/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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.structure.StructureSelectionManager;
*/
private AppJmol appJmolWindow;
- public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ 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 jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment==null) ? appJmolWindow.ap : (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
+ : (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
- fr = new FeatureRenderer(ap);
+ fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
+ }
+ else
+ {
+ ap.updateFeatureRenderer(fr);
}
-
- fr.transferSettings(ap.
- seqPanel.seqCanvas.getFeatureRenderer());
}
return fr;
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ public jalview.api.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()) {
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ if (!isLoadingFromArchive())
+ {
+ colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
}
boolean asPopup)
{
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
- asPopup);
+ jmolpopup = new JmolPopup();
+ jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
}
public void selectionChanged(BitSet arg0)
@Override
public void releaseReferences(Object svl)
{
- if (svl instanceof SeqPanel) {
+ if (svl instanceof SeqPanel)
+ {
appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
- };
+
+ }
+ ;
}
}