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JAL-2034 moved ‘isDefinedGroup’ flag to a test method on AlignViewportI so controller...
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmolBinding.java
diff --git
a/src/jalview/gui/AppJmolBinding.java
b/src/jalview/gui/AppJmolBinding.java
index
131f5bb
..
1c54a5e
100644
(file)
--- a/
src/jalview/gui/AppJmolBinding.java
+++ b/
src/jalview/gui/AppJmolBinding.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-28,12
+28,11
@@
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.structure.StructureSelectionManager;
import java.awt.Container;
import jalview.structure.StructureSelectionManager;
import java.awt.Container;
-import java.util.BitSet;
+import java.util.Map;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
+import org.jmol.java.BS;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
public class AppJmolBinding extends JalviewJmolBinding
{
public class AppJmolBinding extends JalviewJmolBinding
{
@@
-50,16
+49,15
@@
public class AppJmolBinding extends JalviewJmolBinding
}
@Override
}
@Override
- public FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
{
- AlignmentPanel ap = (alignment == null) ? appJmolWindow.getAlignmentPanel()
- : (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow
+ .getAlignmentPanel() : (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
{
if (fr == null)
{
- fr = ap.cloneFeatureRenderer();
+ fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
}
else
{
}
else
{
@@
-71,12
+69,12
@@
public class AppJmolBinding extends JalviewJmolBinding
}
@Override
}
@Override
- public SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
if (console != null)
public void sendConsoleEcho(String strEcho)
{
if (console != null)
@@
-85,6
+83,7
@@
public class AppJmolBinding extends JalviewJmolBinding
}
}
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
if (console != null && strStatus != null)
public void sendConsoleMessage(String strStatus)
{
if (console != null && strStatus != null)
@@
-124,7
+123,7
@@
public class AppJmolBinding extends JalviewJmolBinding
public void updateColours(Object source)
{
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source, topap;
+ AlignmentPanel ap = (AlignmentPanel) source;
// ignore events from panels not used to colour this view
if (!appJmolWindow.isUsedforcolourby(ap))
{
// ignore events from panels not used to colour this view
if (!appJmolWindow.isUsedforcolourby(ap))
{
@@
-132,10
+131,11
@@
public class AppJmolBinding extends JalviewJmolBinding
}
if (!isLoadingFromArchive())
{
}
if (!isLoadingFromArchive())
{
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ colourBySequence(ap);
}
}
}
}
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// todo - script termination doesn't happen ?
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// todo - script termination doesn't happen ?
@@
-149,34
+149,37
@@
public class AppJmolBinding extends JalviewJmolBinding
showUrl(url, "jmol");
}
showUrl(url, "jmol");
}
- public void newJmolPopup(boolean translateLocale, String menuName,
- boolean asPopup)
+ public void newJmolPopup(String menuName)
{
{
- jmolpopup = new JmolPopup();
- jmolpopup.initialize(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
}
{
// TODO Auto-generated method stub
}
+ @Override
public void refreshPdbEntries()
{
// TODO Auto-generated method stub
}
public void refreshPdbEntries()
{
// TODO Auto-generated method stub
}
+ @Override
public void showConsole(boolean b)
{
appJmolWindow.showConsole(b);
}
@Override
public void showConsole(boolean b)
{
appJmolWindow.showConsole(b);
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
Container consolePanel, String buttonsToShow)
{
+ viewer.setJmolCallbackListener(this);
return new AppConsole(viewer, consolePanel, buttonsToShow);
}
return new AppConsole(viewer, consolePanel, buttonsToShow);
}
@@
-195,4
+198,11
@@
public class AppJmolBinding extends JalviewJmolBinding
appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
}
}
appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
}
}
+
+ @Override
+ public Map<String, Object> getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
}
}