-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
+import java.awt.Container;
import java.util.BitSet;
-import java.util.Vector;
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.structure.StructureSelectionManager;
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.api.JmolViewer;
import org.jmol.popup.JmolPopup;
+import org.openscience.jmol.app.jmolpanel.AppConsole;
-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)
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
{
- super(pdbentry, seq, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr=null;
+
+ FeatureRenderer fr = null;
+
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
{
- if (appJmolWindow.ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+ : (AlignmentPanel) alignment;
+ if (ap.av.showSequenceFeatures)
{
if (fr == null)
{
- fr = new FeatureRenderer(appJmolWindow.ap);
+ fr = ap.cloneFeatureRenderer();
+ }
+ else
+ {
+ ap.updateFeatureRenderer(fr);
}
-
- fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
}
return fr;
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer()
+ public jalview.api.SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
{
- return new SequenceRenderer(appJmolWindow.ap.av);
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
public void sendConsoleEcho(String strEcho)
{
- if (appJmolWindow.scriptWindow != null)
+ if (console != null)
{
- appJmolWindow.scriptWindow.sendConsoleEcho(strEcho);
+ console.sendConsoleEcho(strEcho);
}
}
public void sendConsoleMessage(String strStatus)
{
- if (appJmolWindow.scriptWindow!=null && strStatus != null
- )
- // && !strStatus.equals("Script completed"))
- // should we squash the script completed string ?
+ if (console != null && strStatus != null)
+ // && !strStatus.equals("Script completed"))
+ // should we squash the script completed string ?
{
- appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
+ console.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)
+ AlignmentPanel ap = (AlignmentPanel) source, topap;
+ // ignore events from panels not used to colour this view
+ if (!appJmolWindow.isUsedforcolourby(ap))
return;
-
- colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ if (!isLoadingFromArchive())
+ {
+ colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ }
}
public void notifyScriptTermination(String strStatus, int msWalltime)
{
- if (appJmolWindow.scriptWindow != null)
- appJmolWindow.scriptWindow.notifyScriptTermination(strStatus, msWalltime);
+ // todo - script termination doesn't happen ?
+ // if (console != null)
+ // console.notifyScriptTermination(strStatus,
+ // msWalltime);
}
public void showUrl(String url)
{
- showUrl(url,"jmol");
+ showUrl(url, "jmol");
}
public void newJmolPopup(boolean translateLocale, String menuName,
boolean asPopup)
{
- 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;
+ jmolpopup = new JmolPopup();
+ jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
}
public void selectionChanged(BitSet arg0)
{
// TODO Auto-generated method stub
-
+
}
public void refreshPdbEntries()
{
// TODO Auto-generated method stub
-
+
+ }
+
+ public void showConsole(boolean b)
+ {
+ appJmolWindow.showConsole(b);
+ }
+
+ /**
+ * 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);
+ }
+ }
+ }
+
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ Container consolePanel, String buttonsToShow)
+ {
+ return new AppConsole(viewer, consolePanel, buttonsToShow);
+ }
+
+ @Override
+ protected void releaseUIResources()
+ {
+ appJmolWindow = null;
+ if (console != null)
+ {
+ try
+ {
+ console.setVisible(false);
+ } catch (Error e)
+ {
+ } catch (Exception x)
+ {
+ }
+ ;
+ console = null;
+ }
+
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ if (svl instanceof SeqPanel)
+ {
+ appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+
+ }
+ ;
}
-}
\ No newline at end of file
+}
git://source.jalview.org / jalview.git / blobdiff