KEGGtranslator release 1.2 and associated changes.

dist/build.xml

@@ -89,6 +89,7 @@
 <!-- Uncomment for SysBio classes instead of compiled jar. -->
            <fileset dir="${SysBioPath}/bin">
               <exclude name="de/zbit/resources/liftover/*"/>
+           	  <exclude name="de/zbit/mapper/*"/>
             	<exclude name="**/package.html"/>
            </fileset>
 <!-- Achtung, im ersten SysBio release befinden sich bugs in KeggInfos.java ! -->
@@ -103,7 +104,6 @@
             <!-- <zipfileset excludes="META-INF/*.SF" src="${SysBioPath}/lib/Java5/saaj.jar"/>-->
             <!-- <zipfileset excludes="META-INF/*.SF" src="${SysBioPath}/lib/WSDbfetch.jar"/>-->
             <zipfileset excludes="META-INF/*" src="${SysBioPath}/lib/commons-cli-1.1.jar"/>
-            <zipfileset excludes="META-INF/*.SF" src="${SysBioPath}/lib/argparser.jar"/>
 
             <fileset dir="${JSBMLPath}/bin">
               <exclude name="log4j.properties"/> <!-- log4j.properties is in SBML2Latex and jSBML -->

src/de/zbit/kegg/TranslatorTools.java

@@ -29,6 +29,7 @@
 import java.util.logging.Logger;
 
 import y.base.DataMap;
+import y.base.Graph;
 import y.base.Node;
 import y.base.NodeMap;
 import y.view.Graph2D;
@@ -104,6 +105,10 @@ public Map<Integer, List<Node>> getGeneID2NodeMap() {
         break;
       }
     }
+    if (entrez==null) {
+      log.severe("Could not find Node2EntrezID mapping.");
+      return null;
+    }
 
     // build the resulting map
     for (Node n : graph.getNodeArray()) {
@@ -131,4 +136,43 @@ public Map<Integer, List<Node>> getGeneID2NodeMap() {
     return id2node;
   }
 
+  /**
+   * @param n a node
+   * @param descriptor e.g., "keggIds" or "entrezIds". See {@link KEGG2yGraph} for a complete list.
+   * @return the string associated with this node.
+   */
+  @SuppressWarnings("unchecked")
+  public static String getNodeInfoIDs(Node n, String descriptor) {
+    Graph graph = n.getGraph();
+
+    // Get the NodeMap from kegg 2 node.
+    GenericDataMap<DataMap, String> mapDescriptionMap = (GenericDataMap<DataMap, String>) graph.getDataProvider(KEGG2yGraph.mapDescription);
+    NodeMap nodeMap = null;
+    if (mapDescriptionMap==null) return null;
+    for (int i=0; i<graph.getRegisteredNodeMaps().length; i++) {
+      NodeMap nm = graph.getRegisteredNodeMaps()[i];
+      if (mapDescriptionMap.getV(nm).equals(descriptor)) {
+        nodeMap = nm;
+        break;
+      }
+    }
+    if (nodeMap==null) {
+      log.severe("Could not find Node2" + descriptor==null?"null":descriptor + " mapping.");
+      return null;
+    }
+
+    // return kegg id(s)
+    Object id = nodeMap.get(n);
+    return id!=null?id.toString():null;
+
+  }
+
+  /**
+   * @param n
+   * @return kegg ids, separated by a "," for the given node.
+   */
+  public static String getKeggIDs(Node n) {
+    return getNodeInfoIDs(n, "keggIds");
+  }
+
 }

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

@@ -33,6 +33,8 @@
 import java.awt.GridBagLayout;
 import java.awt.Insets;
 import java.awt.Point;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
 import java.awt.event.MouseAdapter;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseMotionAdapter;
@@ -42,10 +44,12 @@
 import javax.swing.BorderFactory;
 import javax.swing.Box;
 import javax.swing.BoxLayout;
+import javax.swing.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.JScrollPane;
 import javax.swing.JTable;
 import javax.swing.JViewport;
+import javax.swing.ToolTipManager;
 import javax.swing.table.DefaultTableModel;
 
 import org.sbml.jsbml.util.StringTools;
@@ -61,11 +65,15 @@
 import y.view.Graph2DSelectionEvent;
 import y.view.Graph2DSelectionListener;
 import y.view.Graph2DView;
+import y.view.HitInfo;
 import y.view.NavigationComponent;
 import y.view.Overview;
 import de.zbit.gui.GUITools;
 import de.zbit.gui.SystemBrowser;
+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;
 
@@ -90,14 +98,44 @@ public class RestrictedEditMode extends EditMode implements Graph2DSelectionList
    */
   JTable propTable=null;
 
+  /**
+   * A panel for the {@link #propTable}.
+   */
   JPanel eastPanel=null;
 
+  /**
+   * This is used to fire openPathway events on double clicks on
+   * pathway reference nodes.
+   */
+  ActionListener aListener = null;
+
+  /**
+   * This is the ActionCommand for actionlisteners to open a new pathway tab.
+   * TODO
+   */
+  public final static String OPEN_PATHWAY = "OPEN_PATHWAY";
+
   public RestrictedEditMode() {
     super();
     //setEditNodeMode(null);
     setCreateEdgeMode(null);
+    /*
+     * The Tooltips of nodes, provding descriptions must be shown
+     * longer than the system default. Let's show them 15 seconds!
+     */
+    ToolTipManager.sharedInstance().setDismissDelay(15000);
   }
 
+  /**
+   * @param listener this is used to fire TODO
+   */
+  public RestrictedEditMode(ActionListener listener) {
+    this();
+    this.aListener = listener;
+  }
+
+
+
   @Override
   protected Node createNode(Graph2D graph, double x, double y) {
     // do nothing
@@ -127,10 +165,84 @@ public static void addBackgroundImage(URL imagePath, Graph2DView pane) {
   /* (non-Javadoc)
    * @see y.view.EditMode#getNodeTip(y.base.Node)
    */
+  @SuppressWarnings("unchecked")
+  @Override
+  protected String getNodeTip(Node n) {
+    // Show a nice ToolTipText for every node.
+    GenericDataMap<DataMap, String> mapDescriptionMap = (GenericDataMap<DataMap, String>) n.getGraph().getDataProvider(KEGG2yGraph.mapDescription);
+    if (mapDescriptionMap==null) return super.getNodeTip(n);
+
+    // Get nodeLabel, description and eventually an image for the ToolTipText
+    String nodeLabel = null;
+    String description = null;
+    String image = "";
+    NodeMap[] nm = n.getGraph().getRegisteredNodeMaps();
+    if (nm!=null) {
+      for (int i=0; i<nm.length;i++) {
+        Object c = nm[i].get(n);
+        if (c==null || c.toString().length()<1) continue;
+        String mapDescription = mapDescriptionMap.getV(nm[i]);
+        if (mapDescription.equals("nodeLabel")) {
+          nodeLabel = "<b>"+c.toString().replace(",", ",<br/>")+"</b><br/>";
+        } else if (mapDescription.equals("description")) {
+          description = "<i>"+c.toString().replace(",", ",<br/>")+"</i><br/>";
+        } else if (mapDescription.equals("keggIds")) {
+          for (String s: c.toString().split(",")) {
+            s=s.toUpperCase().trim();
+            if (s.startsWith("PATH:")) {
+              image+=KEGG2jSBML.getPathwayPreviewPicture(s);
+            } else if (s.startsWith("CPD:")) {
+              // KEGG provides picture for compounds (e.g., "C00118").
+              image+=KEGG2jSBML.getCompoundPreviewPicture(s);
+            }
+          }
+        }
+      }
+    }
+
+    // Merge the three strings to a single tooltip
+    StringBuffer tooltip = new StringBuffer();
+    if (nodeLabel!=null) {
+      tooltip.append(StringUtil.insertLineBreaks(nodeLabel, GUITools.TOOLTIP_LINE_LENGTH, "<br/>"));
+    }
+    if (description!=null) {
+      tooltip.append(StringUtil.insertLineBreaks(description, GUITools.TOOLTIP_LINE_LENGTH, "<br/>"));
+    }
+    if (image!=null && image.length()>0) {
+      tooltip.append("<div align=\"center\">"+image+"</div>");
+    }
+
+    // Append html and return toString.
+    return "<html><body>"+tooltip.toString()+"</body></html>";
+  }
+
+  /* (non-Javadoc)
+   * @see y.view.EditMode#mouseClicked(double, double)
+   */
   @Override
-  protected String getNodeTip(Node arg0) {
-    // TODO Auto-generated method stub
-    return super.getNodeTip(arg0);
+  public void mouseClicked(double x, double y) {
+    MouseEvent ev = lastClickEvent;
+    if (ev.getClickCount() == 2 && aListener!=null) {
+      // Get double clicked node
+      HitInfo allHitObjects = getGraph2D().getHitInfo(x, y, false);
+      Node n = allHitObjects.getHitNode();
+
+      // Ask user if he wants to open the pathway and fire an event.
+      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"});
+        if (ret==0) {
+          ActionEvent e = new ActionEvent(kgId.trim().substring(5).toLowerCase(), JOptionPane.OK_OPTION, OPEN_PATHWAY);
+          aListener.actionPerformed(e);
+        }
+      }
+
+
+    } else {
+      // let EditMode handle the click event
+      super.mouseClicked(x,y);
+    }
   }
 
   /**

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

@@ -140,12 +140,11 @@ public TranslatorPanel(final File inputFile, final Format outputFormat, ActionLi
 
   /**
    * Initiates a download and translation of the given pathway.
-   * @param organism Organism kegg abbreviation (e.g., "mmu")
    * @param pathwayID pathway identifier (e.g., "mmu00010")
    * @param outputFormat
    * @param translationResult
    */
-  public TranslatorPanel(final String organism, final String pathwayID, 
+  public TranslatorPanel(final String pathwayID, 
     final Format outputFormat, ActionListener translationResult) {
     super();
     setLayout(new BorderLayout());
@@ -155,11 +154,11 @@ public TranslatorPanel(final String organism, final String pathwayID,
     this.translationListener = translationResult;
 
     // Execute download and translation in new thread
-    showTemporaryLoadingPanel(pathwayID, organism);
+    showTemporaryLoadingPanel(pathwayID, null);
     final SwingWorker<String, Void> downloadWorker = new SwingWorker<String, Void>() {
       @Override
       protected String doInBackground() throws Exception {
-        return KGMLSelectAndDownload.downloadPathway(organism, pathwayID, false);
+        return KGMLSelectAndDownload.downloadPathway(pathwayID, false);
       }
       protected void done() {
         String localFile=null;
@@ -256,7 +255,7 @@ private void showTemporaryLoadingPanel(String pwName, String organism) {
     removeAll();
     setLayout(new BorderLayout()); // LayoutHelper creates a GridBaglayout, reset it to default.
     final AbstractProgressBar pb = generateLoadingPanel(this, "Downloading '" + pwName + "' " +
-        "for '"+organism+"'...");
+      (organism!=null&&organism.length()>0? "for '"+organism+"'...":""));
     FileDownload.ProgressBar = pb;
     repaint();
   }
@@ -345,7 +344,7 @@ protected void done() {
           pane.setSize(getSize());
           //ViewMode mode = new NavigationMode();
           //pane.addViewMode(mode);
-          EditMode editMode = new RestrictedEditMode();
+          EditMode editMode = new RestrictedEditMode(translationListener);
           editMode.showNodeTips(true);
           pane.addViewMode(editMode);
 

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

@@ -61,6 +61,7 @@
 import de.zbit.gui.prefs.FileSelector;
 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;
@@ -101,6 +102,12 @@ public static enum Action implements ActionCommand {
      * {@link Action} for downloading KGMLs.
      */
 		DOWNLOAD_KGML,
+		/**
+		 * 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.
+		 */
+		OPEN_PATHWAY,
 		/**
 		 * Invisible {@link Action} that should be performed, whenever an
 		 * translation is done.
@@ -386,6 +393,14 @@ public void actionPerformed(ActionEvent e) {
       case NEW_PROGRESSBAR:
         getStatusBar().showProgress((AbstractProgressBar)e.getSource());
         break;
+      case OPEN_PATHWAY:
+        try {
+          tabbedPane.addTab(e.getSource().toString(), new TranslatorPanel(e.getSource().toString(),Format.GraphML,this));
+          tabbedPane.setSelectedIndex(tabbedPane.getTabCount()-1);
+        } catch (Exception e1) {
+          GUITools.showErrorMessage(this, e1);
+        }
+        break;
       default:
         System.out.println(action);
 				break;

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

@@ -30,10 +30,11 @@
 
 import org.sbml.jsbml.Annotation;
 import org.sbml.jsbml.CVTerm;
+import org.sbml.jsbml.CVTerm.Qualifier;
+import org.sbml.jsbml.CVTerm.Type;
 import org.sbml.jsbml.Compartment;
 import org.sbml.jsbml.Creator;
 import org.sbml.jsbml.History;
-import org.sbml.jsbml.JSBML;
 import org.sbml.jsbml.Model;
 import org.sbml.jsbml.ModifierSpeciesReference;
 import org.sbml.jsbml.SBMLDocument;
@@ -42,8 +43,6 @@
 import org.sbml.jsbml.SBaseChangedListener;
 import org.sbml.jsbml.Species;
 import org.sbml.jsbml.SpeciesReference;
-import org.sbml.jsbml.CVTerm.Qualifier;
-import org.sbml.jsbml.CVTerm.Type;
 import org.sbml.jsbml.xml.stax.SBMLWriter;
 
 import de.zbit.kegg.KEGGtranslatorOptions;
@@ -702,8 +701,18 @@ private void addMiriamURNs(Entry entry, Species spec) {
           notes.append(String.format("<p><b>All given names:</b><br/>%s</p>\n",EscapeChars.forHTML(infos.getNames().replace(";", ""))));
         if (infos.getCas() != null)
           notes.append(String.format("<p><b>CAS number:</b> %s</p>\n", infos.getCas()));
-        if (infos.getFormula() != null)
+        if (infos.getFormula() != null) {
           notes.append(String.format("<p><b>Formula:</b> %s</p>\n", EscapeChars.forHTML(infos.getFormula())));
+          String ko_id_uc_t = ko_id.toUpperCase().trim();
+          if (ko_id_uc_t.startsWith("CPD:")) {
+            // KEGG provides picture for compounds (e.g., "C00118").
+            notes.append(getCompoundPreviewPicture(ko_id_uc_t));
+          }
+        }
+        if (entry.getType().equals(EntryType.map)) {
+          // KEGG provides picture for referenced pathways (e.g., "path:hsa00620" => "map00620.gif").
+          notes.append(getPathwayPreviewPicture(ko_id));
+        }
         if (infos.getMass() != null)
           notes.append(String.format("<p><b>Mass:</b> %s</p>\n", infos.getMass()));
         notes.append(notesEndString);
@@ -767,6 +776,24 @@ private void addMiriamURNs(Entry entry, Species spec) {
   }
 
 
+  /**
+   * @param ko_id starting with "cpd:"
+   * @return an html image tag, containing a preview picture for the given compound.
+   */
+  public static String getCompoundPreviewPicture(String ko_id) {
+    return String.format("<img src=\"http://www.kegg.jp/Fig/compound/%s.gif\"/><br/>\n", ko_id.trim().substring(4).toUpperCase() );
+  }
+
+  /** 
+   * @param ko_id starting with "path:"
+   * @return an html image tag, containing a preview picture for the given referenced pathway.
+   */
+  public static String getPathwayPreviewPicture(String ko_id) {
+    // KEGG provides picture for referenced pathways (e.g., "path:hsa00620" => "map00620.gif").
+    String mapNumber = Utils.getNumberFromStringRevAsString(ko_id.length(), ko_id);
+    return String.format("<img src=\"http://www.kegg.jp/kegg/misc/thumbnail/map%s.gif\"/><br/>\n", mapNumber );
+  }
+
   /**
    * Translates the given entry to jSBML.
    *