Moved static variables from the KEGGtranslator interface to the actua…

…l main class "Translator.java".

src/de/zbit/kegg/Translator.java

@@ -56,11 +56,39 @@
  * @version $Rev$
  */
 public class Translator {
+
+  /**
+   * Filename of the KEGG cache file (implemented just
+   * like the browser cache). Must be loaded upon start
+   * and saved upon exit.
+   */
+  public final static String cacheFileName = "keggdb.dat";
+
+  /**
+   * Filename of the KEGG function cache file (implemented just
+   * like the browser cache). Must be loaded upon start
+   * and saved upon exit.
+   */  
+  public final static String cacheFunctionFileName = "keggfc.dat";
+
+  /**
+   * The name of the application.
+   * Removed the final attribute, such that referencing applications can still change this.
+   */
+  public static String APPLICATION_NAME = "KEGGtranslator";
+
+  /**
+   * Version number of this translator
+   */
+  public static final String VERSION_NUMBER = "1.2.0";
+
+
   /**
    * The cache to be used by all KEGG interacting classes.
    * Access via {@link #getManager()}.
    */
   private static KeggInfoManagement manager=null;
+
   /**
    * The cache to be used by all KEGG-Functions interacting classes.
    * Access via {@link #getFunctionManager()}.
@@ -201,14 +229,14 @@ public static boolean translate(Format format, String input, String output)
 	public synchronized static KeggInfoManagement getManager() {
 
 	  // Try to load from cache file
-		if (manager==null && new File(KEGGtranslator.cacheFileName).exists() && new File(KEGGtranslator.cacheFileName).length() > 0) {
+		if (manager==null && new File(Translator.cacheFileName).exists() && new File(Translator.cacheFileName).length() > 0) {
 			try {
-				manager = (KeggInfoManagement) KeggInfoManagement.loadFromFilesystem(KEGGtranslator.cacheFileName);
+				manager = (KeggInfoManagement) KeggInfoManagement.loadFromFilesystem(Translator.cacheFileName);
 			} catch (Throwable e) { // IOException or class cast, if class is moved.
 			  e.printStackTrace();
 			  // Delete invalid cache file
 			  try {
-			    File f = new File(KEGGtranslator.cacheFileName);
+			    File f = new File(Translator.cacheFileName);
 			    if (f.exists() && f.canRead()) {
 			      System.out.println("Deleting invalid cache file " + f.getName());
 			      f.delete();
@@ -229,15 +257,15 @@ public synchronized static KeggInfoManagement getManager() {
 	 public synchronized static KeggFunctionManagement getFunctionManager() {
 
 	    // Try to load from cache file
-	    if (managerFunction==null && new File(KEGGtranslator.cacheFunctionFileName).exists() && new File(KEGGtranslator.cacheFunctionFileName).length() > 0) {
+	    if (managerFunction==null && new File(Translator.cacheFunctionFileName).exists() && new File(Translator.cacheFunctionFileName).length() > 0) {
 	      try {
-	        managerFunction = (KeggFunctionManagement) KeggFunctionManagement.loadFromFilesystem(KEGGtranslator.cacheFunctionFileName);
+	        managerFunction = (KeggFunctionManagement) KeggFunctionManagement.loadFromFilesystem(Translator.cacheFunctionFileName);
 	      } catch (Throwable e) { // IOException or class cast, if class is moved.
 	        e.printStackTrace();
 
 	        // Delete invalid cache file
 	        try {
-	          File f = new File(KEGGtranslator.cacheFunctionFileName);
+	          File f = new File(Translator.cacheFunctionFileName);
 	          if (f.exists() && f.canRead()) {
 	            System.out.println("Deleting invalid cache file " + f.getName());
 	            f.delete();
@@ -259,10 +287,10 @@ public synchronized static KeggFunctionManagement getFunctionManager() {
 	 */
 	public synchronized static void saveCache() {
     if (manager!=null && manager.hasChanged()) {
-      KeggInfoManagement.saveToFilesystem(KEGGtranslator.cacheFileName, manager);
+      KeggInfoManagement.saveToFilesystem(Translator.cacheFileName, manager);
     }
     if (managerFunction!=null && managerFunction.isCacheChangedSinceLastLoading()) {
-      KeggFunctionManagement.saveToFilesystem(KEGGtranslator.cacheFunctionFileName, managerFunction);
+      KeggFunctionManagement.saveToFilesystem(Translator.cacheFunctionFileName, managerFunction);
     }
 	}
 

src/de/zbit/kegg/ext/RestrictedEditMode.java

@@ -70,10 +70,10 @@
 import y.view.Overview;
 import de.zbit.gui.GUITools;
 import de.zbit.gui.SystemBrowser;
+import de.zbit.kegg.Translator;
 import de.zbit.kegg.TranslatorTools;
 import de.zbit.kegg.io.KEGG2jSBML;
 import de.zbit.kegg.io.KEGG2yGraph;
-import de.zbit.kegg.io.KEGGtranslator;
 import de.zbit.util.EscapeChars;
 import de.zbit.util.StringUtil;
 
@@ -231,7 +231,7 @@ public void mouseClicked(double x, double y) {
       String kgId = TranslatorTools.getKeggIDs(n);
       if (kgId.toLowerCase().startsWith("path:")) {
         int ret = GUITools.showQuestionMessage(null, "Do you want to download and open the referenced pathway in a new tab?", 
-          KEGGtranslator.APPLICATION_NAME, new String[]{"Yes", "No"});
+          Translator.APPLICATION_NAME, new String[]{"Yes", "No"});
         if (ret==0) {
           ActionEvent e = new ActionEvent(kgId.trim().substring(5).toLowerCase(), JOptionPane.OK_OPTION, OPEN_PATHWAY);
           aListener.actionPerformed(e);

src/de/zbit/kegg/ext/TranslatorPanelOptions.java

@@ -20,8 +20,8 @@
  */
 package de.zbit.kegg.ext;
 
+import de.zbit.kegg.Translator;
 import de.zbit.kegg.gui.TranslatorPanel;
-import de.zbit.kegg.io.KEGGtranslator;
 import de.zbit.util.prefs.KeyProvider;
 import de.zbit.util.prefs.Option;
 import de.zbit.util.prefs.OptionGroup;
@@ -39,7 +39,7 @@ public abstract interface TranslatorPanelOptions extends KeyProvider{
    * as background image.
    */
   public static final Option<Boolean> SHOW_LOGO_IN_GRAPH_BACKGROUND = new Option<Boolean>("SHOW_LOGO_IN_GRAPH_BACKGROUND",Boolean.class,
-      "If true, shows the " + KEGGtranslator.APPLICATION_NAME + " logo in the background of each graph.", false);
+      "If true, shows the " + Translator.APPLICATION_NAME + " logo in the background of each graph.", false);
 
   /**
    * Shows an overview and navigation panel in every graph frame.

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

@@ -72,7 +72,6 @@
 import de.zbit.kegg.io.BatchKEGGtranslator;
 import de.zbit.kegg.io.KEGG2jSBML;
 import de.zbit.kegg.io.KEGG2yGraph;
-import de.zbit.kegg.io.KEGGtranslator;
 import de.zbit.kegg.io.KEGGtranslatorIOOptions;
 import de.zbit.kegg.io.KEGGtranslatorIOOptions.Format;
 import de.zbit.util.AbstractProgressBar;
@@ -431,7 +430,7 @@ private static AbstractProgressBar generateLoadingPanel(Container parent, String
     } else {
       // Display the panel in an jFrame
       JDialog f = new JDialog();
-      f.setTitle(KEGGtranslator.APPLICATION_NAME);
+      f.setTitle(Translator.APPLICATION_NAME);
       f.setSize(panel.getPreferredSize());
       f.setContentPane(panel);
       f.setPreferredSize(panel.getPreferredSize());
@@ -604,7 +603,7 @@ public void updateButtons(JMenuBar menuBar) {
   public void writeLaTeXReport(File targetFile) {
     if (document==null) return;
     if (!isSBML()) {
-      GUITools.showMessage("This option is only available for SBML documents.", KEGGtranslator.APPLICATION_NAME);
+      GUITools.showMessage("This option is only available for SBML documents.", Translator.APPLICATION_NAME);
       return;
     }
 

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

@@ -62,7 +62,6 @@
 import de.zbit.gui.prefs.PreferencesPanel;
 import de.zbit.kegg.Translator;
 import de.zbit.kegg.ext.RestrictedEditMode;
-import de.zbit.kegg.io.KEGGtranslator;
 import de.zbit.kegg.io.KEGGtranslatorIOOptions;
 import de.zbit.kegg.io.KEGGtranslatorIOOptions.Format;
 import de.zbit.util.AbstractProgressBar;
@@ -105,7 +104,7 @@ public static enum Action implements ActionCommand {
 		/**
 		 * This is coming from {@link RestrictedEditMode#OPEN_PATHWAY} and must be
 		 * renamed accordingly. The source is a kegg pathway id that should be opened
-		 * as new tab, when this action is fired.
+		 * as new tab, when this action is fired. This is an invisible action.
 		 */
 		OPEN_PATHWAY,
 		/**
@@ -325,15 +324,15 @@ private void createNewTab(File inFile, String format) {
 		  if (inFile!=null) {
 		    message = '\'' + inFile.getName() + "' is no valid input file.";
 		  }
-			JOptionPane.showMessageDialog(this, message, KEGGtranslator.APPLICATION_NAME, JOptionPane.WARNING_MESSAGE);
+			JOptionPane.showMessageDialog(this, message, Translator.APPLICATION_NAME, JOptionPane.WARNING_MESSAGE);
 		} else {
 			Format f = null;
 			try {
 				f = Format.valueOf(format);
 			} catch (Throwable exc) {
 			  exc.printStackTrace();
 				JOptionPane.showMessageDialog(this, '\'' + format + "' is no valid output format.",
-						KEGGtranslator.APPLICATION_NAME, JOptionPane.WARNING_MESSAGE);
+						Translator.APPLICATION_NAME, JOptionPane.WARNING_MESSAGE);
 			}
 			if (f != null) {
 				// Tanslate and add tab.
@@ -476,7 +475,7 @@ public File[] openFile(File... files) {
     if ( askOutputFormat || (format == null) || (format.length() < 1)) {
       JLabeledComponent outputFormat = (JLabeledComponent) PreferencesPanel.getJComponentForOption(KEGGtranslatorIOOptions.FORMAT, prefsIO, null);
       outputFormat.setTitle("Please select the output format");
-      JOptionPane.showMessageDialog(this, outputFormat, KEGGtranslator.APPLICATION_NAME, JOptionPane.QUESTION_MESSAGE);
+      JOptionPane.showMessageDialog(this, outputFormat, Translator.APPLICATION_NAME, JOptionPane.QUESTION_MESSAGE);
       format =  outputFormat.getSelectedItem().toString();
     }
 
@@ -718,7 +717,7 @@ public URL getURLOnlineHelp() {
 	 * @see de.zbit.gui.BaseFrame#getApplicationName()
 	 */
 	public String getApplicationName() {
-		return KEGGtranslator.APPLICATION_NAME;
+		return Translator.APPLICATION_NAME;
 	}
 
 	/*
@@ -727,7 +726,7 @@ public String getApplicationName() {
 	 * @see de.zbit.gui.BaseFrame#getDottedVersionNumber()
 	 */
 	public String getDottedVersionNumber() {
-		return KEGGtranslator.VERSION_NUMBER;
+		return Translator.VERSION_NUMBER;
 	}
 
 	/*

src/de/zbit/kegg/io/KEGG2jSBML.java

@@ -48,6 +48,7 @@
 import de.zbit.kegg.KEGGtranslatorOptions;
 import de.zbit.kegg.KeggInfoManagement;
 import de.zbit.kegg.KeggInfos;
+import de.zbit.kegg.Translator;
 import de.zbit.kegg.io.KEGGtranslatorIOOptions.Format;
 import de.zbit.kegg.parser.KeggParser;
 import de.zbit.kegg.parser.pathway.Entry;
@@ -315,7 +316,7 @@ public boolean writeToFile(SBMLDocument doc, String outFile) {
     if (new File(outFile).exists()) lastFileWasOverwritten=true;
     try {
       SBMLWriter writer = new SBMLWriter();
-      writer.write(doc, outFile, KEGGtranslator.APPLICATION_NAME, KEGGtranslator.VERSION_NUMBER);
+      writer.write(doc, outFile, Translator.APPLICATION_NAME, Translator.VERSION_NUMBER);
     } catch (Exception e) {
       e.printStackTrace();
       return false;
@@ -434,7 +435,7 @@ protected SBMLDocument translateWithoutPreprocessing(Pathway p) {
       notes.append("</p>");
     }
     notes.append(String.format("<div align=\"right\"><i><small>This file has been generated by %s version %s</small></i></div><br/>\n", 
-      KEGGtranslator.APPLICATION_NAME, VERSION_NUMBER));
+      Translator.APPLICATION_NAME, Translator.VERSION_NUMBER));
 
     // Save all reaction modifiers in a list. String = reaction id.
     SortedArrayList<Info<String, ModifierSpeciesReference>> reactionModifiers = new SortedArrayList<Info<String, ModifierSpeciesReference>>();
@@ -1177,9 +1178,9 @@ public static void main(String[] args) throws IOException {
     // Speedup Kegg2SBML by loading alredy queried objects. Reduces network
     // load and heavily reduces computation time.
     AbstractKEGGtranslator<SBMLDocument> k2s;
-    if (new File(KEGGtranslator.cacheFileName).exists()
-        && new File(KEGGtranslator.cacheFileName).length() > 0) {
-      KeggInfoManagement manager = (KeggInfoManagement) KeggInfoManagement.loadFromFilesystem(KEGGtranslator.cacheFileName);
+    if (new File(Translator.cacheFileName).exists()
+        && new File(Translator.cacheFileName).length() > 0) {
+      KeggInfoManagement manager = (KeggInfoManagement) KeggInfoManagement.loadFromFilesystem(Translator.cacheFileName);
       k2s = new KEGG2jSBML(manager);
     } else {
       k2s = new KEGG2jSBML();
@@ -1211,7 +1212,7 @@ && new File(KEGGtranslator.cacheFileName).length() > 0) {
 
       // Remember already queried objects (save cache)
       if (k2s.getKeggInfoManager().hasChanged()) {
-        KeggInfoManagement.saveToFilesystem(KEGGtranslator.cacheFileName, k2s.getKeggInfoManager());
+        KeggInfoManagement.saveToFilesystem(Translator.cacheFileName, k2s.getKeggInfoManager());
       }
 
       return;
@@ -1228,7 +1229,7 @@ && new File(KEGGtranslator.cacheFileName).length() > 0) {
 
       // Remember already queried objects
       if (k2s.getKeggInfoManager().hasChanged()) {
-        KeggInfoManagement.saveToFilesystem(KEGGtranslator.cacheFileName, k2s.getKeggInfoManager());
+        KeggInfoManagement.saveToFilesystem(Translator.cacheFileName, k2s.getKeggInfoManager());
       }
 
     } catch (Exception e) {

src/de/zbit/kegg/io/KEGG2yGraph.java

@@ -69,9 +69,10 @@
 import y.view.ShapeNodeRealizer;
 import y.view.hierarchy.GroupNodeRealizer;
 import y.view.hierarchy.HierarchyManager;
+import de.zbit.kegg.KEGGtranslatorOptions;
 import de.zbit.kegg.KeggInfoManagement;
 import de.zbit.kegg.KeggInfos;
-import de.zbit.kegg.KEGGtranslatorOptions;
+import de.zbit.kegg.Translator;
 import de.zbit.kegg.ext.GenericDataMap;
 import de.zbit.kegg.io.KEGGtranslatorIOOptions.Format;
 import de.zbit.kegg.parser.KeggParser;
@@ -1202,9 +1203,9 @@ public static KEGG2yGraph createKEGG2YGF(KeggInfoManagement manager) {
    */
   public static void main(String[] args) throws IOException {
     KeggInfoManagement manager;
-    if (new File(KEGGtranslator.cacheFileName).exists()
-        && new File(KEGGtranslator.cacheFileName).length() > 0) {
-      manager = (KeggInfoManagement) KeggInfoManagement.loadFromFilesystem(KEGGtranslator.cacheFileName);
+    if (new File(Translator.cacheFileName).exists()
+        && new File(Translator.cacheFileName).length() > 0) {
+      manager = (KeggInfoManagement) KeggInfoManagement.loadFromFilesystem(Translator.cacheFileName);
     } else {
       manager = new KeggInfoManagement();
     }
@@ -1236,7 +1237,7 @@ && new File(KEGGtranslator.cacheFileName).length() > 0) {
 
       // Remember already queried objects (save cache)
       if (k2g.getKeggInfoManager().hasChanged()) {
-        KeggInfoManagement.saveToFilesystem(KEGGtranslator.cacheFileName, k2g.getKeggInfoManager());
+        KeggInfoManagement.saveToFilesystem(Translator.cacheFileName, k2g.getKeggInfoManager());
       }
 
       return;
@@ -1253,7 +1254,7 @@ && new File(KEGGtranslator.cacheFileName).length() > 0) {
 
       // Remember already queried objects
       if (k2g.getKeggInfoManager().hasChanged()) {
-        KeggInfoManagement.saveToFilesystem(KEGGtranslator.cacheFileName, k2g.getKeggInfoManager());
+        KeggInfoManagement.saveToFilesystem(Translator.cacheFileName, k2g.getKeggInfoManager());
       }
 
     } catch (Exception e) {

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

@@ -31,29 +31,6 @@
  */
 public interface KEGGtranslator {
 
-  /**
-   * The name of the application.
-   * Removed the final attribute, such that referencing applications can still change this.
-   */
-  public static String APPLICATION_NAME = "KEGGtranslator";
-
-  /**
-   * Version number of this translator
-   */
-  public static final String VERSION_NUMBER = "1.2.0";
-
-  /**
-   * Filename of the KEGG cache file (implemented just
-   * like the browser cache). Must be loaded upon start
-   * and saved upon exit.
-   */
-  public static String cacheFileName = "keggdb.dat";
-  /**
-   * Filename of the KEGG function cache file (implemented just
-   * like the browser cache). Must be loaded upon start
-   * and saved upon exit.
-   */  
-  public static String cacheFunctionFileName = "keggfc.dat";
 
 	/**
 	 * Translate a given KEGG Pathway and write it in the new format to outfile.

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

@@ -31,6 +31,8 @@
 import java.util.HashMap;
 import java.util.Map;
 
+import de.zbit.kegg.Translator;
+
 /**
  * This class creates an {@link OutputStream} that can be used with
  * the yFiles Java library. It ensures that KEGGtranslator name 
@@ -72,8 +74,8 @@ public YFilesWriter(OutputStream out) {
      * </ul>
      * such that no notes of yFiles are being written to the file.
 		 */
-		toReplace.put("yFiles", KEGGtranslator.APPLICATION_NAME);
-		toReplace.put(y.util.YVersion.currentVersionString(), KEGGtranslator.VERSION_NUMBER);
+		toReplace.put("yFiles", Translator.APPLICATION_NAME);
+		toReplace.put(y.util.YVersion.currentVersionString(), Translator.VERSION_NUMBER);
 
 		realOut = out;