JAL-842, Further creation of VARNA classes (probably to much), filled

[jalview.git] / src / jalview / gui / AppVarnaBinding.java

diff --git a/src/jalview/gui/AppVarnaBinding.java b/src/jalview/gui/AppVarnaBinding.java
index 105dd39..5b65b8c 100644 (file)
--- a/src/jalview/gui/AppVarnaBinding.java
+++ b/src/jalview/gui/AppVarnaBinding.java
@@ -17,214 +17,28 @@
  */
 package jalview.gui;
 
-import java.awt.Container;
-import java.awt.event.ComponentEvent;
-import java.awt.event.ComponentListener;
-import java.awt.event.ContainerEvent;
-import java.awt.event.ContainerListener;
-import java.util.BitSet;
+import javax.swing.JFrame;
 
-import javax.swing.JPanel;
+import fr.orsay.lri.varna.applications.*;
 
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.structure.StructureSelectionManager;
-
-import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
-
-public class AppVarnaBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppVarnaBinding// extends jalview.ext.jmol.JalviewJmolBinding
 {
-
-  /**
-   * 
-   */
-  private AppJmol appJmolWindow;
-
-  public AppVarnaBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
-          SequenceI[][] sequenceIs, String[][] chains, String protocol)
-  {
-    super(sSm, pdbentry, sequenceIs, chains, protocol);
-    appJmolWindow = appJmol;
-  }
-
-  FeatureRenderer fr = null;
-
-  @Override
-  public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
-  {
-    AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
-    if (ap.av.showSequenceFeatures)
-    {
-      if (fr == null)
-      {
-        fr = new FeatureRenderer(ap);
-      }
-
-      fr.transferSettings(ap.
-              seqPanel.seqCanvas.getFeatureRenderer());
-    }
-
-    return fr;
-  }
-
-  @Override
-  public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
-  {
-    return new SequenceRenderer(((AlignmentPanel)alignment).av);
-  }
-
-  public void sendConsoleEcho(String strEcho)
-  {
-    if (console != null)
-    {
-      console.sendConsoleEcho(strEcho);
-    }
-  }
-
-  public void sendConsoleMessage(String strStatus)
-  {
-    if (console != null && strStatus != null)
-    // && !strStatus.equals("Script completed"))
-    // should we squash the script completed string ?
-    {
-      console.sendConsoleMessage(strStatus);
-    }
-  }
-
-  @Override
-  public void showUrl(String url, String target)
-  {
-    try
-    {
-      jalview.util.BrowserLauncher.openURL(url);
-    } catch (Exception e)
-    {
-      Cache.log.error("Failed to launch Jmol-associated url " + url, e);
-      // TODO: 2.6 : warn user if browser was not configured.
-    }
-  }
-
-  @Override
-  public void refreshGUI()
-  {
-    // appJmolWindow.repaint();
-    javax.swing.SwingUtilities.invokeLater(new Runnable()
-    {
-      public void run()
-      {
-        appJmolWindow.updateTitleAndMenus();
-        appJmolWindow.revalidate();
-      }
-    });
-  }
-
-  public void updateColours(Object source)
-  {
-    AlignmentPanel ap = (AlignmentPanel) source,topap;
-    // ignore events from unrelated or non-user interactive frames
-    if ((topap=appJmolWindow.getAlignmentPanelFor(ap.av.getAlignment()))==null || topap.alignFrame.getCurrentView() != ap.av || !appJmolWindow.isUsedforcolourby(ap))
-      return;
-    if (!isLoadingFromArchive()) {
-      colourBySequence(ap.av.getShowSequenceFeatures(), ap);
-    }
-  }
-
-  public void notifyScriptTermination(String strStatus, int msWalltime)
-  {
-    // todo - script termination doesn't happen ?
-    // if (console != null)
-    // console.notifyScriptTermination(strStatus,
-    // msWalltime);
-  }
-
-  public void showUrl(String url)
-  {
-    showUrl(url, "jmol");
-  }
-
-  public void newJmolPopup(boolean translateLocale, String menuName,
-          boolean asPopup)
-  {
-
-    jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
-            asPopup);
-  }
-
-  public void selectionChanged(BitSet arg0)
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  public void refreshPdbEntries()
-  {
-    // TODO Auto-generated method stub
-
-  }
-
-  public void showConsole(boolean b)
-  {
-    appJmolWindow.showConsole(b);
-  }
-
-  /**
-   * add the given sequences to the mapping scope for the given pdb file handle
-   * 
-   * @param pdbFile
-   *          - pdbFile identifier
-   * @param seq
-   *          - set of sequences it can be mapped to
-   */
-  public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
-  {
-    for (int pe = 0; pe < pdbentry.length; pe++)
-    {
-      if (pdbentry[pe].getFile().equals(pdbFile))
-      {
-        addSequence(pe, seq);
-      }
-    }
-  }
-
-  @Override
-  protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
-          Container consolePanel, String buttonsToShow)
-  {
-    return new AppConsole(viewer, consolePanel, buttonsToShow);
-  }
-
-  @Override
-  protected void releaseUIResources()
-  {
-    appJmolWindow = null;
-    if (console != null)
-    {
-      try
-      {
-        console.setVisible(false);
-      } catch (Error e)
-      {
-      } catch (Exception x)
-      {
-      }
-      ;
-      console = null;
-    }
-
-  }
-
-  @Override
-  public void releaseReferences(Object svl)
-  {
-    if (svl instanceof SeqPanel) {
-      appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-      
-    };
-  }
+       protected JFrame varnagui;
+  
+       public AppVarnaBinding(){
+               newVarnaGui();
+       }
+               
+       public void newVarnaGui(){
+               varnagui=new VARNAGUI();
+       }       
+       
+       
+       public static void main(String[] args)
+       {
+               AppVarnaBinding vab = new AppVarnaBinding();
+               vab.varnagui.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+               vab.varnagui.pack();
+               vab.varnagui.setVisible(true);  
+       }
 }