X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=eeb48887fb4ee2244ada8e0566f712008fb8a38e;hb=26b115b0a77d521da92a06572d9b7819c2d0d49a;hp=38c9e704720b144c2e45c8547d82d5631a967c85;hpb=153dd62dc91da13ae732600e6ea55ddbe15eab39;p=jalview.git
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index 38c9e70..eeb4888 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,80 +1,66 @@
/*
- * 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.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.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
+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 javajs.util.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)
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
+ DataSourceType protocol)
{
- super(pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer()
+ protected IProgressIndicator getIProgressIndicator()
{
- if (appJmolWindow.ap.av.showSequenceFeatures)
- {
- if (fr == null)
- {
- fr = new FeatureRenderer(appJmolWindow.ap);
- }
-
- fr.transferSettings(appJmolWindow.ap.seqPanel.seqCanvas
- .getFeatureRenderer());
- }
-
- return fr;
+ return appJmolWindow.progressBar;
}
@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)
@@ -83,6 +69,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
if (console != null && strStatus != null)
@@ -110,95 +97,122 @@ 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()
+ {
+ @Override
+ public void run()
+ {
appJmolWindow.updateTitleAndMenus();
appJmolWindow.revalidate();
- }});
+ }
+ });
}
+ @Override
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);
}
+ @Override
public void showUrl(String url)
{
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) {
+ @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)
+ @Override
+ protected JmolAppConsoleInterface createJmolConsole(
+ Container consolePanel, String buttonsToShow)
+ {
+ viewer.setJmolCallbackListener(this);
+ return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow);
+ }
+
+ @Override
+ protected void releaseUIResources()
+ {
+ appJmolWindow = null;
+ closeConsole();
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
{
- for (int pe = 0; pe < pdbentry.length; pe++)
+ if (svl instanceof SeqPanel)
{
- if (pdbentry[pe].getFile().equals(pdbFile))
- {
- addSequence(pe, seq);
- }
+ appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
}
}
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
- Container consolePanel, String buttonsToShow)
+ public Map getJSpecViewProperty(String arg0)
{
- return new AppConsole(viewer, consolePanel, buttonsToShow);
+ // TODO Auto-generated method stub
+ return null;
}
@Override
- protected void releaseUIResources()
+ public JalviewStructureDisplayI getViewer()
{
- appJmolWindow = null;
- if (console!=null) {
- try {
- console.setVisible(false);
- } catch (Error e) {} catch (Exception x) {};
- console=null;
+ return appJmolWindow;
+ }
+
+ @Override
+ public jalview.api.FeatureRenderer getFeatureRenderer(
+ AlignmentViewPanel alignment)
+ {
+ AlignmentPanel ap = (alignment == null)
+ ? appJmolWindow.getAlignmentPanel()
+ : (AlignmentPanel) alignment;
+ if (ap.av.isShowSequenceFeatures())
+ {
+ return ap.av.getAlignPanel().getSeqPanel().seqCanvas.fr;
}
-
+
+ return null;
}
}