-/**
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.util.BitSet;
-
+import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.structure.StructureSelectionManager;
-import org.jmol.popup.JmolPopup;
+import java.awt.Container;
+import java.util.Map;
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
-{
+import org.jmol.api.JmolAppConsoleInterface;
+import org.jmol.java.BS;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
- /**
- *
- */
+public class AppJmolBinding extends JalviewJmolBinding
+{
private AppJmol appJmolWindow;
- public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ private FeatureRenderer fr = null;
+
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
{
- super(pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- if (appJmolWindow.ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow
+ .getAlignmentPanel() : (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
- fr = new FeatureRenderer(appJmolWindow.ap);
+ fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
+ }
+ else
+ {
+ ap.updateFeatureRenderer(fr);
}
-
- fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
}
return fr;
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer()
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- return new SequenceRenderer(appJmolWindow.ap.av);
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
- if (appJmolWindow.scriptWindow != null)
+ if (console != null)
{
- appJmolWindow.scriptWindow.sendConsoleEcho(strEcho);
+ console.sendConsoleEcho(strEcho);
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
- if (appJmolWindow.scriptWindow != null && strStatus != null)
+ if (console != null && strStatus != null)
// && !strStatus.equals("Script completed"))
// should we squash the script completed string ?
{
- appJmolWindow.scriptWindow.sendConsoleMessage(strStatus);
+ console.sendConsoleMessage(strStatus);
}
}
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)
+ // 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);
+ }
}
+ @Override
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");
}
- public void newJmolPopup(boolean translateLocale, String menuName,
- boolean asPopup)
+ public void newJmolPopup(String menuName)
{
-
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
- asPopup);
+ // jmolpopup = new JmolAwtPopup();
+ // jmolpopup.jpiInitialize((viewer), menuName);
}
- public void selectionChanged(BitSet arg0)
+ @Override
+ public void selectionChanged(BS arg0)
{
// TODO Auto-generated method stub
}
+ @Override
public void refreshPdbEntries()
{
// TODO Auto-generated method stub
}
+ @Override
+ 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)
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow)
+ {
+ viewer.setJmolCallbackListener(this);
+ return new AppConsole(viewer, consolePanel, buttonsToShow);
+ }
+
+ @Override
+ protected void releaseUIResources()
{
- for (int pe = 0; pe < pdbentry.length; pe++)
+ appJmolWindow = null;
+ closeConsole();
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ if (svl instanceof SeqPanel)
{
- if (pdbentry[pe].getFile().equals(pdbFile))
- {
- addSequence(pe, seq);
- }
+ appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
}
}
-}
\ No newline at end of file
+ @Override
+ public Map<String, Object> getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff