(hopefully final commit for KEGGtranslator version 2.2.0)

- Added separate format options for SBML_L2V4 and SBML_L3V1
- Massively changed how relations are translated to BioPAX, especially in Level 3:
  o Added support for controller/control combinations
  o Added support for modified proteins with a modificaiton feature, that point to the same protein instance
  o Added complexAssembly and biochemicalReaction for some relations
  o ...
- Various other improvements to 2BioPAX translations
- Added PSI-MI and PSI-MOD ontologies
- Improved command-line usage

Author: Clemens82

src/de/zbit/kegg/Translator.java

@@ -536,5 +536,22 @@ protected boolean addCopyrightToSplashScreen() {
 	public Window initGUI(AppConf appConf) {
 		return new TranslatorUI(appConf);
 	}
+	
+	/**
+	 * Decide whether to show the gui or not.
+	 */
+	@Override
+  public boolean showsGUI() {
+    SBProperties props = getCommandLineArgs();
+    boolean showGUI = (props.size() < 1) || props.getBooleanProperty(GUIOptions.GUI);
+    if (!showGUI) {
+      // Check if an input file is given. This is required for and will trigger the command-line mode.
+      String inputFile = props.getProperty(KEGGtranslatorIOOptions.INPUT);
+      if (inputFile==null || inputFile.length()<1) {
+        showGUI = true;
+      }
+    }
+    return showGUI;
+  }
 
 }

src/de/zbit/kegg/gui/TranslatorPanelTools.java

@@ -50,7 +50,7 @@ public static TranslatorPanel<?> createPanel(final File inputFile, final Format
     TranslatorPanel<?> panel = null;
 
     switch (outputFormat) {
-      case SBML: case SBML_QUAL: case SBML_CORE_AND_QUAL: /*case LaTeX: */
+      case SBML: case SBML_QUAL: case SBML_CORE_AND_QUAL: case SBML_L2V4: case SBML_L3V1: /*case LaTeX: */
         panel = new TranslatorSBMLPanel(inputFile, outputFormat, translationResult);
         break;
 
@@ -80,7 +80,7 @@ public static TranslatorPanel<?> createPanel(final String pathwayID, final Forma
     TranslatorPanel<?> panel = null;
 
     switch (outputFormat) {
-      case SBML: case SBML_QUAL: case SBML_CORE_AND_QUAL: /*case LaTeX: */
+      case SBML: case SBML_QUAL: case SBML_CORE_AND_QUAL: case SBML_L2V4: case SBML_L3V1: /*case LaTeX: */
         panel = new TranslatorSBMLPanel(pathwayID, outputFormat, translationResult);
         break;
 

src/de/zbit/kegg/gui/TranslatorUI.java

@@ -66,6 +66,7 @@
 import de.zbit.gui.prefs.FileSelector;
 import de.zbit.gui.prefs.PreferencesPanel;
 import de.zbit.io.filefilter.SBFileFilter;
+import de.zbit.kegg.KEGGtranslatorOptions;
 import de.zbit.kegg.Translator;
 import de.zbit.kegg.ext.KEGGTranslatorPanelOptions;
 import de.zbit.kegg.io.KEGG2jSBML;
@@ -275,6 +276,11 @@ public void actionPerformed(ActionEvent e) {
 				// Get selected file and format
 				File inFile = getInputFile(r);
 				String format = getOutputFileFormat(r);
+				
+				// Check if it is conform with current settings
+				if (!checkSettingsAndIssueWarning(format)) {
+				  return;
+				}
 
 				// Translate
 				createNewTab(inFile, format);
@@ -290,8 +296,38 @@ public void actionPerformed(ActionEvent e) {
 	}
 
 	/**
+	 * Checks if the current application preferences are conform
+	 * with the currently selected format and eventually 
+	 * issues a warning.
+   * @param format
+   * @return <code>FALSE</code> if the translation should be
+   * stopped.
+   */
+  protected boolean checkSettingsAndIssueWarning(String format) {
+    
+    Format f = Format.valueOf(format);
+    if (f==null) {
+      GUITools.showErrorMessage(this, "Unknown output format: " + format);
+      return false;
+    } else if (f == Format.SBML_L2V4) {
+      // Check if Level 2 and extensions are selected.
+      SBPreferences prefs = SBPreferences.getPreferencesFor(KEGGtranslatorOptions.class);
+      if (KEGGtranslatorOptions.ADD_LAYOUT_EXTENSION.getValue(prefs) ||
+          KEGGtranslatorOptions.USE_GROUPS_EXTENSION.getValue(prefs)) {
+        String message = "SBML supports extensions since Level 3. You've chosen to translate a document to Level 2 including the layout or groups extension, what is not possible.\nDo you want to deactivate the extensions for this translation?";
+        int ret = GUITools.showQuestionMessage(this, message, "Conflict between selected Level and extension support", JOptionPane.OK_CANCEL_OPTION);
+        if (ret == JOptionPane.CANCEL_OPTION) {
+          return false;
+        }
+      }
+    }
+    
+    return true;
+  }
+
+  /**
 	 * Searches for any JComponent with
-	 * "TranslatorOptions.FORMAT.getOptionName()" on it and returns the selected
+	 * {@link KEGGtranslatorIOOptions#FORMAT}.getOptionName() on it and returns the selected
 	 * format. Use it e.g. with {@link #translateToolBar}.
 	 * 
 	 * @param r
@@ -774,7 +810,6 @@ public URL getURLOnlineHelp() {
 	/* (non-Javadoc)
 	 * @see java.beans.PropertyChangeListener#propertyChange(java.beans.PropertyChangeEvent)
 	 */
-	@Override
 	public void propertyChange(PropertyChangeEvent evt) {
 		logger.fine(evt.toString());
 	}

src/de/zbit/kegg/io/AbstractKEGGtranslator.java

@@ -802,8 +802,8 @@ protected static String firstName(String name) {
    */
   protected String NameToSId(String name) {
     /*
-     * letter ::= �a�..�z�,�A�..�Z� digit ::= �0�..�9� idChar ::= letter |
-     * digit | �_� SId ::= ( letter | �_� ) idChar*
+     * letter = a-z,A-Z; digit = 0-9; idChar = (letter | digit | _ );
+     * SId = ( letter | _ ) idChar*
      */
     String ret;
     if (name == null || name.trim().length() == 0) {
@@ -848,7 +848,7 @@ protected String NameToSId(String name) {
    * @return
    */
   private static boolean isLetter(char c) {
-    // Unfortunately Character.isLetter also acceps ß, but SBML doesn't.
+    // Unfortunately Character.isLetter also accepts ß, but SBML doesn't.
     // a-z or A-Z
     return (c>=97 && c<=122) || (c>=65 && c<=90);
   }

src/de/zbit/kegg/io/BatchKEGGtranslator.java

@@ -294,6 +294,8 @@ private boolean writeAsJPG(Object translatedDoc, Pathway originalPW, String outF
         break;
 
       case SBML:
+      case SBML_L2V4:
+      case SBML_L3V1:
         myGraph = new SBML2GraphML().createGraph((org.sbml.jsbml.SBMLDocument) translatedDoc);
         break;
 
@@ -331,6 +333,12 @@ public static KEGGtranslator<?> getTranslator(Format outFormat, KeggInfoManageme
 		case SBML:
 			translator = new KEGG2jSBML(manager);
 			break;
+	  case SBML_L2V4:
+      translator = new KEGG2jSBML(manager, 2, 4);
+      break;
+	  case SBML_L3V1:
+      translator = new KEGG2jSBML(manager, 3, 1);
+      break;
     case SBML_QUAL:
       translator = new KEGG2SBMLqual(manager);
       break;