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JAL-192 show reference sequence position and residue in ruler
[jalview.git]
/
src
/
jalview
/
appletgui
/
AppletJmolBinding.java
diff --git
a/src/jalview/appletgui/AppletJmolBinding.java
b/src/jalview/appletgui/AppletJmolBinding.java
index
650693d
..
6ec5b4d
100644
(file)
--- a/
src/jalview/appletgui/AppletJmolBinding.java
+++ b/
src/jalview/appletgui/AppletJmolBinding.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.
*
@@
-23,16
+23,19
@@
package jalview.appletgui;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+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 javajs.awt.Dimension;
import org.jmol.api.JmolAppConsoleInterface;
import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
+import org.jmol.console.AppletConsole;
+import org.jmol.java.BS;
-class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+class AppletJmolBinding extends JalviewJmolBinding
{
/**
{
/**
@@
-48,11
+51,12
@@
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
appletJmolBinding = appletJmol;
}
appletJmolBinding = appletJmol;
}
+ @Override
public jalview.api.FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
AlignmentPanel ap = (AlignmentPanel) alignment;
public jalview.api.FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
AlignmentPanel ap = (AlignmentPanel) alignment;
- if (appletJmolBinding.ap.av.showSequenceFeatures)
+ if (appletJmolBinding.ap.av.isShowSequenceFeatures())
{
if (appletJmolBinding.fr == null)
{
{
if (appletJmolBinding.fr == null)
{
@@
-68,35
+72,42
@@
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
return appletJmolBinding.fr;
}
return appletJmolBinding.fr;
}
+ @Override
public jalview.api.SequenceRenderer getSequenceRenderer(
AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
public jalview.api.SequenceRenderer getSequenceRenderer(
AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
if (appletJmolBinding.scriptWindow == null)
public void sendConsoleEcho(String strEcho)
{
if (appletJmolBinding.scriptWindow == null)
+ {
appletJmolBinding.showConsole(true);
appletJmolBinding.showConsole(true);
+ }
- appletJmolBinding.history.append("\n" + strEcho);
+ appletJmolBinding.addToHistory(strEcho);
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
if (appletJmolBinding.history != null && strStatus != null
&& !strStatus.equals("Script completed"))
{
public void sendConsoleMessage(String strStatus)
{
if (appletJmolBinding.history != null && strStatus != null
&& !strStatus.equals("Script completed"))
{
- appletJmolBinding.history.append("\n" + strStatus);
+ appletJmolBinding.addToHistory(strStatus);
}
}
}
}
+ @Override
public void showUrl(String url, String target)
{
appletJmolBinding.ap.alignFrame.showURL(url, target);
}
public void showUrl(String url, String target)
{
appletJmolBinding.ap.alignFrame.showURL(url, target);
}
+ @Override
public void refreshGUI()
{
appletJmolBinding.updateTitleAndMenus();
public void refreshGUI()
{
appletJmolBinding.updateTitleAndMenus();
@@
-105,7
+116,7
@@
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ colourBySequence(ap);
}
public void showUrl(String url)
}
public void showUrl(String url)
@@
-122,26
+133,26
@@
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
public void newJmolPopup(boolean translateLocale, String menuName,
boolean asPopup)
{
public void newJmolPopup(boolean translateLocale, String menuName,
boolean asPopup)
{
-
- jmolpopup = new JmolPopup();
- jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
+ // jmolpopup = new JmolAwtPopup(); // is this used?
+ // jmolpopup.jpiInitialize((viewer), menuName);
}
}
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// do nothing.
}
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// do nothing.
}
- public void selectionChanged(BitSet arg0)
+ public void selectionChanged(BS arg0)
{
// TODO Auto-generated method stub
}
{
// TODO Auto-generated method stub
}
+ @Override
public void refreshPdbEntries()
{
public void refreshPdbEntries()
{
- // TODO Auto-generated method stub
-
+ // noop
}
@Override
}
@Override
@@
-151,12
+162,11
@@
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
@Override
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
Container consolePanel, String buttonsToShow)
{
- // return new org.jmol.console.AppletConsole(viewer2, consolePanel);
- JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole()
- .getAppConsole(viewer2);
+ JmolAppConsoleInterface appc = new AppletConsole();
+ appc.start(viewer);
return appc;
}
return appc;
}
@@
-164,20
+174,7
@@
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
protected void releaseUIResources()
{
appletJmolBinding = null;
protected void releaseUIResources()
{
appletJmolBinding = null;
- if (console != null)
- {
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
- }
-
+ closeConsole();
}
@Override
}
@Override
@@
-186,9
+183,16
@@
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
@Override
}
@Override
- public void resizeInnerPanel(String data)
+ public Dimension resizeInnerPanel(String data)
{
// TODO Auto-generated method stub
{
// TODO Auto-generated method stub
+ return null;
+ }
+ @Override
+ public Map<String, Object> getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
}
}
}
}