*/
package jalview.gui;
-import java.util.Locale;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import java.awt.Font;
import java.awt.Graphics;
+import java.awt.Graphics2D;
+import java.awt.RenderingHints;
import java.io.File;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
+import java.util.concurrent.Executors;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
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.datamodel.StructureViewerModel.StructureData;
-import jalview.fts.service.alphafold.AlphafoldRestClient;
import jalview.gui.ImageExporter.ImageWriterI;
import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.exceptions.ImageOutputException;
import jalview.structure.StructureCommand;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.BrowserLauncher;
import jalview.util.ImageMaker;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
+import jalview.util.imagemaker.BitmapImageSizing;
public class AppJmol extends StructureViewerBase
{
}
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);
}
jmb.executeCommand(new StructureCommand(command), false);
jmb.executeCommand(new StructureCommand("set hoverDelay=0.1"), false);
+ jmb.executeCommand(new StructureCommand("set antialiasdisplay on"),
+ false);
jmb.setFinishedInit(true);
}
} catch (OutOfMemoryError oomerror)
{
new OOMWarning("When trying to open the Jmol viewer!", oomerror);
- Cache.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
} catch (Exception ex)
{
- Cache.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.debug("File locations are " + filesString);
+ Console.debug("File locations are " + filesString);
return;
} catch (Exception ex)
{
- Cache.error("Couldn't add files to Jmol viewer!", ex);
+ Console.error("Couldn't add files to Jmol viewer!", ex);
ex.printStackTrace();
return;
}
{
try
{
- Cache.debug("Waiting around for jmb notify.");
+ Console.debug("Waiting around for jmb notify.");
waitTotal += waitFor;
// Thread.sleep() throws an exception in JS
}
if (waitTotal > waitMax)
{
- System.err.println("Timed out waiting for Jmol to load files after "
- + waitTotal + "ms");
- // System.err.println("finished: " + jmb.isFinishedInit()
+ jalview.bin.Console.errPrintln(
+ "Timed out waiting for Jmol to load files after "
+ + waitTotal + "ms");
+ // jalview.bin.Console.errPrintln("finished: " + jmb.isFinishedInit()
// + "; loaded: " + Arrays.toString(jmb.getPdbFile())
// + "; files: " + files.toString());
jmb.getStructureFiles();
@Override
public void makePDBImage(ImageMaker.TYPE type)
{
+ try
+ {
+ makePDBImage(null, type, null,
+ BitmapImageSizing.defaultBitmapImageSizing());
+ } catch (ImageOutputException ioex)
+ {
+ Console.error("Unexpected error whilst writing " + type.toString(),
+ ioex);
+ }
+ }
+
+ public void makePDBImage(File file, ImageMaker.TYPE type, String renderer,
+ BitmapImageSizing userBis) throws ImageOutputException
+ {
int width = getWidth();
int height = getHeight();
+
+ BitmapImageSizing bis = ImageMaker.getScaleWidthHeight(width, height,
+ userBis);
+ float usescale = bis.scale();
+ int usewidth = bis.width();
+ int useheight = bis.height();
+
ImageWriterI writer = new ImageWriterI()
{
@Override
public void exportImage(Graphics g) throws Exception
{
- jmb.jmolViewer.renderScreenImage(g, width, height);
+ Graphics2D ig2 = (Graphics2D) g;
+ ig2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ if (type == TYPE.PNG && usescale > 0.0f)
+ {
+ // for a scaled image, this scales down a bigger image to give the
+ // right resolution
+ if (usescale > 0.0f)
+ {
+ ig2.scale(1 / usescale, 1 / usescale);
+ }
+ }
+
+ jmb.jmolViewer.requestRepaintAndWait("image export");
+ jmb.jmolViewer.renderScreenImage(ig2, usewidth, useheight);
}
};
- String view = MessageManager.getString("action.view").toLowerCase(Locale.ROOT);
- ImageExporter exporter = new ImageExporter(writer,
+ String view = MessageManager.getString("action.view")
+ .toLowerCase(Locale.ROOT);
+ final ImageExporter exporter = new ImageExporter(writer,
getProgressIndicator(), type, getTitle());
- exporter.doExport(null, this, width, height, view);
+
+ final Throwable[] exceptions = new Throwable[1];
+ exceptions[0] = null;
+ final AppJmol us = this;
+ try
+ {
+ Thread runner = Executors.defaultThreadFactory()
+ .newThread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ try
+ {
+ exporter.doExport(file, us, width, height, view,
+ renderer, userBis);
+ } catch (Throwable t)
+ {
+ exceptions[0] = t;
+ }
+ }
+ });
+ runner.start();
+ long time = 0;
+ do
+ {
+ Thread.sleep(25);
+ } while (runner.isAlive() && time++ < 4000);
+ if (time >= 4000)
+ {
+ runner.interrupt();
+ throw new ImageOutputException(
+ "Jmol took too long to export. Waited for 100 seconds.");
+ }
+ } catch (Throwable e)
+ {
+ throw new ImageOutputException(
+ "Unexpected error when generating image", e);
+ }
+ if (exceptions[0] != null)
+ {
+ if (exceptions[0] instanceof ImageOutputException)
+ {
+ throw ((ImageOutputException) exceptions[0]);
+ }
+ else
+ {
+ throw new ImageOutputException(
+ "Unexpected error when generating image", exceptions[0]);
+ }
+ }
}
@Override
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());
+ jalview.bin.Console
+ .errPrintln("Show Jmol help failed with: " + ex.getMessage());
}
}
}
}
}
- 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);
git://source.jalview.org / jalview.git / blobdiff