*/
package jalview.gui;
+import java.awt.Container;
+import java.io.File;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.JComponent;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+
import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
-
-import java.awt.Container;
-import java.util.Map;
-
-import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
-import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+import jalview.util.Platform;
+import javajs.util.BS;
public class AppJmolBinding extends JalviewJmolBinding
{
- private AppJmol appJmolWindow;
-
- private FeatureRenderer fr = null;
-
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- super(sSm, pdbentry, sequenceIs, chains, protocol);
- appJmolWindow = appJmol;
- }
-
- @Override
- public FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
- {
- AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
- : (AlignmentPanel) alignment;
- if (ap.av.isShowSequenceFeatures())
- {
- if (fr == null)
- {
- fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
- }
- else
- {
- ap.updateFeatureRenderer(fr);
- }
- }
-
- return fr;
+ super(sSm, pdbentry, sequenceIs, protocol);
+ setViewer(appJmol);
}
@Override
- public SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
// appJmolWindow.repaint();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- appJmolWindow.updateTitleAndMenus();
- appJmolWindow.revalidate();
+ JalviewStructureDisplayI theViewer = getViewer();
+ // invokes colourbySequence() via seqColour_ActionPerformed()
+ theViewer.updateTitleAndMenus();
+ ((JComponent) theViewer).revalidate();
}
});
}
- public void updateColours(Object source)
- {
- AlignmentPanel ap = (AlignmentPanel) source;
- // ignore events from panels not used to colour this view
- if (!appJmolWindow.isUsedforcolourby(ap))
- {
- return;
- }
- if (!isLoadingFromArchive())
- {
- colourBySequence(ap);
- }
- }
-
@Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// msWalltime);
}
+ @Override
public void showUrl(String url)
{
showUrl(url, "jmol");
@Override
public void selectionChanged(BS arg0)
{
- // TODO Auto-generated method stub
-
- }
-
- @Override
- public void refreshPdbEntries()
- {
- // TODO Auto-generated method stub
-
}
@Override
public void showConsole(boolean b)
{
- appJmolWindow.showConsole(b);
+ getViewer().showConsole(b);
}
@Override
protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
- viewer.setJmolCallbackListener(this);
- return new AppConsole(viewer, consolePanel, buttonsToShow);
+ jmolViewer.setJmolCallbackListener(this);
+ // BH comment: can't do this yet [for JS only, or generally?]
+ return Platform.isJS() ? null
+ : new AppConsole(jmolViewer, consolePanel, buttonsToShow);
}
@Override
protected void releaseUIResources()
{
- appJmolWindow = null;
+ setViewer(null);
closeConsole();
}
{
if (svl instanceof SeqPanel)
{
- appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+ getViewer().removeAlignmentPanel(((SeqPanel) svl).ap);
}
}
// TODO Auto-generated method stub
return null;
}
+
+ @SuppressWarnings("unused")
+ public void cacheFiles(List<File> files)
+ {
+ if (files == null)
+ {
+ return;
+ }
+ for (File f : files)
+ {
+ Platform.cacheFileData(f);
+ }
+ }
}