import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileParse;
+import jalview.io.StructureFile;
import jalview.schemes.BuriedColourScheme;
import jalview.schemes.HelixColourScheme;
import jalview.schemes.HydrophobicColourScheme;
import java.util.List;
import java.util.Vector;
+import org.jmol.util.Logger;
+
public class AppletJmol extends EmbmenuFrame implements
// StructureListener,
KeyListener, ActionListener, ItemListener
{
this.ap = ap;
jmb = new AppletJmolBinding(this, ap.getStructureSelectionManager(),
- new PDBEntry[]
- { pdbentry }, new SequenceI[][]
- { seq }, new String[][]
- { chains }, protocol);
+ new PDBEntry[] { pdbentry }, new SequenceI[][] { seq },
+ new String[][] { chains }, protocol);
jmb.setColourBySequence(true);
if (pdbentry.getId() == null || pdbentry.getId().length() < 1)
{
String alreadyMapped = StructureSelectionManager
.getStructureSelectionManager(ap.av.applet)
.alreadyMappedToFile(pdbentry.getId());
- MCview.PDBfile reader = null;
+ StructureFile reader = null;
if (alreadyMapped != null)
{
reader = StructureSelectionManager.getStructureSelectionManager(
jmb.allocateViewer(renderPanel, true, ap.av.applet.getName()
+ "_jmol_", ap.av.applet.getDocumentBase(),
ap.av.applet.getCodeBase(), "-applet", scriptWindow, null);
+ Logger.setLogLevel(Logger.LEVEL_WARN);
} catch (Exception e)
{
System.err
this.addWindowListener(new WindowAdapter()
{
+ @Override
public void windowClosing(WindowEvent evt)
{
closeViewer();
}
if (freader == null)
{
- throw new Exception(MessageManager.getString("exception.invalid_datasource_couldnt_obtain_reader"));
+ throw new Exception(
+ MessageManager
+ .getString("exception.invalid_datasource_couldnt_obtain_reader"));
}
jmb.viewer.openReader(pdbentry.getFile(), pdbentry.getId(),
freader);
this.setVisible(false);
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
if (evt.getSource() == mappingMenuItem)
jmb.setColourBySequence(itm == seqColour);
}
+ @Override
public void itemStateChanged(ItemEvent evt)
{
if (evt.getSource() == jmolColour)
}
}
+ @Override
public void keyPressed(KeyEvent evt)
{
if (evt.getKeyCode() == KeyEvent.VK_ENTER && scriptWindow.isVisible())
{
jmb.eval(inputLine.getText());
- history.append("\n$ " + inputLine.getText());
+ addToHistory("$ " + inputLine.getText());
inputLine.setText("");
}
}
+ @Override
public void keyTyped(KeyEvent evt)
{
}
+ @Override
public void keyReleased(KeyEvent evt)
{
}
{
Dimension currentSize = new Dimension();
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
currentSize = this.getSize();
}
return ap;
}
+
+ /**
+ * Append the given text to the history object
+ *
+ * @param text
+ */
+ public void addToHistory(String text)
+ {
+ // actually currently never initialised
+ if (history != null)
+ {
+ history.append("\n" + text);
+ }
+ }
}