package jalview.gui;
import java.util.BitSet;
-import java.util.Vector;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import org.jmol.popup.JmolPopup;
-class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
{
/**
private AppJmol appJmolWindow;
public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
- SequenceI[] seq, String[] chains, String protocol)
+ SequenceI[][] sequenceIs, String[][] chains, String protocol)
{
- super(pdbentry, seq, chains, protocol);
+ super(pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr=null;
+
+ FeatureRenderer fr = null;
+
@Override
public jalview.api.FeatureRenderer getFeatureRenderer()
{
}
fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
+ .getFeatureRenderer());
}
return fr;
public void sendConsoleMessage(String strStatus)
{
- if (appJmolWindow.scriptWindow!=null && strStatus != null
- )
- // && !strStatus.equals("Script completed"))
- // should we squash the script completed string ?
+ if (appJmolWindow.scriptWindow != null && strStatus != null)
+ // && !strStatus.equals("Script completed"))
+ // should we squash the script completed string ?
{
appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
}
@Override
public void showUrl(String url, String target)
{
- try {
+ try
+ {
jalview.util.BrowserLauncher.openURL(url);
- } catch (Exception e) {
+ } 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 updateUI()
+ public void refreshGUI()
{
// appJmolWindow.repaint();
- appJmolWindow.updateTitleAndMenus();
+ javax.swing.SwingUtilities.invokeLater(new Runnable() {
+ public void run() {
+ appJmolWindow.updateTitleAndMenus();
+ appJmolWindow.revalidate();
+ }});
}
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- if (appJmolWindow.ap.alignFrame.getCurrentView()!=ap.av)
+ if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
return;
-
+
colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
}
public void notifyScriptTermination(String strStatus, int msWalltime)
{
if (appJmolWindow.scriptWindow != null)
- appJmolWindow.scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+ appJmolWindow.scriptWindow.notifyScriptTermination(strStatus,
+ msWalltime);
}
public void showUrl(String url)
{
- showUrl(url,"jmol");
+ showUrl(url, "jmol");
}
public void newJmolPopup(boolean translateLocale, String menuName,
jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
asPopup);
}
- public synchronized void addSequence(SequenceI[] seq)
- {
- Vector v = new Vector();
- for (int i = 0; i < sequence.length; i++)
- v.addElement(sequence[i]);
-
- for (int i = 0; i < seq.length; i++)
- if (!v.contains(seq[i]))
- v.addElement(seq[i]);
-
- SequenceI[] tmp = new SequenceI[v.size()];
- v.copyInto(tmp);
- sequence = tmp;
- }
public void selectionChanged(BitSet arg0)
{
// TODO Auto-generated method stub
-
+
}
public void refreshPdbEntries()
{
// TODO Auto-generated method stub
-
+
}
+
+
+ /**
+ * 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);
+ }
+ }
+ }
+
}
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