Bug fixes, added support for L2V5, correct indentation of generated S…

…BML files, and new third-party libraries:

* New libs JSBML and SysBio
* JSBML lib is smaller in parts because unused packages are no longer in this JAR, but I added the tidy project for correct indentation.
* Fixed bugs: groups extension wasn't correctly used and duplicate ids were often generated (also in other cases).
* Bug with incorrect links; I added a replacement of ampersent characters for encoding these links.
* Added more try-catch blocks to avoid crashing of the program upon one error.

src/de/zbit/graph/SearchSupport.java

@@ -126,9 +126,9 @@ public void onGraphEvent( final GraphEvent e ) {
   }
 
   /**
-   * Returns the <code>Graph2DView</code> that is associated to the search
+   * Returns the {@code Graph2DView} that is associated to the search
    * suuport.
-   * @return the <code>Graph2DView</code> that is associated to the search
+   * @return the {@code Graph2DView} that is associated to the search
    * suuport.
    */
   public Graph2DView getView() {
@@ -464,9 +464,9 @@ public void actionPerformed( final ActionEvent e ) {
 
   /**
    * Creates a preconfigured action map for the support's
-   * <em>find next match</em> and <em>clear result</code> actions.
+   * <em>find next match</em> and <em>clear result} actions.
    * @return a preconfigured action map for the support's
-   * <em>find next match</em> and <em>clear result</code> actions.
+   * <em>find next match</em> and <em>clear result} actions.
    * @see #getClearAction()
    * @see #getNextAction()
    */
@@ -479,12 +479,12 @@ public ActionMap createActionMap() {
 
   /**
    * Creates a preconfigured input map for the support's
-   * <em>find next match</em> and <em>clear result</code> actions.
+   * <em>find next match</em> and <em>clear result} actions.
    * The default implementation maps the <em>find next match</em> action
-   * to the <code>F3</code> function key and the <em>clear search result</em>
-   * action to the <code>ESCAPE</code> key.
+   * to the {@code F3} function key and the <em>clear search result</em>
+   * action to the {@code ESCAPE} key.
    * @return a preconfigured input map for the support's
-   * <em>find next match</em> and <em>clear result</code> actions.
+   * <em>find next match</em> and <em>clear result} actions.
    * @see #getClearAction()
    * @see #getNextAction()
    */
@@ -500,7 +500,7 @@ public InputMap createDefaultInputMap() {
   private static final Color HIGHLIGHT_COLOR = new Color(202,227,255);
 
   /**
-   * <code>Drawable</code> that highlights search results by drawing a thick,
+   * {@code Drawable} that highlights search results by drawing a thick,
    * colored border around search result nodes.
    */
   private final class Marker implements Drawable {
@@ -576,7 +576,7 @@ public static final class SearchResult {
 
     /**
      * Add the specified node to the search result set.
-     * @param node   the <code>Node</code> to add.
+     * @param node   the {@code Node} to add.
      */
     void add( final Node node ) {
       nodes.add(node);
@@ -648,16 +648,16 @@ public void emphasizePrevious() {
     /**
      * Sorts the nodes in the search result set according to the order
      * induced by the specified comparator.
-     * @param c   the <code>Comparator</code> to sort the nodes in the search
+     * @param c   the {@code Comparator} to sort the nodes in the search
      * result set.
      */
     void sort( final Comparator c ) {
       nodes.sort(c);
     }
 
     /**
-     * Returns a <code>Collection</code> handle for the search result.
-     * @return a <code>Collection</code> handle for the search result.
+     * Returns a {@code Collection} handle for the search result.
+     * @return a {@code Collection} handle for the search result.
      */
     Collection asCollection() {
       return nodes;
@@ -671,9 +671,9 @@ public static interface SearchCriterion {
     /**
      * Returns {@code true} if the specified node should be included
      * in the search result and {@code false} otherwise.
-     * @param graph   the <code>Graph2D</code> to which the specified node
+     * @param graph   the {@code Graph2D} to which the specified node
      * belongs.
-     * @param node   the <code>Node</code> to test for inclusion in the
+     * @param node   the {@code Node} to test for inclusion in the
      * search result.
      * @return {@code true} if the specified node should be included
      * in the search result and {@code false} otherwise.

src/de/zbit/graph/StackingNodeLayout.java

@@ -117,7 +117,7 @@ private StackingNodeLayout(Graph2D graph, Node group, boolean recursive) {
 
   /**
    * Perform a simply stacking layout with {@link #cols} columns.
-   * @param graph graph in which <code>groupNode</code> is contained
+   * @param graph graph in which {@code groupNode} is contained
    * @param groupNode the group node whose childs should be stacked
    */
   public static void doLayout(Graph2D graph, Node groupNode) {
@@ -128,7 +128,7 @@ public static void doLayout(Graph2D graph, Node groupNode) {
    * Perform a simply stacking layout with {@link #cols} columns.
    * Perform also a stacking layout for all group nodes in this
    * group node.
-   * @param graph graph in which <code>groupNode</code> is contained
+   * @param graph graph in which {@code groupNode} is contained
    * @param groupNode the group node whose childs should be stacked
    */
   public static void doRecursiveLayout(Graph2D graph, Node groupNode) {
@@ -202,7 +202,7 @@ private void layoutGroupNode(Node group) {
 
   /**
    * @param group
-   * @return all children of the given <code>group</code> node.
+   * @return all children of the given {@code group} node.
    */
   @SuppressWarnings("unchecked")
   public List<Node> getChildren(Node group) {
@@ -220,7 +220,7 @@ public List<Node> getChildren(Node group) {
    * The order of the returned list is fixed: First grouped nodes
    * than ungrouped nodes!
    * @param group
-   * @return all children of the given <code>group</code>
+   * @return all children of the given {@code group}
    * node and all group nodes in this group node.
    */
   public List<Node> getChildrenDeep(Node group) {

src/de/zbit/kegg/Translator.java

@@ -526,7 +526,7 @@ public URL getURLOnlineUpdate() {
    */
   @Override
   public String getVersionNumber() {
-    return "2.4.0";
+    return "2.5";
   }
 
   /* (non-Javadoc)

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

@@ -55,7 +55,7 @@ public abstract interface KEGGTranslatorPanelOptions extends de.zbit.graph.gui.o
       "Select percentage for brightening the KEGG background image.", new Range<Integer>(Integer.class, "{[0,100]}"), 65, SHOW_KEGG_PICTURE_IN_GRAPH_BACKGROUND, TRUE_RANGE);
 
   /**
-   * <code>TRUE</code> if the image should be converted to a greyscale image.
+   * {@code true} if the image should be converted to a greyscale image.
    */
   public static final Option<Boolean> GREYSCALE_KEGG_BACKGROUND_IMAGE = new Option<Boolean>("GREYSCALE_KEGG_BACKGROUND_IMAGE", Boolean.class,
       "If true, converts the KEGG background image to a greyscale picture.", true, SHOW_KEGG_PICTURE_IN_GRAPH_BACKGROUND, TRUE_RANGE);

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

@@ -48,7 +48,12 @@ 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 SBML_L2V4: case SBML_L3V1: /*case LaTeX: */
+      case SBML:
+      case SBML_QUAL:
+      case SBML_CORE_AND_QUAL:
+      case SBML_L2V4:
+      case SBML_L2V5:
+      case SBML_L3V1: /*case LaTeX: */
         panel = new TranslatorSBMLPanel(inputFile, outputFormat, translationResult);
         break;
 

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

@@ -335,7 +335,7 @@ public void actionPerformed(ActionEvent e) {
    * with the currently selected format and eventually
    * issues a warning.
    * @param format
-   * @return <code>FALSE</code> if the translation should be
+   * @return {@code false} if the translation should be
    * stopped.
    */
   protected boolean checkSettingsAndIssueWarning(String format) {
@@ -412,7 +412,7 @@ private File getInputFile(JComponent r) {
 
   /**
    * A method to set the value of a currently displayed {@link FileSelector}
-   * corresponding to the <code>KEGGtranslatorIOOptions.INPUT</code> option.
+   * corresponding to the {@code KEGGtranslatorIOOptions.INPUT} option.
    * @param r the JComponent on which the component for the mentioned
    * optioned is placed.
    * @param file the file to set

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

@@ -466,10 +466,10 @@ public void translate(String infile, String outfile) throws Exception {
 
   /**
    * This method converts a given KGML file into the
-   * specified <code>OutputFormat</code>.
+   * specified {@code OutputFormat}.
    * 
    * @param f the input file.
-   * @return the generated document in <code>OutputFormat</code>.
+   * @return the generated document in {@code OutputFormat}.
    * @throws IOException if the input file is not readable.
    */
   @Override

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

@@ -350,6 +350,9 @@ public static KEGGtranslator<?> getTranslator(Format outFormat, KeggInfoManageme
       case SBML_L2V4:
         translator = new KEGG2jSBML(manager, 2, 4);
         break;
+      case SBML_L2V5:
+        translator = new KEGG2jSBML(manager, 2, 5);
+        break;
       case SBML_L3V1:
         translator = new KEGG2jSBML(manager, 3, 1);
         break;

src/de/zbit/kegg/io/KEGG2BioPAX.java

@@ -342,7 +342,7 @@ public BioPAXElement createXRef(IdentifierDatabases db, String id, int type) {
 
   /**
    * Creates a biosource, corresponding to the organism/species of
-   * the input pathway <code>p</code>.
+   * the input pathway {@code p}.
    * <p> Please call this method only once per model and save the
    * result somewhere, in case you need it multiple times.
    * 
@@ -881,7 +881,7 @@ public void createReactions(Pathway p) {
    * set.
    * <br/>But these entries might be reused in relations (i.e., relations involving
    * reactions) and thus, this method will set the custom attribute of an {@link Entry}
-   * to the BioPAX reaction given as <code>reaction</code> .
+   * to the BioPAX reaction given as {@code reaction} .
    * @param p
    * @param r KEGG reaction
    * @param reaction BioPAX reaction
@@ -1078,7 +1078,7 @@ protected BioPAXElement getInteractionVocuabulary(SubType st) {
    * This method tries to denote the vocabulary with an identifiers.org URI.
    * This has been suggested by Igor R.
    * @param st the corresponding subtype
-   * @param proteinModification {@code TRUE} ONLY for modification
+   * @param proteinModification {@code true} ONLY for modification
    * vocabularies, such as {@link SequenceModificationVocabulary}.
    * @return an RDF-ID of the vocabulary element.
    */
@@ -1155,7 +1155,7 @@ public boolean isGraphicalOutput() {
 
   /**
    * Please implement this method to add the given {@link Entry}
-   * <code>e</code> as appropriate BioPAX entity to the {@link #model}.
+   * {@code e} as appropriate BioPAX entity to the {@link #model}.
    * @param e
    * @param p
    * @return created {@link BioPAXElement}
@@ -1164,7 +1164,7 @@ public boolean isGraphicalOutput() {
 
   /**
    * Please implement this method to add the given {@link Reaction}
-   * <code>r</code> as appropriate BioPAX entity to the {@link #model}.
+   * {@code r} as appropriate BioPAX entity to the {@link #model}.
    * @param r
    * @param p
    * @return created {@link BioPAXElement}
@@ -1173,7 +1173,7 @@ public boolean isGraphicalOutput() {
 
   /**
    * Please implement this method to add the given {@link Relation}
-   * <code>r</code> as appropriate BioPAX entity to the {@link #model}.
+   * {@code r} as appropriate BioPAX entity to the {@link #model}.
    * @param r
    * @param p
    * @return created {@link BioPAXElement}

src/de/zbit/kegg/io/KEGG2BioPAX_level2.java

@@ -354,7 +354,7 @@ public BioPAXElement addEntry(Entry entry, Pathway p) {
 
   /**
    * Searches for the {@link physicalEntityParticipant} represented by the given
-   * {@link BioPAXElement} <code>ceb</code>.
+   * {@link BioPAXElement} {@code ceb}.
    * @param ceb
    * @return instance of {@link physicalEntityParticipant}
    */

src/de/zbit/kegg/io/KEGG2SBMLGroupExtension.java

@@ -31,7 +31,6 @@
 import org.sbml.jsbml.NamedSBase;
 import org.sbml.jsbml.SBMLDocument;
 import org.sbml.jsbml.ext.groups.Group;
-import org.sbml.jsbml.ext.groups.GroupKind;
 import org.sbml.jsbml.ext.groups.GroupsConstants;
 import org.sbml.jsbml.ext.groups.GroupsModelPlugin;
 import org.sbml.jsbml.ext.groups.Member;
@@ -68,42 +67,44 @@ public class KEGG2SBMLGroupExtension {
    * @param p
    * @param model
    * @param entry
+   * @param groupId
    * @return
    */
-  public static Group createGroup(Pathway p, Model model, Entry entry) {
+  public static Group createGroup(Pathway p, Model model, Entry entry, String groupId) {
     GroupsModelPlugin groupModel = getGroupsModelPlugin(model);
 
     // Get all group-members
     List<String> componentSpeciesIDs = new ArrayList<String>();
     if (entry.hasComponents()) {
-      for (int c:entry.getComponents()) {
+      for (int c : entry.getComponents()) {
         Entry ce = p.getEntryForId(c);
-        if (ce!=null && ce.getCustom()!=null && ce.getCustom() instanceof NamedSBase) {
+        if ((ce != null) && (ce.getCustom() != null) && (ce.getCustom() instanceof NamedSBase)) {
           String speciesID = ((NamedSBase)ce.getCustom()).getId();
           componentSpeciesIDs.add(speciesID);
         }
       }
     }
 
     // Create group and add all members
-    Group g = groupModel.createGroup();
+    Group g = groupModel.createGroup(groupId);
     for (String id: componentSpeciesIDs) {
-      try{
-        g.createMember(id);
+      try {
+        Member member = g.createMember(g.getId() + "_member_" + id);
+        member.setIdRef(id);
       } catch (Throwable e) {
         log.log(Level.WARNING, "Duplicated component species ID: " + id);
       }
     }
 
     // The KIND attribute is required. Possible values are listed in GroupKind
-    g.setKind(GroupKind.collection);
+    g.setKind(Group.Kind.collection);
 
     return g;
   }
 
 
   /**
-   * Clones the given group <code>g</code>
+   * Clones the given group {@code g}
    * @param id the id of the new group
    * @param g
    * @param prefixForMembers this will be prepended to all member symbols
@@ -138,7 +139,7 @@ public static Group cloneGroup(String id, Group g, String prefixForMembers) {
   }
 
   /**
-   * Duplicates all members of the given group <code>g</code> and
+   * Duplicates all members of the given group {@code g} and
    * adds a prefix to all duplicated members.
    * @param g
    * @param prefixForMembers
@@ -159,7 +160,8 @@ public static void cloneGroupComponents(Group g, String prefixForMembers) {
       if (prefixForMembers!=null) {
         if (!symbol.startsWith(prefixForMembers)) {
           symbol = prefixForMembers + symbol;
-          g.createMember(symbol);
+          Member member = g.createMember(g.getId() + "_member_" + symbol);
+          member.setIdRef(symbol);
         }
       }
     }

src/de/zbit/kegg/io/KEGG2SBMLLayoutExtension.java

@@ -135,7 +135,12 @@ public static void addLayoutExtension(Pathway p, SBMLDocument doc, Model model,
     // => track min and max values.
     MinAndMaxTracker tracker = new MinAndMaxTracker();
 
-    Map<String, Integer> idCounts = new HashMap<String, Integer>();
+    String keyWord = "KEGGtranslator_idCounts";
+    Map<String, Integer> idCounts = (Map<String, Integer>) doc.getUserObject(keyWord);
+    if (idCounts == null) {
+      idCounts = new HashMap<String, Integer>();
+      doc.putUserObject(keyWord, idCounts);
+    }
     Map<String, ReactionGlyph> keggReactionName2glyph = new HashMap<String, ReactionGlyph>();
 
     // First, create a glyph for each reaction
@@ -171,7 +176,7 @@ public static void addLayoutExtension(Pathway p, SBMLDocument doc, Model model,
     // Create a glyph for each entry (In KGML, only entries have graph objects)
     for (Entry e : p.getEntries()) {
       Object s = e.getCustom();
-      if (s!=null && e.hasGraphics()) {
+      if ((s != null) && e.hasGraphics()) {
         Graphics g = e.getGraphics();
         boolean isLineGraphic = g.getType().equals(GraphicsType.line);
         if (isLineGraphic) {