X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=98787cbb749edd01f9eb5e9859940ba57fa9146a;hb=refs%2Fheads%2Ffeature%2FJAL-3551Pymol;hp=b8b60bcba81fa60f9133c6dcf8980f9f2734f0bf;hpb=59d682209891099d46b960509907c79e3fb276fe;p=jalview.git
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index b8b60bc..98787cb 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,89 +1,63 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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.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 java.io.File;
+import java.util.List;
+import java.util.Map;
-import javax.swing.JPanel;
+import javax.swing.JComponent;
+
+import org.jmol.api.JmolAppConsoleInterface;
+import org.openscience.jmol.app.jmolpanel.console.AppConsole;
import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
+import javajs.util.BS;
-import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.api.JmolViewer;
-import org.jmol.popup.JmolPopup;
-import org.openscience.jmol.app.jmolpanel.AppConsole;
-
-public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
+public class AppJmolBinding extends JalviewJmolBinding
{
-
- /**
- *
- */
- private AppJmol appJmolWindow;
-
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
- PDBEntry[] pdbentry, SequenceI[][] sequenceIs, String[][] chains,
- String protocol)
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- super(sSm, pdbentry, sequenceIs, chains, protocol);
- appJmolWindow = appJmol;
- }
-
- FeatureRenderer fr = null;
-
- @Override
- public jalview.api.FeatureRenderer getFeatureRenderer(
- AlignmentViewPanel alignment)
- {
- AlignmentPanel ap = (alignment == null) ? appJmolWindow.ap
- : (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
- {
- if (fr == null)
- {
- fr = ap.cloneFeatureRenderer();
- }
- else
- {
- ap.updateFeatureRenderer(fr);
- }
- }
-
- return fr;
+ super(sSm, pdbentry, sequenceIs, protocol);
+ setViewer(appJmol);
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer(
- AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+ @Override
public void sendConsoleEcho(String strEcho)
{
if (console != null)
@@ -92,6 +66,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
if (console != null && strStatus != null)
@@ -118,29 +93,26 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
@Override
public void refreshGUI()
{
+ if (getMappedStructureCount() == 0)
+ {
+ // too soon!
+ return;
+ }
// appJmolWindow.repaint();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- appJmolWindow.updateTitleAndMenus();
- appJmolWindow.revalidate();
+ JalviewStructureDisplayI theViewer = getViewer();
+ // invokes colourbySequence() via seqColour_ActionPerformed()
+ theViewer.updateTitleAndMenus();
+ ((JComponent) theViewer).revalidate();
}
});
}
- public void updateColours(Object source)
- {
- AlignmentPanel ap = (AlignmentPanel) source, topap;
- // ignore events from panels not used to colour this view
- if (!appJmolWindow.isUsedforcolourby(ap))
- return;
- if (!isLoadingFromArchive())
- {
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
- }
- }
-
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// todo - script termination doesn't happen ?
@@ -149,80 +121,44 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
// msWalltime);
}
+ @Override
public void showUrl(String url)
{
showUrl(url, "jmol");
}
- public void newJmolPopup(boolean translateLocale, String menuName,
- boolean asPopup)
- {
-
- jmolpopup = new JmolPopup();
- jmolpopup.initialize(viewer, translateLocale, menuName, asPopup);
- }
-
- public void selectionChanged(BitSet arg0)
+ public void newJmolPopup(String menuName)
{
- // TODO Auto-generated method stub
-
+ // jmolpopup = new JmolAwtPopup();
+ // jmolpopup.jpiInitialize((viewer), menuName);
}
- public void refreshPdbEntries()
+ @Override
+ public void selectionChanged(BS arg0)
{
- // TODO Auto-generated method stub
-
}
+ @Override
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)
- {
- for (int pe = 0; pe < pdbentry.length; pe++)
- {
- if (pdbentry[pe].getFile().equals(pdbFile))
- {
- addSequence(pe, seq);
- }
- }
+ getViewer().showConsole(b);
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
- return new AppConsole(viewer, consolePanel, buttonsToShow);
+ jmolViewer.setJmolCallbackListener(this);
+ // BH comment: can't do this yet [for JS only, or generally?]
+ return Platform.isJS() ? null
+ : new AppConsole(jmolViewer, consolePanel, buttonsToShow);
}
@Override
protected void releaseUIResources()
{
- appJmolWindow = null;
- if (console != null)
- {
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
- }
-
+ setViewer(null);
+ closeConsole();
}
@Override
@@ -230,9 +166,27 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
{
if (svl instanceof SeqPanel)
{
- appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
+ getViewer().removeAlignmentPanel(((SeqPanel) svl).ap);
+ }
+ }
+ @Override
+ public Map getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
+ @SuppressWarnings("unused")
+ public void cacheFiles(List files)
+ {
+ if (files == null)
+ {
+ return;
+ }
+ for (File f : files)
+ {
+ Platform.cacheFileData(f);
}
- ;
}
}