*/
package jalview.gui;
+import java.util.Locale;
+
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import javax.swing.event.InternalFrameEvent;
import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.datamodel.StructureViewerModel;
import jalview.util.ImageMaker;
import jalview.util.MessageManager;
import jalview.util.Platform;
-
public class AppJmol extends StructureViewerBase
{
// ms to wait for Jmol to load files
.toArray(new SequenceI[sequencesForPdb.size()]);
i++;
}
-
// TODO: check if protocol is needed to be set, and if chains are
// autodiscovered.
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
seqColour.setSelected(true);
viewerColour.setSelected(false);
}
-
this.setBounds(viewerModel.getX(), viewerModel.getY(),
viewerModel.getWidth(), viewerModel.getHeight());
setViewId(viewid);
{
super.initMenus();
+
viewerColour
.setText(MessageManager.getString("label.colour_with_jmol"));
viewerColour.setToolTipText(MessageManager
}
private void openNewJmol(AlignmentPanel ap, boolean alignAdded,
- PDBEntry[] pdbentrys,
- SequenceI[][] seqs)
+ PDBEntry[] pdbentrys, SequenceI[][] seqs)
{
setProgressIndicator(ap.alignFrame);
jmb = new AppJmolBinding(this, ap.getStructureSelectionManager(),
openNewJmol(ap, alignAdded, pe, seqs);
}
-
void initJmol(String command)
{
jmb.setFinishedInit(false);
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Jmol viewer!", ex);
+ Console.error("Couldn't open Jmol viewer!", ex);
ex.printStackTrace();
return;
}
{
new OOMWarning("When trying to add structures to the Jmol viewer!",
oomerror);
- Cache.log.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
return;
} catch (Exception ex)
{
- Cache.log.error("Couldn't add files to Jmol viewer!", ex);
+ Console.error("Couldn't add files to Jmol viewer!", ex);
ex.printStackTrace();
return;
}
{
try
{
- Cache.log.debug("Waiting around for jmb notify.");
+ Console.debug("Waiting around for jmb notify.");
waitTotal += waitFor;
// Thread.sleep() throws an exception in JS
jmb.jmolViewer.renderScreenImage(g, width, height);
}
};
- String view = MessageManager.getString("action.view").toLowerCase();
+ String view = MessageManager.getString("action.view")
+ .toLowerCase(Locale.ROOT);
ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
exporter.doExport(null, this, width, height, view);
try
{
BrowserLauncher // BH 2018
- .openURL("http://wiki.jmol.org");//http://jmol.sourceforge.net/docs/JmolUserGuide/");
+ .openURL("http://wiki.jmol.org");// http://jmol.sourceforge.net/docs/JmolUserGuide/");
} catch (Exception ex)
{
System.err.println("Show Jmol help failed with: " + ex.getMessage());
@Override
public void showConsole(boolean showConsole)
{
+
if (showConsole)
{
if (splitPane == null)
}
}
}
- else if (jmb == null || jmb.jmolViewer == null || !jmb.isFinishedInit())
+ else if (jmb == null || jmb.jmolViewer == null
+ || !jmb.isFinishedInit())
{
g.setColor(Color.black);
g.fillRect(0, 0, currentSize.width, currentSize.height);