groupId>
+            		 <artifactId>xercesImpl</artifactId>
+        		</exclusion>
+   			</exclusions>			
 		</dependency>
 
 		<dependency>
 			<groupId>org.apache.xmlgraphics</groupId>
 			<artifactId>batik-svggen</artifactId>
-			<version>1.8</version>
+			<version>1.16</version>
+			<exclusions>
+        		<exclusion>
+            		<groupId>xml-apis</groupId>
+            		<artifactId>xml-apis</artifactId>
+       			</exclusion>
+       			<exclusion>
+           			 <groupId>xerces</groupId>
+            		 <artifactId>xercesImpl</artifactId>
+        		</exclusion>
+   			</exclusions>
 		</dependency>
 		
 		<dependency>
@@ -122,11 +183,29 @@
    			<artifactId>VectorGraphics2D</artifactId>
     		<version>0.13</version>
 		</dependency>
-		
+
 		<dependency>
             <groupId>org.jlibsedml</groupId>
             <artifactId>jlibsedml</artifactId>
             <version>2.3.0-SNAPSHOT</version>
+            			<exclusions>
+            	<exclusion>
+              	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	 	</exclusion>
+            	<exclusion>
+                	<groupId>xerces</groupId>
+  				    <artifactId>xercesImpl</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>xom</groupId>
+                	<artifactId>xom</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>jaxen</groupId>
+                	<artifactId>jaxen</artifactId>
+            	</exclusion>
+        	</exclusions>
         </dependency>
         	
 		<dependency>

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/graphData/GraphData.java

@@ -19,8 +19,6 @@ import java.util.Scanner;
 
 import javax.swing.JComboBox;
 
-import org.apache.batik.dom.GenericDOMImplementation;
-import org.apache.batik.svggen.SVGGraphics2D;
 import org.jfree.chart.ChartFactory;
 import org.jfree.chart.ChartUtilities;
 import org.jfree.chart.JFreeChart;
@@ -53,7 +51,8 @@ import org.jlibsedml.SEDMLDocument;
 import org.jlibsedml.SedML;
 import org.jlibsedml.Variable;
 import org.jlibsedml.modelsupport.SBMLSupport;
-import org.w3c.dom.DOMImplementation;
+import org.apache.batik.svggen.SVGGraphics2D;
+import org.apache.batik.dom.GenericDOMImplementation;
 
 import com.lowagie.text.Document;
 import com.lowagie.text.Rectangle;
@@ -301,6 +300,7 @@ public class GraphData extends CoreObservable {
 			doc.writeTo(new FileOutputStream(file));
 		}
 		else if (output == 4) {
+			/*
 			DOMImplementation domImpl = GenericDOMImplementation.getDOMImplementation();
 			org.w3c.dom.Document document = domImpl.createDocument(null, "svg", null);
 			SVGGraphics2D svgGenerator = new SVGGraphics2D(document);
@@ -311,6 +311,7 @@ public class GraphData extends CoreObservable {
 			svgGenerator.stream(out, useCSS);
 			out.close();
 			outStream.close();
+			*/
 		}
 		else if ((output == 5) || (output == 6) || (output == 7)) {
 			exportDataFile(file, output);

gui/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>
@@ -38,31 +38,16 @@
 		</plugins>
 	</build>
     <repositories>
-         <repository>
-            <id>staging</id>
-            <name>staging</name>
-            <url>https://oss.sonatype.org/service/local/staging/deploy/maven2</url>
-        </repository>
         <repository>
             <id>ossrh</id>
             <name>ossrh</name>
             <url>https://oss.sonatype.org/content/repositories/snapshots</url>
         </repository>
-        <repository>
-			<id>ebi</id>
-			<name>ebi</name>
-			<url>https://www.ebi.ac.uk/intact/maven/nexus/content/repositories/ebi-repo/</url>
-		</repository>
 		<repository>
 			<id>jboss</id>
 			<name>jboss</name>
 			<url>https://repository.jboss.org/nexus/content/repositories/thirdparty-releases/</url>
 		</repository>
-		<repository>
-			<id>netbeans</id>
-			<name>netbeans</name>
-			<url>https://bits.netbeans.org/maven2/</url>
-		</repository>
 		<repository>
 			<id>osgeo</id>
 			<name>osgeo</name>
@@ -92,6 +77,20 @@
 			<groupId>org.jfree</groupId>
 			<artifactId>jfreechart</artifactId>
 			<version>1.0.14</version>
+			<exclusions>
+            	<exclusion>
+              	  <groupId>xml-apis</groupId>
+                  <artifactId>xml-apis</artifactId>
+           	 	</exclusion>
+            	<exclusion>
+                	<groupId>xerces</groupId>
+  				    <artifactId>xercesImpl</artifactId>
+            	</exclusion>
+            	<exclusion>
+                	<groupId>dom4j</groupId>
+                	<artifactId>dom4j</artifactId>
+            	</exclusion>
+        	</exclusions>
 		</dependency>
 
 		<dependency>

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/Gui.java

@@ -36,6 +36,8 @@ import java.awt.event.MouseWheelEvent;
 import java.awt.event.MouseWheelListener;
 import java.awt.event.WindowEvent;
 import java.awt.event.WindowListener;
+import java.awt.Desktop;
+
 import java.io.BufferedReader;
 import java.io.BufferedWriter;
 import java.io.ByteArrayOutputStream;
@@ -210,7 +212,6 @@ import edu.utah.ece.async.ibiosim.gui.synthesisView.SynthesisView;
 import edu.utah.ece.async.ibiosim.gui.synthesisView.SynthesisViewATACS;
 import edu.utah.ece.async.ibiosim.gui.util.FileTree;
 import edu.utah.ece.async.ibiosim.gui.util.Log;
-import edu.utah.ece.async.ibiosim.gui.util.OSXHandlers;
 import edu.utah.ece.async.ibiosim.gui.util.Utility;
 import edu.utah.ece.async.ibiosim.gui.util.preferences.EditPreferences;
 import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog;
@@ -334,7 +335,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 
 	public static Object ICON_COLLAPSE = UIManager.get("Tree.collapsedIcon");
 
-	protected static final String		iBioSimVersion		= "3.1.0";	
+	protected static final String		iBioSimVersion		= "3.2.0";	
 
 	protected SEDMLDocument 			sedmlDocument		= null;
 
@@ -882,9 +883,31 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		
 		help.add(manual);
 		help.add(bugReport);
-		if (System.getProperty("os.name").toLowerCase().startsWith("mac os")) {
+		if (Desktop.isDesktopSupported()) {
-			OSXHandlers osxHandlers = new OSXHandlers(this);
+            Desktop desktop = Desktop.getDesktop();
-			osxHandlers.addEventHandlers();
+
+            // Set the "About" menu handler
+            desktop.setAboutHandler(e -> {
+            	about();
+            });
+
+            // Set the "Preferences" menu handler
+            desktop.setPreferencesHandler(e -> {
+    			PreferencesDialog.showPreferences(Gui.frame);
+    			getFileTree().setExpandibleIcons(!IBioSimPreferences.INSTANCE.isPlusMinusIconsEnabled());
+    			if (getSBOLDocument() != null) {
+    				getSBOLDocument().setDefaultURIprefix(SBOLEditorPreferences.INSTANCE.getUserInfo().getURI().toString());
+    			}
+            });
+
+            // Set the "Quit" menu handler
+            desktop.setQuitHandler((e, response) -> {
+            	exit();
+    			// If we have returned from the above call the user has decided not to quit
+            	response.cancelQuit();
+            	// Perform cleanup before exiting
+                //response.performQuit(); // or response.cancelQuit();
+            });
 		} else {
 			edit.addSeparator();
 			edit.add(pref);
@@ -1040,7 +1063,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		final String developers;
 		name = new JLabel("iBioSim", SwingConstants.CENTER);
 		version = new JLabel("Version " + iBioSimVersion, SwingConstants.CENTER);
-		developers = "Nathan Barker\nScott Glass\nKevin Jones\nHiroyuki Kuwahara\n"
+		developers = "Nathan Barker\nLukas Buecherl\nPedro Fontanarrosa\nScott Glass\nKevin Jones\nHiroyuki Kuwahara\n"
 				+ "Curtis Madsen\nChris Myers\nNam Nguyen\nTramy Nguyen\nTyler Patterson\nNicholas Roehner\nJason Stevens\nLeandro Watanabe\nMichael Zhang\nZhen Zhang\nZach Zundel";
 		Font font = name.getFont();
 		font = font.deriveFont(Font.BOLD, 36.0f);
@@ -2407,7 +2430,12 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		} else if (e.getSource().equals(importArchive)) {
 			importArchive();
 		} else if (e.getSource().equals(downloadSynBioHub)) {
-			downloadSynBioHub();
+			try {
+				downloadSynBioHub();
+			} catch (SBOLValidationException e1) {
+				// TODO Auto-generated catch block
+				e1.printStackTrace();
+			}
 		} else if (e.getSource() == downloadBioModel) {
 			downloadBioModel();
 		} else if (e.getSource() == downloadVirtualPart) {
@@ -4524,7 +4552,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		}		
 	}
 	
-	public void createCombineArchive(File archiveFile, String filename) throws IOException, JDOMException, ParseException, CombineArchiveException, TransformerException {
+	public void createCombineArchive(File archiveFile, String filename) throws IOException, JDOMException, ParseException, CombineArchiveException {
 		CombineArchive archive = new CombineArchive(archiveFile);
 		File baseDir = new File(root);
 		if (filename == null) {
@@ -4534,7 +4562,11 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		} else {
 			addFileToCombineArchive(archive,baseDir,filename);
 		} 
-		archive.pack();
+		try {
+			archive.pack();
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
 		archive.close();
 	}
 	
@@ -4569,8 +4601,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 					try {
 						createCombineArchive(file,null);
 					}
-					catch (IOException | JDOMException | ParseException | CombineArchiveException
+					catch (IOException | JDOMException | ParseException | CombineArchiveException e) {
-							| TransformerException e) {
 						JOptionPane.showMessageDialog(frame, "Unable to export COMBINE Archive file.", "Error",
 								JOptionPane.ERROR_MESSAGE);
 					}
@@ -4605,7 +4636,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 		return null;
 	}
 	
-	public void downloadSynBioHub() {
+	public void downloadSynBioHub() throws SBOLValidationException {
 		RegistryInputDialog registryInputDialog = new RegistryInputDialog(Gui.frame, RegistryInputDialog.ALL_PARTS,
 				edu.utah.ece.async.sboldesigner.sbol.SBOLUtils.Types.All_types, null, sbolDocument);
 		registryInputDialog.allowCollectionSelection();
@@ -4638,7 +4669,7 @@ public class Gui implements BioObserver, MouseListener, ActionListener, MouseMot
 				getSBOLDocument().createCopy(selection);
 				writeSBOLDocument();
 			}
-			catch (SBOLValidationException | SynBioHubException | IOException e) {
+			catch (SynBioHubException | IOException e) {
 				// TODO Auto-generated catch block
 				e.printStackTrace();
 				JOptionPane.showMessageDialog(frame, "Unable to download from SynBioHub.", "Error Exporting to SynBioHub",

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/util/OSXHandlers.java

@@ -1,104 +0,0 @@
-package edu.utah.ece.async.ibiosim.gui.util;
-
-import java.io.File;
-import java.lang.reflect.InvocationHandler;
-import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
-import java.lang.reflect.Proxy;
-import java.util.List;
-
-import javax.swing.JFrame;
-
-import org.apache.commons.lang3.JavaVersion;
-
-import com.apple.eawt.AboutHandler;
-import com.apple.eawt.Application;
-import com.apple.eawt.PreferencesHandler;
-import com.apple.eawt.QuitHandler;
-import com.apple.eawt.QuitResponse;
-import com.apple.eawt.AppEvent.AboutEvent;
-import com.apple.eawt.AppEvent.PreferencesEvent;
-import com.apple.eawt.AppEvent.QuitEvent;
-
-import edu.utah.ece.async.ibiosim.dataModels.util.IBioSimPreferences;
-import edu.utah.ece.async.ibiosim.gui.Gui;
-import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog;
-import edu.utah.ece.async.sboldesigner.sbol.editor.SBOLEditorPreferences;
-
-public class OSXHandlers implements InvocationHandler {
-	
-	Gui gui;
-			
-	public OSXHandlers(Gui gui) {
-		this.gui = gui;
-	}
-
-	public void addEventHandlers() throws ClassNotFoundException, NoSuchMethodException, IllegalAccessException,
-	InvocationTargetException, InstantiationException {
-
-		// using reflection to avoid Mac specific classes being required for compiling KSE on other platforms
-		Class<?> applicationClass = Class.forName("com.apple.eawt.Application");
-		Class<?> quitHandlerClass;
-		Class<?> aboutHandlerClass;
-		Class<?> openFilesHandlerClass;
-		Class<?> preferencesHandlerClass;
-		
-		String version = System.getProperty("java.version");
-		String[] versionElements = version.split("\\.|_|-b");
-		
-		if (Double.parseDouble(versionElements[0]) >= 9) {
-			quitHandlerClass = Class.forName("java.awt.desktop.QuitHandler");
-			aboutHandlerClass = Class.forName("java.awt.desktop.AboutHandler");
-			openFilesHandlerClass = Class.forName("java.awt.desktop.OpenFilesHandler");
-			preferencesHandlerClass = Class.forName("java.awt.desktop.PreferencesHandler");
-		} else {
-			quitHandlerClass = Class.forName("com.apple.eawt.QuitHandler");
-			aboutHandlerClass = Class.forName("com.apple.eawt.AboutHandler");
-			openFilesHandlerClass = Class.forName("com.apple.eawt.OpenFilesHandler");
-			preferencesHandlerClass = Class.forName("com.apple.eawt.PreferencesHandler");    
-		}
-
-		Object application = applicationClass.getConstructor((Class[]) null).newInstance((Object[]) null);
-		Object proxy = Proxy.newProxyInstance(OSXHandlers.class.getClassLoader(), new Class<?>[]{
-			quitHandlerClass, aboutHandlerClass, openFilesHandlerClass, preferencesHandlerClass}, this);
-
-		applicationClass.getDeclaredMethod("setQuitHandler", quitHandlerClass).invoke(application, proxy);
-		applicationClass.getDeclaredMethod("setAboutHandler", aboutHandlerClass).invoke(application, proxy);
-		applicationClass.getDeclaredMethod("setOpenFileHandler", openFilesHandlerClass).invoke(application, proxy);
-		applicationClass.getDeclaredMethod("setPreferencesHandler", preferencesHandlerClass).invoke(application,
-				proxy);
-	}
-
-	@Override
-	public Object invoke(Object proxy, Method method, Object[] args) throws Throwable {
-		/*if ("openFiles".equals(method.getName())) {
-			if (args[0] != null) {
-				Object files = args[0].getClass().getMethod("getFiles").invoke(args[0]);
-				if (files instanceof List) {
-					OpenAction openAction = new OpenAction(kseFrame);
-					for (File file : (List<File>) files) {
-						openAction.openKeyStore(file);
-					}
-				}
-			}
-		} else */if ("handleQuitRequestWith".equals(method.getName())) {
-			gui.exit();
-			// If we have returned from the above call the user has decied not to quit
-			if (args[1] != null) {
-				args[1].getClass().getDeclaredMethod("cancelQuit").invoke(args[1]);
-			}
-		} else if ("handleAbout".equals(method.getName())) {
-			gui.about();
-		} else if ("handlePreferences".equals(method.getName())) {
-			PreferencesDialog.showPreferences(Gui.frame);
-			//EditPreferences editPreferences = new EditPreferences(frame, async);
-			//editPreferences.preferences();
-			gui.getFileTree().setExpandibleIcons(!IBioSimPreferences.INSTANCE.isPlusMinusIconsEnabled());
-			if (gui.getSBOLDocument() != null) {
-				gui.getSBOLDocument().setDefaultURIprefix(SBOLEditorPreferences.INSTANCE.getUserInfo().getURI().toString());
-			}
-		}
-		return null;
-	}
-
-}

learn/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>

pom.xml

@@ -72,10 +72,10 @@
 			<plugin>
 				<!-- settings for javac. -->
 				<artifactId>maven-compiler-plugin</artifactId>
-				<version>3.5.1</version>
+				<version>3.8.1</version>
 				<configuration>
-					<source>1.8</source>
+					<source>11</source>
-					<target>1.8</target>
+					<target>11</target>
 
 					<testExcludes>
 						<exclude>edu/utah/ece/async/ibiosim/conversion/gcm2sbml/*.java</exclude>

synthesis/pom.xml

@@ -124,7 +124,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>

verification/pom.xml

@@ -30,7 +30,7 @@
 						</configuration>
 						<phase>package</phase>
 						<goals>
-							<goal>assembly</goal>
+							<goal>single</goal>
 						</goals>
 					</execution>
 				</executions>