/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * 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.
- *
+ * 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/>.
+ * 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.awt.event.ComponentEvent;
-import java.awt.event.ComponentListener;
-import java.awt.event.ContainerEvent;
-import java.awt.event.ContainerListener;
-import java.util.BitSet;
-
-import javax.swing.JPanel;
-
import jalview.api.AlignmentViewPanel;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
import jalview.structure.StructureSelectionManager;
+import java.awt.Container;
+import java.util.BitSet;
+
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolViewer;
import org.jmol.popup.JmolPopup;
import org.openscience.jmol.app.jmolpanel.AppConsole;
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
{
-
- /**
- *
- */
private AppJmol appJmolWindow;
- public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, 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(sSm, pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ public FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+ : (AlignmentPanel) alignment;
if (ap.av.showSequenceFeatures)
{
if (fr == null)
{
- fr = new FeatureRenderer(ap);
+ fr = ap.cloneFeatureRenderer();
+ }
+ else
+ {
+ ap.updateFeatureRenderer(fr);
}
-
- fr.transferSettings(ap.
- seqPanel.seqCanvas.getFeatureRenderer());
}
return fr;
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
{
- return new SequenceRenderer(((AlignmentPanel)alignment).av);
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
public void sendConsoleEcho(String strEcho)
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source,topap;
+ AlignmentPanel ap = (AlignmentPanel) source, topap;
// ignore events from panels not used to colour this view
if (!appJmolWindow.isUsedforcolourby(ap))
+ {
return;
- if (!isLoadingFromArchive()) {
+ }
+ if (!isLoadingFromArchive())
+ {
colourBySequence(ap.av.getShowSequenceFeatures(), ap);
}
}
public void newJmolPopup(boolean translateLocale, String menuName,
boolean asPopup)
{
-
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
- asPopup);
+ jmolpopup = new JmolPopup();
+ jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
}
public void selectionChanged(BitSet arg0)
*/
public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
+ for (int pe = 0; pe < getPdbCount(); pe++)
{
- if (pdbentry[pe].getFile().equals(pdbFile))
+ if (getPdbEntry(pe).getFile().equals(pdbFile))
{
addSequence(pe, seq);
}
protected void releaseUIResources()
{
appJmolWindow = null;
- if (console != null)
- {
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
- }
-
+ closeConsole();
}
@Override
public void releaseReferences(Object svl)
{
- if (svl instanceof SeqPanel) {
+ if (svl instanceof SeqPanel)
+ {
appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
- };
+ }
}
}