X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fappletgui%2FAppletJmolBinding.java;h=f7a121c518b98e75da846417abf4e0bba77b3654;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=3fccad754bd9d2ea3e9cc89e0a4759957c6cc016;hpb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;p=jalview.git
diff --git a/src/jalview/appletgui/AppletJmolBinding.java b/src/jalview/appletgui/AppletJmolBinding.java
index 3fccad7..f7a121c 100644
--- a/src/jalview/appletgui/AppletJmolBinding.java
+++ b/src/jalview/appletgui/AppletJmolBinding.java
@@ -1,37 +1,41 @@
/*
- * 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 2.9)
+ * Copyright (C) 2015 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.ext.jmol.JalviewJmolBinding;
import jalview.structure.StructureSelectionManager;
+import java.awt.Container;
+import java.util.Map;
+
+import javajs.awt.Dimension;
+
import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.applet.AppletConsole;
-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
{
/**
@@ -39,17 +43,20 @@ 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)
+ @Override
+ 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)
{
@@ -65,34 +72,42 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
return appletJmolBinding.fr;
}
- public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
+ @Override
+ public jalview.api.SequenceRenderer getSequenceRenderer(
+ AlignmentViewPanel alignment)
{
- return new SequenceRenderer(((AlignmentPanel)alignment).av);
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
if (appletJmolBinding.scriptWindow == null)
+ {
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"))
{
- appletJmolBinding.history.append("\n" + strStatus);
+ appletJmolBinding.addToHistory(strStatus);
}
}
+ @Override
public void showUrl(String url, String target)
{
appletJmolBinding.ap.alignFrame.showURL(url, target);
}
+ @Override
public void refreshGUI()
{
appletJmolBinding.updateTitleAndMenus();
@@ -101,7 +116,7 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ colourBySequence(ap);
}
public void showUrl(String url)
@@ -118,26 +133,26 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
public void newJmolPopup(boolean translateLocale, String menuName,
boolean asPopup)
{
-
- jmolpopup = JmolPopup.newJmolPopup(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 selectionChanged(BitSet arg0)
+ public void selectionChanged(BS arg0)
{
// TODO Auto-generated method stub
}
+ @Override
public void refreshPdbEntries()
{
- // TODO Auto-generated method stub
-
+ // noop
}
@Override
@@ -147,30 +162,19 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
- return new AppletConsole(viewer2, consolePanel);
+ JmolAppConsoleInterface appc = new AppletConsole();
+ appc.start(viewer);
+ 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 +182,17 @@ class AppletJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
{
}
+ @Override
+ public Dimension resizeInnerPanel(String data)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @Override
+ public Map getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
}