Start of redo of preferences.

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/util/IBioSimPreferences.java

@@ -0,0 +1,257 @@
+/*
+ * Copyright (c) 2012 - 2015, Clark & Parsia, LLC. <http://www.clarkparsia.com>
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.utah.ece.async.ibiosim.dataModels.util;
+
+import java.util.prefs.Preferences;
+
+import edu.utah.ece.async.ibiosim.dataModels.util.Infos;
+import edu.utah.ece.async.ibiosim.dataModels.util.PersonInfo;
+
+public enum IBioSimPreferences {
+	INSTANCE;
+
+	private PersonInfo userInfo = null;
+
+	public PersonInfo getUserInfo() {
+		if (userInfo == null) {
+			Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("user");
+			String name = prefs.get("name", "");
+			String email = prefs.get("email", "");
+			String uri = prefs.get("uri", "http://www.dummy.org");
+			userInfo = Infos.forPerson(uri, name, email);
+		}
+
+		return userInfo;
+	}
+
+	public void saveUserInfo(PersonInfo userInfo) {
+		this.userInfo = userInfo;
+
+		Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("user");
+
+		try {
+			if (userInfo == null) {
+				prefs.removeNode();
+			} else {
+				prefs.put("uri", userInfo.getURI().toString());
+				prefs.put("name", userInfo.getName());
+				if (userInfo.getEmail() != null) {
+					prefs.put("email", userInfo.getEmail().toString());
+				} else {
+					prefs.put("email", "");
+				}
+			}
+
+			prefs.flush();
+		} catch (Exception e) {
+			e.printStackTrace();
+		}
+	}
+
+	public boolean getValidate() {
+		return false;
+	}
+
+	private Boolean enableFileDialog = null;
+	
+	public boolean isFileDialogEnabled() {
+		if (enableFileDialog == null) {
+			enableFileDialog = Preferences.userRoot().get("biosim.general.file_browser", "").equals("FileDialog");
+		}
+
+		return enableFileDialog;
+	}
+
+	public void setFileDialogEnabled(boolean enableFileDialog) {
+		this.enableFileDialog = enableFileDialog;
+		if (enableFileDialog) {
+			Preferences.userRoot().put("biosim.general.file_browser", "FileDialog");
+		} else {
+			Preferences.userRoot().put("biosim.general.file_browser", "JFileChooser");
+		}
+	}
+
+	private Boolean enablePlusMinusIcons = null;
+	
+	public boolean isPlusMinusIconsEnabled() {
+		if (enablePlusMinusIcons == null) {
+			enablePlusMinusIcons = Preferences.userRoot().get("biosim.general.tree_icons", "").equals("plus_minus");
+		}
+
+		return enablePlusMinusIcons;
+	}
+
+	public void setPlusMinusIconsEnabled(boolean enablePlusMinusIcons) {
+		this.enablePlusMinusIcons = enablePlusMinusIcons;
+		if (enablePlusMinusIcons) {
+			Preferences.userRoot().put("biosim.general.tree_icons", "plus_minus");
+		} else {
+			Preferences.userRoot().put("biosim.general.tree_icons", "default");
+		}
+	}
+	
+	private Boolean enableNoConfirm = null;
+	
+	public boolean isNoConfirmEnabled() {
+		if (enableNoConfirm == null) {
+			enableNoConfirm = Preferences.userRoot().get("biosim.general.delete", "").equals("noconfirm");
+		}
+
+		return enableNoConfirm;
+	}
+
+	public void setNoConfirmEnabled(boolean enableNoConfirm) {
+		this.enableNoConfirm = enableNoConfirm;
+		if (enableNoConfirm) {
+			Preferences.userRoot().put("biosim.general.delete", "noconfirm");
+		} else {
+			Preferences.userRoot().put("biosim.general.delete", "confirm");
+		}
+	}
+	
+	private Boolean enableLibSBMLFlatten = null;
+	
+	public boolean isLibSBMLFlattenEnabled() {
+		if (enableLibSBMLFlatten == null) {
+			enableLibSBMLFlatten = Preferences.userRoot().get("biosim.general.flatten", "").equals("libsbml");
+		}
+
+		return enableLibSBMLFlatten;
+	}
+
+	public void setLibSBMLFlattenEnabled(boolean enableLibSBMLFlatten) {
+		this.enableLibSBMLFlatten = enableLibSBMLFlatten;
+		if (enableLibSBMLFlatten) {
+			Preferences.userRoot().put("biosim.general.flatten", "libsbml");
+		} else {
+			Preferences.userRoot().put("biosim.general.flatten", "default");
+		}
+	}
+	
+	private Boolean enableLibSBMLValidate = null;
+	
+	public boolean isLibSBMLValidateEnabled() {
+		if (enableLibSBMLValidate == null) {
+			enableLibSBMLValidate = Preferences.userRoot().get("biosim.general.validate", "").equals("libsbml");
+		}
+
+		return enableLibSBMLValidate;
+	}
+
+	public void setLibSBMLValidateEnabled(boolean enableLibSBMLValidate) {
+		this.enableLibSBMLValidate = enableLibSBMLValidate;
+		if (enableLibSBMLValidate) {
+			Preferences.userRoot().put("biosim.general.validate", "libsbml");
+		} else {
+			Preferences.userRoot().put("biosim.general.validate", "default");
+		}
+	}
+
+	private Boolean enableWarnings = null;
+	
+	public boolean isWarningsEnabled() {
+		if (enableWarnings == null) {
+			enableWarnings = Preferences.userRoot().get("biosim.general.warnings", "").equals("true");
+		}
+
+		return enableWarnings;
+	}
+
+	public void setWarningsEnabled(boolean enableWarnings) {
+		this.enableWarnings = enableWarnings;
+		if (enableWarnings) {
+			Preferences.userRoot().put("biosim.general.warnings", "true");
+		} else {
+			Preferences.userRoot().put("biosim.general.warnings", "false");
+		}
+	}
+
+	private Boolean enableBranching = null;
+	private Boolean enableVersioning = null;
+	
+	public boolean isBranchingEnabled() {
+		if (enableBranching == null) {
+			Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("versioning");
+			enableBranching = prefs.getBoolean("enableBranching", false);
+		}
+
+		return enableBranching;
+	}
+
+	public void setBranchingEnabled(boolean enableBranching) {
+		Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("versioning");
+		prefs.putBoolean("enableBranching", enableBranching);
+	}
+
+	public boolean isVersioningEnabled() {
+		if (enableVersioning == null) {
+			Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("versioning");
+			// versioning is no longer supported
+			enableVersioning = prefs.getBoolean("enable", false);
+		}
+
+		return enableVersioning;
+	}
+
+	public void setVersioningEnabled(boolean enableVersioning) {
+		Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("versioning");
+		prefs.putBoolean("enable", enableVersioning);
+	}
+
+	private Integer seqBehavior = null;
+
+	/**
+	 * askUser is 0, overwrite is 1, and keep is 2
+	 */
+	public Integer getSeqBehavior() {
+		if (seqBehavior == null) {
+			Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("settings");
+			seqBehavior = prefs.getInt("seqBehavior", 2);
+		}
+		return seqBehavior;
+	}
+
+	/**
+	 * askUser is 0, overwrite is 1, and keep is 2
+	 */
+	public void setSeqBehavior(int seqBehavior) {
+		Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("settings");
+		prefs.putInt("seqBehavior", seqBehavior);
+		this.seqBehavior = seqBehavior;
+	}
+
+	private Integer nameDisplayIdBehavior = null;
+
+	/**
+	 * show name is 0, show displayId is 1
+	 */
+	public Integer getNameDisplayIdBehavior() {
+		if (nameDisplayIdBehavior == null) {
+			Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("settings");
+			nameDisplayIdBehavior = prefs.getInt("nameDisplayIdBehavior", 0);
+		}
+		return nameDisplayIdBehavior;
+	}
+
+	/**
+	 * show name is 0, show displayId is 1
+	 */
+	public void setNameDisplayIdBehavior(int showNameOrDisplayId) {
+		Preferences prefs = Preferences.userNodeForPackage(IBioSimPreferences.class).node("settings");
+		prefs.putInt("nameDisplayIdBehavior", showNameOrDisplayId);
+		this.nameDisplayIdBehavior = showNameOrDisplayId;
+	}
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/util/Infos.java

@@ -0,0 +1,75 @@
+/*
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.utah.ece.async.ibiosim.dataModels.util;
+
+import java.net.URI;
+
+import com.google.common.base.Preconditions;
+
+public class Infos {	
+	public static PersonInfo forPerson(String uri) {
+		return forPerson(URI.create(uri), "", null);
+	}
+	
+	public static PersonInfo forPerson(URI uri) {
+		return forPerson(uri, "", null);
+	}
+	
+	public static PersonInfo forPerson(String uri, String name, String email) {
+		return forPerson(URI.create(uri), name, email);
+	}
+	
+	public static PersonInfo forPerson(URI uri, String name, String email) {
+		return new ImmutablePersonInfo(uri, name, email);
+	}
+	
+	private static class ImmutablePersonInfo implements PersonInfo {
+		private final URI uri;
+		private final String name;
+		private final String email;
+
+		public ImmutablePersonInfo(URI user, String name, String email) {
+			Preconditions.checkNotNull(user, "Person URI cannot be null");
+			this.uri = user;
+			this.name = name;
+			this.email = email;
+		}
+
+		@Override
+		public URI getURI() {
+		    return uri;
+		}
+		
+		@Override
+		public String getName() {
+			return name;
+		}
+
+		@Override
+		public String getEmail() {
+			return email;
+		}
+
+		@Override
+	    public String toString() {
+			StringBuilder sb = new StringBuilder();
+			sb.append(name);
+			if (email != null) {
+				sb.append(" <").append(email.toString()).append(">");
+			}
+		    return sb.toString();
+	    }	
+	}
+
+}

dataModels/src/main/java/edu/utah/ece/async/ibiosim/dataModels/util/PersonInfo.java

@@ -0,0 +1,26 @@
+/*
+ * Copyright (c) 2012 - 2015, Clark & Parsia, LLC. <http://www.clarkparsia.com>
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.utah.ece.async.ibiosim.dataModels.util;
+
+import java.net.URI;
+
+public interface PersonInfo {
+	public URI getURI();
+	
+	public String getName();
+	
+	public String getEmail();
+}

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

@@ -156,7 +156,6 @@ import com.apple.eawt.PreferencesHandler;
 import com.apple.eawt.QuitHandler;
 import com.apple.eawt.QuitResponse;
 import edu.utah.ece.async.sboldesigner.sbol.editor.SBOLDesignerPlugin;
-
 import uk.ac.ebi.biomodels.ws.BioModelsWSClient;
 import uk.ac.ebi.biomodels.ws.BioModelsWSException;
 import de.unirostock.sems.cbarchive.CombineArchive;
@@ -186,10 +185,11 @@ import edu.utah.ece.async.ibiosim.gui.modelEditor.schematic.Utils;
 import edu.utah.ece.async.ibiosim.gui.sbolBrowser.SBOLBrowser2;
 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.EditPreferences;
 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.Utility;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.EditPreferences;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog;
 import edu.utah.ece.async.ibiosim.gui.util.tabs.CloseAndMaxTabbedPane;
 import edu.utah.ece.async.ibiosim.gui.verificationView.AbstractionPanel;
 import edu.utah.ece.async.ibiosim.gui.verificationView.VerificationView;
@@ -339,6 +339,7 @@ public class Gui implements Observer, MouseListener, ActionListener, MouseMotion
 
 		app.setPreferencesHandler(new PreferencesHandler() {
 			public void handlePreferences(PreferencesEvent pe) {
+				PreferencesDialog.showPreferences(frame);
 				EditPreferences editPreferences = new EditPreferences(frame, async, tree);
 				editPreferences.preferences();
 				if (sbolDocument != null) {
@@ -2947,6 +2948,7 @@ public class Gui implements Observer, MouseListener, ActionListener, MouseMotion
 		}
 		// if the open project menu item is selected
 		else if (e.getSource() == pref) {
+			PreferencesDialog.showPreferences(frame);
 			EditPreferences editPreferences = new EditPreferences(frame, async, tree);
 			editPreferences.preferences();
 			if (sbolDocument != null) {
@@ -6279,6 +6281,7 @@ public class Gui implements Observer, MouseListener, ActionListener, MouseMotion
 				addTab(sbolDesignerPlugin.getRootDisplayId(), sbolDesignerPlugin, "SBOL Designer");
 			}
 		} catch (Exception e) {
+			e.printStackTrace();
 			JOptionPane.showMessageDialog(Gui.frame, "SBOL file at " + fileName + " is invalid.", "Invalid SBOL",
 					JOptionPane.ERROR_MESSAGE);
 		}

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/sbol/SBOLAssociationPanel2.java

@@ -36,7 +36,7 @@ import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.SBOLException;
 import edu.utah.ece.async.ibiosim.gui.Gui;
 import edu.utah.ece.async.ibiosim.gui.modelEditor.schematic.ModelEditor;
 import edu.utah.ece.async.ibiosim.gui.sbolBrowser.SBOLBrowser2;
-import edu.utah.ece.async.ibiosim.gui.util.EditPreferences;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.EditPreferences;
 
 import java.net.URI;
 import java.net.URISyntaxException;

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/sbol/SBOLDescriptorPanel2.java

@@ -40,7 +40,7 @@ import edu.utah.ece.async.ibiosim.dataModels.sbol.SBOLIdentityManager;
 import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
 import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.SBOLException;
 import edu.utah.ece.async.ibiosim.gui.Gui;
-import edu.utah.ece.async.ibiosim.gui.util.EditPreferences;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.EditPreferences;
 
 /**
  * 

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/sbol/SBOLField2.java

@@ -42,7 +42,7 @@ import edu.utah.ece.async.ibiosim.dataModels.sbol.SBOLUtility;
 import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
 import edu.utah.ece.async.ibiosim.gui.Gui;
 import edu.utah.ece.async.ibiosim.gui.modelEditor.schematic.ModelEditor;
-import edu.utah.ece.async.ibiosim.gui.util.EditPreferences;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.EditPreferences;
 import edu.utah.ece.async.sboldesigner.sbol.editor.dialog.PartEditDialog;
 
 public class SBOLField2 extends JPanel implements ActionListener {

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/schematic/BioGraph.java

@@ -69,7 +69,6 @@ import com.mxgraph.view.mxStylesheet;
 import edu.utah.ece.async.ibiosim.dataModels.biomodel.annotation.AnnotationUtility;
 import edu.utah.ece.async.ibiosim.dataModels.biomodel.parser.BioModel;
 import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;
-import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.Utility;
 import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
 import edu.utah.ece.async.ibiosim.gui.Gui;
 import edu.utah.ece.async.ibiosim.gui.ResourceManager;

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/schematic/ModelEditor.java

@@ -28,7 +28,6 @@ import java.io.PrintStream;
 import java.io.UnsupportedEncodingException;
 import java.util.ArrayList;
 import java.util.HashMap;
-import java.util.HashSet;
 import java.util.Observable;
 import java.util.Observer;
 import java.util.Scanner;
@@ -142,9 +141,9 @@ import edu.utah.ece.async.ibiosim.gui.modelEditor.util.AbstractRunnableNamedButt
 import edu.utah.ece.async.ibiosim.gui.modelEditor.util.PropertyList;
 import edu.utah.ece.async.ibiosim.gui.modelEditor.util.Runnable;
 import edu.utah.ece.async.ibiosim.gui.modelEditor.util.UndoManager;
-import edu.utah.ece.async.ibiosim.gui.util.EditPreferences;
 import edu.utah.ece.async.ibiosim.gui.util.Log;
 import edu.utah.ece.async.ibiosim.gui.util.SpringUtilities;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.EditPreferences;
 import edu.utah.ece.async.ibiosim.synthesis.assembly.Assembler2;
 import edu.utah.ece.async.ibiosim.synthesis.assembly.AssemblyGraph2;
 import edu.utah.ece.async.ibiosim.synthesis.assembly.SequenceTypeValidator;
@@ -725,8 +724,11 @@ public class ModelEditor extends JPanel implements ActionListener, MouseListener
 		//String submissionVersion = cd.isSetVersion() ? cd.getVersion() : "1";
 
 		JComboBox registries = new JComboBox();
+
 		registries.addItem("http://synbiohub.org");
 		registries.addItem("http://synbiohub.utah.edu");
+		registries.addItem("http://cidarlab.org:7777");
+		registries.addItem("https://synbiohub.cidarlab.org");
 		registries.addItem("http://localhost:7777");
 		registries.addItem("http://14compsci099.ncl.ac.uk:7777");
 		JTextField userField = new JTextField(12);
@@ -785,7 +787,7 @@ public class ModelEditor extends JPanel implements ActionListener, MouseListener
 						"Submission Error", JOptionPane.ERROR_MESSAGE);
 				error = true;
 			}
-			String password = passwordField.getText().trim();
+			String password = passwordField.getPassword().toString().trim();
 			if (password.equals("")) {
 				JOptionPane.showMessageDialog(Gui.frame, "Password Required",
 						"Submission Error", JOptionPane.ERROR_MESSAGE);
@@ -2005,7 +2007,7 @@ public class ModelEditor extends JPanel implements ActionListener, MouseListener
 
 	private static void updateValue(SBMLDocument d,String id,String factor,String paramId,String value,String type) {
 		SBase sbase = SBMLutilities.getElementBySId(d, id);
-		if (d.getModel().getInitialAssignment(id)!=null) {
+		if (d.getModel().getInitialAssignmentBySymbol(id)!=null) {
 			d.getModel().getListOfInitialAssignments().remove(id);
 		}
 		if (sbase != null) {
@@ -3362,7 +3364,7 @@ public class ModelEditor extends JPanel implements ActionListener, MouseListener
 					if (lower!=upper) {
 						bound = "[" + lower + "," + upper + "]";
 					}
-					InitialAssignment ia = flatSBML.getModel().getInitialAssignment(p.getId());
+					InitialAssignment ia = flatSBML.getModel().getInitialAssignmentBySymbol(p.getId());
 					if (ia != null) {
 						ASTNode math = ia.getMath();
 						if (math.getType()==ASTNode.Type.FUNCTION && math.getName().equals("uniform")) {
@@ -3393,7 +3395,7 @@ public class ModelEditor extends JPanel implements ActionListener, MouseListener
 								if (lrate!=urate) {
 									boundRate = "[" + lrate + "," + urate + "]";
 								}
-								ia = flatSBML.getModel().getInitialAssignment(rp.getId());
+								ia = flatSBML.getModel().getInitialAssignmentBySymbol(rp.getId());
 								if (ia != null) {
 									ASTNode math = ia.getMath();
 									if (math.getType()==ASTNode.Type.FUNCTION && math.getName().equals("uniform")) {
@@ -3469,7 +3471,7 @@ public class ModelEditor extends JPanel implements ActionListener, MouseListener
 				for (int j = 0; j < postset.size(); j++) {
 					t.addPostset(lpn.getPlace(postset.get(j)));
 				}
-				Rule r = sbml.getModel().getRule(GlobalConstants.TRIGGER + "_" + e.getId());
+				Rule r = sbml.getModel().getRuleByVariable(GlobalConstants.TRIGGER + "_" + e.getId());
 				if (r != null) {
 					t.setPersistent(true);
 					ASTNode triggerMath = r.getMath();

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/schematic/Schematic.java

@@ -101,7 +101,6 @@ import com.mxgraph.util.mxRectangle;
 import edu.utah.ece.async.ibiosim.dataModels.biomodel.annotation.AnnotationUtility;
 import edu.utah.ece.async.ibiosim.dataModels.biomodel.parser.BioModel;
 import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;
-import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.Utility;
 import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
 import edu.utah.ece.async.ibiosim.gui.Gui;
 import edu.utah.ece.async.ibiosim.gui.ResourceManager;

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/modelEditor/schematic/Utils.java

@@ -13,7 +13,6 @@
  *******************************************************************************/
 package edu.utah.ece.async.ibiosim.gui.modelEditor.schematic;
 
-import java.awt.Dimension;
 import java.awt.event.ActionListener;
 import java.io.IOException;
 import java.net.URL;
@@ -59,8 +58,6 @@ import org.sbml.jsbml.ext.arrays.ArraysSBasePlugin;
 import org.sbml.jsbml.ext.arrays.util.ArraysMath;
 import org.sbml.jsbml.ext.arrays.validator.ArraysValidator;
 import org.sbml.jsbml.validator.SBMLValidator;
-import org.sbml.jsbml.validator.SBMLValidator.CHECK_CATEGORY;
-import org.sbml.libsbml.SBMLReader;
 import org.sbml.libsbml.libsbmlConstants;
 
 import edu.utah.ece.async.ibiosim.dataModels.biomodel.util.SBMLutilities;

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/sbolBrowser/SBOLBrowser2.java

@@ -31,7 +31,7 @@ import org.sbolstandard.core2.Collection;
 import edu.utah.ece.async.ibiosim.dataModels.sbol.SBOLUtility;
 import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
 import edu.utah.ece.async.ibiosim.gui.Gui;
-import edu.utah.ece.async.ibiosim.gui.util.EditPreferences;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.EditPreferences;
 
 /**
  * 

gui/src/main/java/edu/utah/ece/async/ibiosim/gui/synthesisView/SynthesisView.java

@@ -53,9 +53,9 @@ import edu.utah.ece.async.ibiosim.dataModels.sbol.SBOLFileManager;
 import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
 import edu.utah.ece.async.ibiosim.dataModels.util.exceptions.SBOLException;
 import edu.utah.ece.async.ibiosim.gui.Gui;
-import edu.utah.ece.async.ibiosim.gui.util.EditPreferences;
 import edu.utah.ece.async.ibiosim.gui.util.Log;
 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.synthesis.SBMLTechMapping.SynthesisGraph;
 import edu.utah.ece.async.ibiosim.synthesis.SBMLTechMapping.Synthesizer;
 

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

@@ -0,0 +1,98 @@
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
+
+import java.awt.Component;
+
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JRadioButton;
+
+import edu.utah.ece.async.ibiosim.dataModels.util.IBioSimPreferences;
+import edu.utah.ece.async.ibiosim.gui.ResourceManager;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog.PreferencesTab;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Images;
+import edu.utah.ece.async.sboldesigner.swing.FormBuilder;
+
+public enum AnalysisPreferencesTab implements PreferencesTab {
+	INSTANCE;
+
+	// askUser is 0, overwrite is 1, and keep is 2
+	private JRadioButton seqAskUser = new JRadioButton("Ask", IBioSimPreferences.INSTANCE.getSeqBehavior() == 0);
+	private JRadioButton seqOverwrite = new JRadioButton("Overwrite",
+			IBioSimPreferences.INSTANCE.getSeqBehavior() == 1);
+	private JRadioButton seqKeep = new JRadioButton("Keep", IBioSimPreferences.INSTANCE.getSeqBehavior() == 2);
+
+	// show name is 0, show displayId is 1
+	private JRadioButton showName = new JRadioButton("Show name when set",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 0);
+	private JRadioButton showDisplayId = new JRadioButton("Show displayId",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 1);
+
+	@Override
+	public String getTitle() {
+		return "Analysis";
+	}
+
+	@Override
+	public String getDescription() {
+		return "Default Analysis Settings";
+	}
+
+	@Override
+	public Icon getIcon() {
+		return ResourceManager.getImageIcon("simulation.jpg");
+	}
+
+	@Override
+	public Component getComponent() {
+		JLabel impliedSequence = new JLabel(
+				"<html>Every time the implied sequence is shorter than the original <br>sequence, would you like to overwrite or keep the original sequence?</html>");
+		ButtonGroup seqGroup = new ButtonGroup();
+		seqGroup.add(seqAskUser);
+		seqGroup.add(seqOverwrite);
+		seqGroup.add(seqKeep);
+
+		JLabel showNameOrDisplayId = new JLabel("<html>Always show displayId or always show name when set?</html>");
+		ButtonGroup nameDisplayIdGroup = new ButtonGroup();
+		nameDisplayIdGroup.add(showName);
+		nameDisplayIdGroup.add(showDisplayId);
+
+		FormBuilder builder = new FormBuilder();
+		builder.add("", impliedSequence);
+		builder.add("", seqAskUser);
+		builder.add("", seqOverwrite);
+		builder.add("", seqKeep);
+		builder.add("", showNameOrDisplayId);
+		builder.add("", showName);
+		builder.add("", showDisplayId);
+
+		return builder.build();
+	}
+
+	@Override
+	public void save() {
+		int seqBehavior = 0;
+		if (seqAskUser.isSelected()) {
+			seqBehavior = 0;
+		} else if (seqOverwrite.isSelected()) {
+			seqBehavior = 1;
+		} else if (seqKeep.isSelected()) {
+			seqBehavior = 2;
+		}
+		IBioSimPreferences.INSTANCE.setSeqBehavior(seqBehavior);
+
+		int showNameOrDisplayId = 0;
+		if (showName.isSelected()) {
+			showNameOrDisplayId = 0;
+		} else if (showDisplayId.isSelected()) {
+			showNameOrDisplayId = 1;
+		}
+		IBioSimPreferences.INSTANCE.setNameDisplayIdBehavior(showNameOrDisplayId);
+	}
+
+	@Override
+	public boolean requiresRestart() {
+		return false;
+	}
+}

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

@@ -11,7 +11,7 @@
  * and also available online at <http://www.async.ece.utah.edu/ibiosim/License>.
  *  
  *******************************************************************************/
-package edu.utah.ece.async.ibiosim.gui.util;
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
 
 import java.awt.BorderLayout;
 import java.awt.Color;
@@ -44,6 +44,7 @@ import edu.utah.ece.async.ibiosim.dataModels.biomodel.parser.CompatibilityFixer;
 import edu.utah.ece.async.ibiosim.dataModels.sbol.SBOLUtility;
 import edu.utah.ece.async.ibiosim.dataModels.util.GlobalConstants;
 import edu.utah.ece.async.ibiosim.gui.Gui;
+import edu.utah.ece.async.ibiosim.gui.util.FileTree;
 
 /**
  * 
@@ -779,10 +780,10 @@ public class EditPreferences {
 		return biosimrc.get(GlobalConstants.SBOL_AUTHORITY_PREFERENCE, GlobalConstants.SBOL_AUTHORITY_DEFAULT);
 	}
 	
-	private JPanel assemblyPreferences(Preferences biosimrc) {	
+	private JPanel SBOLPreferences(Preferences biosimrc) {	
 		// assembly preferences
 		JPanel assemblyLabels = new JPanel(new GridLayout(13, 1));
-		assemblyLabels.add(new JLabel("URI Authority"));
+		assemblyLabels.add(new JLabel("Namespace"));
 		assemblyLabels.add(new JLabel("Assemble Complete Genetic Construct"));
 		assemblyLabels.add(new JLabel("Regex for Complete Genetic Construct"));
 		assemblyLabels.add(new JLabel("Validate Assembled Constructs"));
@@ -1405,7 +1406,7 @@ public class EditPreferences {
 		return problem;
 	}
 	
-	private boolean saveAssemblyPreferences(Preferences biosimrc) {
+	private boolean saveSBOLPreferences(Preferences biosimrc) {
 		boolean problem = false;
 		if (!uriField.getText().trim().equals("")) {
 			biosimrc.put(GlobalConstants.SBOL_AUTHORITY_PREFERENCE, uriField.getText().trim());
@@ -1456,7 +1457,7 @@ public class EditPreferences {
 		JPanel generalPrefs = generalPreferences(biosimrc);
 		JPanel schematicPrefs = schematicPreferences(biosimrc);
 		JPanel modelPrefs = modelPreferences(biosimrc);
-		JPanel assemblyPrefs = assemblyPreferences(biosimrc);
+		JPanel assemblyPrefs = SBOLPreferences(biosimrc);
 		JPanel analysisPrefs = analysisPreferences(biosimrc);
 		JPanel learnPrefs = learnPreferences(biosimrc);
 
@@ -1484,7 +1485,7 @@ public class EditPreferences {
 				if (!problem) problem = saveModelPreferences(biosimrc);
 				if (!problem) problem = saveAnalysisPreferences(biosimrc);
 				if (!problem) problem = saveLearnPreferences(biosimrc);
-				if (!problem) problem = saveAssemblyPreferences(biosimrc);
+				if (!problem) problem = saveSBOLPreferences(biosimrc);
 				try {
 					biosimrc.sync();
 				}

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

@@ -0,0 +1,98 @@
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
+
+import java.awt.Component;
+
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JRadioButton;
+
+import edu.utah.ece.async.ibiosim.dataModels.util.IBioSimPreferences;
+import edu.utah.ece.async.ibiosim.gui.ResourceManager;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog.PreferencesTab;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Images;
+import edu.utah.ece.async.sboldesigner.swing.FormBuilder;
+
+public enum GeneralPreferencesTab implements PreferencesTab {
+	INSTANCE;
+
+	// askUser is 0, overwrite is 1, and keep is 2
+	private JRadioButton seqAskUser = new JRadioButton("Ask", IBioSimPreferences.INSTANCE.getSeqBehavior() == 0);
+	private JRadioButton seqOverwrite = new JRadioButton("Overwrite",
+			IBioSimPreferences.INSTANCE.getSeqBehavior() == 1);
+	private JRadioButton seqKeep = new JRadioButton("Keep", IBioSimPreferences.INSTANCE.getSeqBehavior() == 2);
+
+	// show name is 0, show displayId is 1
+	private JRadioButton showName = new JRadioButton("Show name when set",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 0);
+	private JRadioButton showDisplayId = new JRadioButton("Show displayId",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 1);
+
+	@Override
+	public String getTitle() {
+		return "General";
+	}
+
+	@Override
+	public String getDescription() {
+		return "General Preferences";
+	}
+
+	@Override
+	public Icon getIcon() {
+		return ResourceManager.getImageIcon("general.png");
+	}
+
+	@Override
+	public Component getComponent() {
+		JLabel impliedSequence = new JLabel(
+				"<html>Every time the implied sequence is shorter than the original <br>sequence, would you like to overwrite or keep the original sequence?</html>");
+		ButtonGroup seqGroup = new ButtonGroup();
+		seqGroup.add(seqAskUser);
+		seqGroup.add(seqOverwrite);
+		seqGroup.add(seqKeep);
+
+		JLabel showNameOrDisplayId = new JLabel("<html>Always show displayId or always show name when set?</html>");
+		ButtonGroup nameDisplayIdGroup = new ButtonGroup();
+		nameDisplayIdGroup.add(showName);
+		nameDisplayIdGroup.add(showDisplayId);
+
+		FormBuilder builder = new FormBuilder();
+		builder.add("", impliedSequence);
+		builder.add("", seqAskUser);
+		builder.add("", seqOverwrite);
+		builder.add("", seqKeep);
+		builder.add("", showNameOrDisplayId);
+		builder.add("", showName);
+		builder.add("", showDisplayId);
+
+		return builder.build();
+	}
+
+	@Override
+	public void save() {
+		int seqBehavior = 0;
+		if (seqAskUser.isSelected()) {
+			seqBehavior = 0;
+		} else if (seqOverwrite.isSelected()) {
+			seqBehavior = 1;
+		} else if (seqKeep.isSelected()) {
+			seqBehavior = 2;
+		}
+		IBioSimPreferences.INSTANCE.setSeqBehavior(seqBehavior);
+
+		int showNameOrDisplayId = 0;
+		if (showName.isSelected()) {
+			showNameOrDisplayId = 0;
+		} else if (showDisplayId.isSelected()) {
+			showNameOrDisplayId = 1;
+		}
+		IBioSimPreferences.INSTANCE.setNameDisplayIdBehavior(showNameOrDisplayId);
+	}
+
+	@Override
+	public boolean requiresRestart() {
+		return false;
+	}
+}

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

@@ -0,0 +1,98 @@
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
+
+import java.awt.Component;
+
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JRadioButton;
+
+import edu.utah.ece.async.ibiosim.dataModels.util.IBioSimPreferences;
+import edu.utah.ece.async.ibiosim.gui.ResourceManager;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog.PreferencesTab;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Images;
+import edu.utah.ece.async.sboldesigner.swing.FormBuilder;
+
+public enum LearnPreferencesTab implements PreferencesTab {
+	INSTANCE;
+
+	// askUser is 0, overwrite is 1, and keep is 2
+	private JRadioButton seqAskUser = new JRadioButton("Ask", IBioSimPreferences.INSTANCE.getSeqBehavior() == 0);
+	private JRadioButton seqOverwrite = new JRadioButton("Overwrite",
+			IBioSimPreferences.INSTANCE.getSeqBehavior() == 1);
+	private JRadioButton seqKeep = new JRadioButton("Keep", IBioSimPreferences.INSTANCE.getSeqBehavior() == 2);
+
+	// show name is 0, show displayId is 1
+	private JRadioButton showName = new JRadioButton("Show name when set",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 0);
+	private JRadioButton showDisplayId = new JRadioButton("Show displayId",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 1);
+
+	@Override
+	public String getTitle() {
+		return "Learn";
+	}
+
+	@Override
+	public String getDescription() {
+		return "Default Learn Settings";
+	}
+
+	@Override
+	public Icon getIcon() {
+		return ResourceManager.getImageIcon("learn.jpg");
+	}
+
+	@Override
+	public Component getComponent() {
+		JLabel impliedSequence = new JLabel(
+				"<html>Every time the implied sequence is shorter than the original <br>sequence, would you like to overwrite or keep the original sequence?</html>");
+		ButtonGroup seqGroup = new ButtonGroup();
+		seqGroup.add(seqAskUser);
+		seqGroup.add(seqOverwrite);
+		seqGroup.add(seqKeep);
+
+		JLabel showNameOrDisplayId = new JLabel("<html>Always show displayId or always show name when set?</html>");
+		ButtonGroup nameDisplayIdGroup = new ButtonGroup();
+		nameDisplayIdGroup.add(showName);
+		nameDisplayIdGroup.add(showDisplayId);
+
+		FormBuilder builder = new FormBuilder();
+		builder.add("", impliedSequence);
+		builder.add("", seqAskUser);
+		builder.add("", seqOverwrite);
+		builder.add("", seqKeep);
+		builder.add("", showNameOrDisplayId);
+		builder.add("", showName);
+		builder.add("", showDisplayId);
+
+		return builder.build();
+	}
+
+	@Override
+	public void save() {
+		int seqBehavior = 0;
+		if (seqAskUser.isSelected()) {
+			seqBehavior = 0;
+		} else if (seqOverwrite.isSelected()) {
+			seqBehavior = 1;
+		} else if (seqKeep.isSelected()) {
+			seqBehavior = 2;
+		}
+		IBioSimPreferences.INSTANCE.setSeqBehavior(seqBehavior);
+
+		int showNameOrDisplayId = 0;
+		if (showName.isSelected()) {
+			showNameOrDisplayId = 0;
+		} else if (showDisplayId.isSelected()) {
+			showNameOrDisplayId = 1;
+		}
+		IBioSimPreferences.INSTANCE.setNameDisplayIdBehavior(showNameOrDisplayId);
+	}
+
+	@Override
+	public boolean requiresRestart() {
+		return false;
+	}
+}

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

@@ -0,0 +1,98 @@
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
+
+import java.awt.Component;
+
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JRadioButton;
+
+import edu.utah.ece.async.ibiosim.dataModels.util.IBioSimPreferences;
+import edu.utah.ece.async.ibiosim.gui.ResourceManager;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog.PreferencesTab;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Images;
+import edu.utah.ece.async.sboldesigner.swing.FormBuilder;
+
+public enum ModelEditorPreferencesTab implements PreferencesTab {
+	INSTANCE;
+
+	// askUser is 0, overwrite is 1, and keep is 2
+	private JRadioButton seqAskUser = new JRadioButton("Ask", IBioSimPreferences.INSTANCE.getSeqBehavior() == 0);
+	private JRadioButton seqOverwrite = new JRadioButton("Overwrite",
+			IBioSimPreferences.INSTANCE.getSeqBehavior() == 1);
+	private JRadioButton seqKeep = new JRadioButton("Keep", IBioSimPreferences.INSTANCE.getSeqBehavior() == 2);
+
+	// show name is 0, show displayId is 1
+	private JRadioButton showName = new JRadioButton("Show name when set",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 0);
+	private JRadioButton showDisplayId = new JRadioButton("Show displayId",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 1);
+
+	@Override
+	public String getTitle() {
+		return "Model Editor";
+	}
+
+	@Override
+	public String getDescription() {
+		return "Preferences for Model Editor Schematic";
+	}
+
+	@Override
+	public Icon getIcon() {
+		return ResourceManager.getImageIcon("sbml.jpg");
+	}
+
+	@Override
+	public Component getComponent() {
+		JLabel impliedSequence = new JLabel(
+				"<html>Every time the implied sequence is shorter than the original <br>sequence, would you like to overwrite or keep the original sequence?</html>");
+		ButtonGroup seqGroup = new ButtonGroup();
+		seqGroup.add(seqAskUser);
+		seqGroup.add(seqOverwrite);
+		seqGroup.add(seqKeep);
+
+		JLabel showNameOrDisplayId = new JLabel("<html>Always show displayId or always show name when set?</html>");
+		ButtonGroup nameDisplayIdGroup = new ButtonGroup();
+		nameDisplayIdGroup.add(showName);
+		nameDisplayIdGroup.add(showDisplayId);
+
+		FormBuilder builder = new FormBuilder();
+		builder.add("", impliedSequence);
+		builder.add("", seqAskUser);
+		builder.add("", seqOverwrite);
+		builder.add("", seqKeep);
+		builder.add("", showNameOrDisplayId);
+		builder.add("", showName);
+		builder.add("", showDisplayId);
+
+		return builder.build();
+	}
+
+	@Override
+	public void save() {
+		int seqBehavior = 0;
+		if (seqAskUser.isSelected()) {
+			seqBehavior = 0;
+		} else if (seqOverwrite.isSelected()) {
+			seqBehavior = 1;
+		} else if (seqKeep.isSelected()) {
+			seqBehavior = 2;
+		}
+		IBioSimPreferences.INSTANCE.setSeqBehavior(seqBehavior);
+
+		int showNameOrDisplayId = 0;
+		if (showName.isSelected()) {
+			showNameOrDisplayId = 0;
+		} else if (showDisplayId.isSelected()) {
+			showNameOrDisplayId = 1;
+		}
+		IBioSimPreferences.INSTANCE.setNameDisplayIdBehavior(showNameOrDisplayId);
+	}
+
+	@Override
+	public boolean requiresRestart() {
+		return false;
+	}
+}

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

@@ -0,0 +1,98 @@
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
+
+import java.awt.Component;
+
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JRadioButton;
+
+import edu.utah.ece.async.ibiosim.dataModels.util.IBioSimPreferences;
+import edu.utah.ece.async.ibiosim.gui.ResourceManager;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog.PreferencesTab;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Images;
+import edu.utah.ece.async.sboldesigner.swing.FormBuilder;
+
+public enum ModelPreferencesTab implements PreferencesTab {
+	INSTANCE;
+
+	// askUser is 0, overwrite is 1, and keep is 2
+	private JRadioButton seqAskUser = new JRadioButton("Ask", IBioSimPreferences.INSTANCE.getSeqBehavior() == 0);
+	private JRadioButton seqOverwrite = new JRadioButton("Overwrite",
+			IBioSimPreferences.INSTANCE.getSeqBehavior() == 1);
+	private JRadioButton seqKeep = new JRadioButton("Keep", IBioSimPreferences.INSTANCE.getSeqBehavior() == 2);
+
+	// show name is 0, show displayId is 1
+	private JRadioButton showName = new JRadioButton("Show name when set",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 0);
+	private JRadioButton showDisplayId = new JRadioButton("Show displayId",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 1);
+
+	@Override
+	public String getTitle() {
+		return "Model";
+	}
+
+	@Override
+	public String getDescription() {
+		return "Default Model Parameters";
+	}
+
+	@Override
+	public Icon getIcon() {
+		return ResourceManager.getImageIcon("dot.jpg");
+	}
+
+	@Override
+	public Component getComponent() {
+		JLabel impliedSequence = new JLabel(
+				"<html>Every time the implied sequence is shorter than the original <br>sequence, would you like to overwrite or keep the original sequence?</html>");
+		ButtonGroup seqGroup = new ButtonGroup();
+		seqGroup.add(seqAskUser);
+		seqGroup.add(seqOverwrite);
+		seqGroup.add(seqKeep);
+
+		JLabel showNameOrDisplayId = new JLabel("<html>Always show displayId or always show name when set?</html>");
+		ButtonGroup nameDisplayIdGroup = new ButtonGroup();
+		nameDisplayIdGroup.add(showName);
+		nameDisplayIdGroup.add(showDisplayId);
+
+		FormBuilder builder = new FormBuilder();
+		builder.add("", impliedSequence);
+		builder.add("", seqAskUser);
+		builder.add("", seqOverwrite);
+		builder.add("", seqKeep);
+		builder.add("", showNameOrDisplayId);
+		builder.add("", showName);
+		builder.add("", showDisplayId);
+
+		return builder.build();
+	}
+
+	@Override
+	public void save() {
+		int seqBehavior = 0;
+		if (seqAskUser.isSelected()) {
+			seqBehavior = 0;
+		} else if (seqOverwrite.isSelected()) {
+			seqBehavior = 1;
+		} else if (seqKeep.isSelected()) {
+			seqBehavior = 2;
+		}
+		IBioSimPreferences.INSTANCE.setSeqBehavior(seqBehavior);
+
+		int showNameOrDisplayId = 0;
+		if (showName.isSelected()) {
+			showNameOrDisplayId = 0;
+		} else if (showDisplayId.isSelected()) {
+			showNameOrDisplayId = 1;
+		}
+		IBioSimPreferences.INSTANCE.setNameDisplayIdBehavior(showNameOrDisplayId);
+	}
+
+	@Override
+	public boolean requiresRestart() {
+		return false;
+	}
+}

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

@@ -0,0 +1,98 @@
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
+
+import java.awt.Component;
+
+import javax.swing.ButtonGroup;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JLabel;
+import javax.swing.JRadioButton;
+
+import edu.utah.ece.async.ibiosim.dataModels.util.IBioSimPreferences;
+import edu.utah.ece.async.ibiosim.gui.ResourceManager;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog.PreferencesTab;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Images;
+import edu.utah.ece.async.sboldesigner.swing.FormBuilder;
+
+public enum PartEditorPreferencesTab implements PreferencesTab {
+	INSTANCE;
+
+	// askUser is 0, overwrite is 1, and keep is 2
+	private JRadioButton seqAskUser = new JRadioButton("Ask", IBioSimPreferences.INSTANCE.getSeqBehavior() == 0);
+	private JRadioButton seqOverwrite = new JRadioButton("Overwrite",
+			IBioSimPreferences.INSTANCE.getSeqBehavior() == 1);
+	private JRadioButton seqKeep = new JRadioButton("Keep", IBioSimPreferences.INSTANCE.getSeqBehavior() == 2);
+
+	// show name is 0, show displayId is 1
+	private JRadioButton showName = new JRadioButton("Show name when set",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 0);
+	private JRadioButton showDisplayId = new JRadioButton("Show displayId",
+			IBioSimPreferences.INSTANCE.getNameDisplayIdBehavior() == 1);
+
+	@Override
+	public String getTitle() {
+		return "Part Editor";
+	}
+
+	@Override
+	public String getDescription() {
+		return "Settings for SBOLDesigner Plugin";
+	}
+
+	@Override
+	public Icon getIcon() {
+		return ResourceManager.getImageIcon("sbol.jpg");
+	}
+
+	@Override
+	public Component getComponent() {
+		JLabel impliedSequence = new JLabel(
+				"<html>Every time the implied sequence is shorter than the original <br>sequence, would you like to overwrite or keep the original sequence?</html>");
+		ButtonGroup seqGroup = new ButtonGroup();
+		seqGroup.add(seqAskUser);
+		seqGroup.add(seqOverwrite);
+		seqGroup.add(seqKeep);
+
+		JLabel showNameOrDisplayId = new JLabel("<html>Always show displayId or always show name when set?</html>");
+		ButtonGroup nameDisplayIdGroup = new ButtonGroup();
+		nameDisplayIdGroup.add(showName);
+		nameDisplayIdGroup.add(showDisplayId);
+
+		FormBuilder builder = new FormBuilder();
+		builder.add("", impliedSequence);
+		builder.add("", seqAskUser);
+		builder.add("", seqOverwrite);
+		builder.add("", seqKeep);
+		builder.add("", showNameOrDisplayId);
+		builder.add("", showName);
+		builder.add("", showDisplayId);
+
+		return builder.build();
+	}
+
+	@Override
+	public void save() {
+		int seqBehavior = 0;
+		if (seqAskUser.isSelected()) {
+			seqBehavior = 0;
+		} else if (seqOverwrite.isSelected()) {
+			seqBehavior = 1;
+		} else if (seqKeep.isSelected()) {
+			seqBehavior = 2;
+		}
+		IBioSimPreferences.INSTANCE.setSeqBehavior(seqBehavior);
+
+		int showNameOrDisplayId = 0;
+		if (showName.isSelected()) {
+			showNameOrDisplayId = 0;
+		} else if (showDisplayId.isSelected()) {
+			showNameOrDisplayId = 1;
+		}
+		IBioSimPreferences.INSTANCE.setNameDisplayIdBehavior(showNameOrDisplayId);
+	}
+
+	@Override
+	public boolean requiresRestart() {
+		return false;
+	}
+}

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

@@ -0,0 +1,167 @@
+/*
+ * Copyright (c) 2012 - 2015, Clark & Parsia, LLC. <http://www.clarkparsia.com>
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
+
+import java.awt.BorderLayout;
+import java.awt.CardLayout;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyEvent;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.DefaultListModel;
+import javax.swing.Icon;
+import javax.swing.JButton;
+import javax.swing.JComponent;
+import javax.swing.JDialog;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.KeyStroke;
+import javax.swing.ListSelectionModel;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+
+import com.google.common.base.Objects;
+
+/**
+ * 
+ * @author Evren Sirin
+ */
+public class PreferencesDialog extends JDialog implements ActionListener {
+	private static final String TITLE = "Preferences";
+
+	private static final PreferencesTab[] TABS = { UserInfoTab.INSTANCE, RegistryPreferencesTab.INSTANCE,
+			GeneralPreferencesTab.INSTANCE, PartEditorPreferencesTab.INSTANCE, ModelEditorPreferencesTab.INSTANCE, 
+			ModelPreferencesTab.INSTANCE, AnalysisPreferencesTab.INSTANCE, LearnPreferencesTab.INSTANCE 
+			/**
+			 * SOMappingTab.INSTANCE,
+			 * VersioningPreferencesTab.INSTANCE
+			 **/
+	};
+
+	public static void showPreferences(Component parent) {
+		showPreferences(parent, null);
+	}
+
+	public static void showPreferences(Component parent, String selectTab) {
+		PreferencesDialog dialog = new PreferencesDialog(parent, selectTab);
+		dialog.setVisible(true);
+	}
+
+	private PreferencesDialog(Component parent, String selectTab) {
+		super(JOptionPane.getFrameForComponent(parent), TITLE, true);
+
+		final JButton closeButton = new JButton("Close");
+		closeButton.addActionListener(this);
+		closeButton.registerKeyboardAction(this, KeyStroke.getKeyStroke(KeyEvent.VK_ESCAPE, 0),
+				JComponent.WHEN_IN_FOCUSED_WINDOW);
+		getRootPane().setDefaultButton(closeButton);
+
+		// Create the panel that contains the "cards".
+		final JPanel cards = new JPanel(new CardLayout());
+		DefaultListModel<PreferencesTab> listModel = new DefaultListModel<PreferencesTab>();
+		int selectedIndex = 0;
+		for (PreferencesTab tab : TABS) {
+			cards.add(new JScrollPane(tab.getComponent()), tab.getTitle());
+			if (Objects.equal(tab.getTitle(), selectTab)) {
+				selectedIndex = listModel.size();
+			}
+			listModel.addElement(tab);
+		}
+
+		final JList<PreferencesTab> list = new JList<PreferencesTab>(listModel);
+		list.setFocusable(false);
+		list.setPreferredSize(new Dimension(100, 100));
+		list.setCellRenderer(new DefaultListCellRenderer() {
+			public Component getListCellRendererComponent(JList<?> list, // the
+																			// list
+					Object value, // value to display
+					int index, // cell index
+					boolean isSelected, // is the cell selected
+					boolean cellHasFocus) // does the cell have focus
+			{
+				super.getListCellRendererComponent(list, value, index, isSelected, cellHasFocus);
+				PreferencesTab tab = (PreferencesTab) value;
+				setText(tab.getTitle());
+				setIcon(tab.getIcon());
+				setToolTipText(tab.getDescription());
+				return this;
+			}
+		});
+
+		list.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+		list.addListSelectionListener(new ListSelectionListener() {
+			@Override
+			public void valueChanged(ListSelectionEvent event) {
+				if (!event.getValueIsAdjusting()) {
+					CardLayout layout = (CardLayout) cards.getLayout();
+					layout.show(cards, ((PreferencesTab) list.getSelectedValue()).getTitle());
+				}
+			}
+		});
+		list.setSelectedIndex(selectedIndex);
+
+		JPanel buttonPane = new JPanel();
+		buttonPane.setLayout(new BoxLayout(buttonPane, BoxLayout.LINE_AXIS));
+		buttonPane.setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10));
+		buttonPane.add(Box.createHorizontalGlue());
+		buttonPane.add(closeButton);
+
+		Container contentPane = getContentPane();
+		contentPane.add(new JScrollPane(list), BorderLayout.WEST);
+		contentPane.add(cards, BorderLayout.CENTER);
+		contentPane.add(buttonPane, BorderLayout.SOUTH);
+
+		setSize(600, 450);
+		setLocationRelativeTo(getOwner());
+	}
+
+	public void actionPerformed(ActionEvent e) {
+		boolean restart = false;
+		for (PreferencesTab tab : TABS) {
+			restart = tab.requiresRestart();
+			tab.save();
+		}
+
+		if (restart) {
+			JOptionPane.showMessageDialog(this, "Your changes will take effect next time the program is started");
+		}
+
+		setVisible(false);
+	}
+
+	interface PreferencesTab {
+		String getTitle();
+
+		String getDescription();
+
+		Icon getIcon();
+
+		Component getComponent();
+
+		void save();
+
+		boolean requiresRestart();
+	}
+}

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

@@ -0,0 +1,246 @@
+/*
+ * Copyright (c) 2012 - 2015, Clark & Parsia, LLC. <http://www.clarkparsia.com>
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.Container;
+import java.awt.Dimension;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.BoxLayout;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTable;
+import javax.swing.ListSelectionModel;
+import javax.swing.event.ListSelectionEvent;
+import javax.swing.event.ListSelectionListener;
+import javax.swing.table.AbstractTableModel;
+import javax.swing.table.TableRowSorter;
+
+import edu.utah.ece.async.ibiosim.gui.ResourceManager;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog.PreferencesTab;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Images;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Registries;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Registry;
+import edu.utah.ece.async.sboldesigner.sbol.editor.dialog.RegistryAddDialog;
+
+public enum RegistryPreferencesTab implements PreferencesTab {
+	INSTANCE;
+
+	@Override
+	public String getTitle() {
+		return "Registries";
+	}
+
+	@Override
+	public String getDescription() {
+		return "Configuration options for part registries";
+	}
+
+	@Override
+	public Icon getIcon() {
+		return ResourceManager.getImageIcon("registry.png");
+	}
+
+	@Override
+	public Component getComponent() {
+		final RegistryTableModel tableModel = new RegistryTableModel();
+		final JTable table = new JTable(tableModel);
+		table.setSelectionMode(ListSelectionModel.SINGLE_SELECTION);
+
+		ActionListener listener = new ActionListener() {
+			public void actionPerformed(ActionEvent e) {
+				RegistryTableModel model = (RegistryTableModel) table.getModel();
+				Action action = Action.valueOf(e.getActionCommand());
+				switch (action) {
+				case ADD:
+					Registry registry = new RegistryAddDialog(table, null).getInput();
+					if (registry != null) {
+						model.add(registry);
+						Registries.get().save();
+					}
+					break;
+				case REMOVE:
+					int row = table.convertRowIndexToModel(table.getSelectedRow());
+					model.remove(row);
+					Registries.get().save();
+					break;
+				case RESTORE:
+					model.restoreDefaults();
+					Registries.get().save();
+					break;
+				case EDIT:
+					row = table.convertRowIndexToModel(table.getSelectedRow());
+					if (row > model.getRowCount()) {
+						return;
+					} else {
+						Registry oldRegistry = model.getComponent(row);
+						registry = new RegistryAddDialog(table, oldRegistry).getInput();
+						if (registry != null) {
+							model.remove(row);
+							model.add(registry);
+							Registries.get().save();
+						}
+					}
+					break;
+				}
+			}
+		};
+
+		final JButton addButton = new JButton("Add");
+		addButton.setActionCommand(Action.ADD.toString());
+		addButton.addActionListener(listener);
+
+		final JButton editButton = new JButton("Edit");
+		editButton.setActionCommand(Action.EDIT.toString());
+		editButton.addActionListener(listener);
+		editButton.setEnabled(false);
+
+		final JButton removeButton = new JButton("Remove");
+		removeButton.setActionCommand(Action.REMOVE.toString());
+		removeButton.addActionListener(listener);
+		removeButton.setEnabled(false);
+
+		final JButton restoreButton = new JButton("Restore defaults");
+		restoreButton.setActionCommand(Action.RESTORE.toString());
+		restoreButton.addActionListener(listener);
+		restoreButton.setEnabled(true);
+
+		table.getSelectionModel().addListSelectionListener(new ListSelectionListener() {
+			@Override
+			public void valueChanged(ListSelectionEvent event) {
+				// Everything can be removed/edited except Built-In parts.
+				removeButton.setEnabled(table.getSelectedRow() >= 2);
+				editButton.setEnabled(table.getSelectedRow() >= 2);
+			}
+		});
+
+		//OldInputDialog.setWidthAsPercentages(table, 0.2, 0.2, 0.6);
+
+		TableRowSorter<RegistryTableModel> sorter = new TableRowSorter<RegistryTableModel>(tableModel);
+		table.setRowSorter(sorter);
+
+		JScrollPane tableScroller = new JScrollPane(table);
+		tableScroller.setPreferredSize(new Dimension(450, 200));
+		tableScroller.setAlignmentX(Component.LEFT_ALIGNMENT);
+
+		JPanel tablePane = new JPanel();
+		tablePane.setLayout(new BoxLayout(tablePane, BoxLayout.PAGE_AXIS));
+		JLabel label = new JLabel("Registry list");
+		label.setLabelFor(table);
+		tablePane.add(label);
+		tablePane.add(Box.createRigidArea(new Dimension(0, 5)));
+		tablePane.add(tableScroller);
+		tablePane.setBorder(BorderFactory.createEmptyBorder(10, 10, 10, 10));
+
+		JPanel buttonPane = new JPanel();
+		buttonPane.setLayout(new BoxLayout(buttonPane, BoxLayout.LINE_AXIS));
+		buttonPane.setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10));
+		buttonPane.add(addButton);
+		buttonPane.add(editButton);
+		buttonPane.add(removeButton);
+		buttonPane.add(Box.createHorizontalGlue());
+		buttonPane.add(restoreButton);
+
+		Container contentPane = new JPanel(new BorderLayout());
+		contentPane.add(tablePane, BorderLayout.CENTER);
+		contentPane.add(buttonPane, BorderLayout.SOUTH);
+		return contentPane;
+	}
+
+	@Override
+	public void save() {
+	}
+
+	@Override
+	public boolean requiresRestart() {
+		return false;
+	}
+
+	private static enum Action {
+		ADD, REMOVE, RESTORE, EDIT
+	}
+
+	private static class RegistryTableModel extends AbstractTableModel {
+		private static final String[] COLUMNS = { "Name", "URL/Path", "Description" };
+		private Registries registries;
+
+		public RegistryTableModel() {
+			this.registries = Registries.get();
+		}
+
+		public void restoreDefaults() {
+			registries.restoreDefaults();
+			fireTableDataChanged();
+		}
+
+		public void add(Registry registry) {
+			registries.add(registry);
+			fireTableDataChanged();
+		}
+
+		public void remove(int row) {
+			registries.remove(row);
+			fireTableDataChanged();
+		}
+
+		public int getColumnCount() {
+			return COLUMNS.length;
+		}
+
+		public int getRowCount() {
+			return registries.size();
+		}
+
+		public String getColumnName(int col) {
+			return COLUMNS[col];
+		}
+
+		public Registry getComponent(int row) {
+			return registries.get(row);
+		}
+
+		public Object getValueAt(int row, int col) {
+			Registry registry = getComponent(row);
+			switch (col) {
+			case 0:
+				return registry.getName();
+			case 1:
+				return registry.getLocation();
+			case 2:
+				return registry.getDescription();
+			default:
+				throw new IndexOutOfBoundsException();
+			}
+		}
+
+		public Class<?> getColumnClass(int col) {
+			return Object.class;
+		}
+
+		public boolean isCellEditable(int row, int col) {
+			return false;
+		}
+	}
+}

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

@@ -0,0 +1,117 @@
+/*
+ * Copyright (c) 2012 - 2015, Clark & Parsia, LLC. <http://www.clarkparsia.com>
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package edu.utah.ece.async.ibiosim.gui.util.preferences;
+
+import java.awt.BorderLayout;
+import java.awt.Component;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.net.URI;
+
+import javax.swing.BorderFactory;
+import javax.swing.Box;
+import javax.swing.Icon;
+import javax.swing.ImageIcon;
+import javax.swing.JButton;
+import javax.swing.JPanel;
+import javax.swing.JTextField;
+
+import com.google.common.base.Strings;
+
+import edu.utah.ece.async.ibiosim.dataModels.util.IBioSimPreferences;
+import edu.utah.ece.async.ibiosim.dataModels.util.Infos;
+import edu.utah.ece.async.ibiosim.dataModels.util.PersonInfo;
+import edu.utah.ece.async.ibiosim.gui.ResourceManager;
+import edu.utah.ece.async.ibiosim.gui.util.preferences.PreferencesDialog.PreferencesTab;
+import edu.utah.ece.async.sboldesigner.sbol.editor.Images;
+import edu.utah.ece.async.sboldesigner.swing.FormBuilder;
+
+public enum UserInfoTab implements PreferencesTab {
+	INSTANCE;
+
+	private JTextField name;
+	private JTextField email;
+	private JTextField uri;
+
+	@Override
+	public String getTitle() {
+		return "User";
+	}
+
+	@Override
+	public String getDescription() {
+		return "User information added to designs";
+	}
+
+	@Override
+	public Icon getIcon() {
+		return ResourceManager.getImageIcon("user.png");
+	}
+
+	@Override
+	public Component getComponent() {
+		PersonInfo info = IBioSimPreferences.INSTANCE.getUserInfo();
+		FormBuilder builder = new FormBuilder();
+		name = builder.addTextField("Full name", info == null ? null : info.getName());
+		email = builder.addTextField("Email",
+				info == null || info.getEmail() == null ? null : info.getEmail().toString());
+		uri = builder.addTextField("Namespace [required]", info == null ? null : info.getURI().toString());
+		JPanel formPanel = builder.build();
+
+		JButton deleteInfo = new JButton("Delete user info");
+		deleteInfo.addActionListener(new ActionListener() {
+			@Override
+			public void actionPerformed(ActionEvent e) {
+				PersonInfo userInfo = Infos.forPerson(uri.getText());
+				IBioSimPreferences.INSTANCE.saveUserInfo(userInfo);
+				name.setText(null);
+				email.setText(null);
+			}
+		});
+		deleteInfo.setAlignmentX(Component.RIGHT_ALIGNMENT);
+		deleteInfo.setEnabled(info != null);
+
+		Box buttonPanel = Box.createHorizontalBox();
+		buttonPanel.setBorder(BorderFactory.createEmptyBorder(0, 10, 10, 10));
+		buttonPanel.add(Box.createHorizontalGlue());
+		buttonPanel.add(deleteInfo);
+
+		JPanel p = new JPanel(new BorderLayout());
+		p.add(formPanel, BorderLayout.NORTH);
+		p.add(buttonPanel, BorderLayout.SOUTH);
+
+		return p;
+	}
+
+	@Override
+	public void save() {
+		boolean noURI = Strings.isNullOrEmpty(uri.getText());
+		boolean noName = Strings.isNullOrEmpty(name.getText());
+		boolean noEmail = Strings.isNullOrEmpty(email.getText());
+		if (!(noURI && noName && noEmail)) {
+			URI personURI = URI.create(uri.getText());
+			String personName = noName ? "" : name.getText();
+			String personEmail = noEmail ? null : email.getText();
+			PersonInfo info = Infos.forPerson(personURI, personName, personEmail);
+			IBioSimPreferences.INSTANCE.saveUserInfo(info);
+		}
+	}
+
+	@Override
+	public boolean requiresRestart() {
+		return false;
+	}
+}

manifast

@@ -0,0 +1,2 @@
+Manifest-Version: 1.0
+