X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=80fafe3697fefc143b7a608bf42338d31e56401b;hb=ad15cff29620f960119f80176f1fd443da9f6763;hp=ffe00b54f535937c457a89fc577f8bb9d3aa902b;hpb=362f2db1b01f3562784864a1d6ac5f7b9be0a18a;p=jalview.git
diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index ffe00b5..80fafe3 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,34 +1,35 @@
/*
- * 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
-import java.awt.Container;
-import java.util.BitSet;
-
import jalview.api.AlignmentViewPanel;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
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.applet.AppletConsole;
import org.jmol.popup.JmolPopup;
class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
@@ -39,17 +40,19 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
*/
private AppletJmol appletJmolBinding;
- public AppletJmolBinding(AppletJmol appletJmol, StructureSelectionManager sSm, PDBEntry[] pdbentry,
+ public AppletJmolBinding(AppletJmol appletJmol,
+ StructureSelectionManager sSm, PDBEntry[] pdbentry,
SequenceI[][] seq, String[][] chains, String protocol)
{
super(sSm, pdbentry, seq, chains, protocol);
appletJmolBinding = appletJmol;
}
- public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (AlignmentPanel)alignment;
- if (appletJmolBinding.ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (AlignmentPanel) alignment;
+ if (appletJmolBinding.ap.av.isShowSequenceFeatures())
{
if (appletJmolBinding.fr == null)
{
@@ -65,15 +68,18 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
return appletJmolBinding.fr;
}
- 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)
{
if (appletJmolBinding.scriptWindow == null)
+ {
appletJmolBinding.showConsole(true);
+ }
appletJmolBinding.history.append("\n" + strEcho);
}
@@ -101,7 +107,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
public void showUrl(String url)
@@ -119,8 +125,8 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
boolean asPopup)
{
- jmolpopup = JmolPopup.newJmolPopup(viewer, translateLocale, menuName,
- asPopup);
+ jmolpopup = new JmolPopup();
+ jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
}
public void notifyScriptTermination(String strStatus, int msWalltime)
@@ -134,10 +140,10 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
+ @Override
public void refreshPdbEntries()
{
- // TODO Auto-generated method stub
-
+ // noop
}
@Override
@@ -150,27 +156,17 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
Container consolePanel, String buttonsToShow)
{
- return new AppletConsole(viewer2, consolePanel);
+ // return new org.jmol.console.AppletConsole(viewer2, consolePanel);
+ JmolAppConsoleInterface appc = new org.jmol.console.AppletConsole()
+ .getAppConsole(viewer2);
+ return appc;
}
@Override
protected void releaseUIResources()
{
appletJmolBinding = null;
- if (console != null)
- {
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
- }
-
+ closeConsole();
}
@Override
@@ -178,4 +174,10 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
{
}
+ @Override
+ public void resizeInnerPanel(String data)
+ {
+ // TODO Auto-generated method stub
+
+ }
}