X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=eb15a651246d1705184426f7d4c8e8a8f18594a3;hb=9876fdccf311378e690c1f9e18db52675d427b89;hp=f051838f30ab6875c281d086ac8ae9dbbdc8f6ca;hpb=1b5f1de68f3f4dadcd4eecc80a5db17441eb7ab6;p=jalview.git
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index f051838..eb15a65 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,66 +1,80 @@
-/**
+/*
+ * 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.
+ *
+ * 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 .
+ * 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.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.structure.StructureSelectionManager;
+
+import java.awt.Container;
+import java.util.Map;
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 jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
{
-
- /**
- *
- */
private AppJmol appJmolWindow;
- public AppJmolBinding(AppJmol appJmol, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ private FeatureRenderer fr = null;
+
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
+ String protocol)
{
- super(pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, chains, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ public FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
{
- if (appJmolWindow.ap.av.showSequenceFeatures)
+ AlignmentPanel ap = (alignment == null) ? appJmolWindow
+ .getAlignmentPanel() : (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
- fr = new FeatureRenderer(appJmolWindow.ap);
+ fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
+ }
+ else
+ {
+ ap.updateFeatureRenderer(fr);
}
-
- fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
}
return fr;
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer()
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
- return new SequenceRenderer(appJmolWindow.ap.av);
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
if (console != null)
@@ -69,6 +83,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
if (console != null && strStatus != null)
@@ -96,28 +111,37 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
public void refreshGUI()
{
// appJmolWindow.repaint();
- javax.swing.SwingUtilities.invokeLater(new Runnable() {
- public void run() {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
appJmolWindow.updateTitleAndMenus();
appJmolWindow.revalidate();
- }});
+ }
+ });
}
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
- if (appJmolWindow.ap.alignFrame.getCurrentView() != ap.av)
+ // ignore events from panels not used to colour this view
+ if (!appJmolWindow.isUsedforcolourby(ap))
+ {
return;
-
- colourBySequence(ap.av.getShowSequenceFeatures(), ap.av.alignment);
+ }
+ if (!isLoadingFromArchive())
+ {
+ colourBySequence(ap);
+ }
}
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// todo - script termination doesn't happen ?
- //if (console != null)
- //console.notifyScriptTermination(strStatus,
- // msWalltime);
+ // if (console != null)
+ // console.notifyScriptTermination(strStatus,
+ // msWalltime);
}
public void showUrl(String url)
@@ -125,53 +149,37 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
showUrl(url, "jmol");
}
- public void newJmolPopup(boolean translateLocale, String menuName,
- boolean asPopup)
+ public void newJmolPopup(String menuName)
{
-
- jmolpopup = JmolPopup.newJmolPopup(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
}
+ @Override
public void refreshPdbEntries()
{
// TODO Auto-generated method stub
}
- public void showConsole(boolean b) {
- appJmolWindow.showConsole(b);
- }
-
- /**
- * add the given sequences to the mapping scope for the given pdb file handle
- *
- * @param pdbFile
- * - pdbFile identifier
- * @param seq
- * - set of sequences it can be mapped to
- */
- public void addSequenceForStructFile(String pdbFile, SequenceI[] seq)
+ @Override
+ public void showConsole(boolean b)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
- {
- if (pdbentry[pe].getFile().equals(pdbFile))
- {
- addSequence(pe, seq);
- }
- }
+ appJmolWindow.showConsole(b);
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
+ viewer.setJmolCallbackListener(this);
return new AppConsole(viewer, consolePanel, buttonsToShow);
}
@@ -179,12 +187,22 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
protected void releaseUIResources()
{
appJmolWindow = null;
- if (console!=null) {
- try {
- console.setVisible(false);
- } catch (Error e) {} catch (Exception x) {};
- console=null;
+ closeConsole();
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ if (svl instanceof SeqPanel)
+ {
+ appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
}
-
}
-}
\ No newline at end of file
+
+ @Override
+ public Map getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+}