X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAppJmolBinding.java;h=f822358ebd1990c0e53a0a413374389349604fcc;hb=136c0793b90b72b928c4d77dc109dd5c644e00d3;hp=df62eabe1b33c15475b192dd86e03c4784e883d6;hpb=7ef02aa7c7559f3a37f2f0524243c52b00335294;p=jalview.git
diff --git a/src/jalview/gui/AppJmolBinding.java b/src/jalview/gui/AppJmolBinding.java
index df62eab..f822358 100644
--- a/src/jalview/gui/AppJmolBinding.java
+++ b/src/jalview/gui/AppJmolBinding.java
@@ -1,83 +1,59 @@
/*
- * 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 ($$Version-Rel$$)
+ * 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.AlignmentI;
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 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, StructureSelectionManager sSm, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
+ PDBEntry[] pdbentry, SequenceI[][] sequenceIs, DataSourceType protocol)
{
- super(sSm, pdbentry, sequenceIs, chains, protocol);
+ super(sSm, pdbentry, sequenceIs, protocol);
appJmolWindow = appJmol;
}
- FeatureRenderer fr = null;
-
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer(AlignmentViewPanel alignment)
+ public SequenceRenderer getSequenceRenderer(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;
+ return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
@Override
- public jalview.api.SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
- {
- return new SequenceRenderer(((AlignmentPanel)alignment).av);
- }
-
public void sendConsoleEcho(String strEcho)
{
if (console != null)
@@ -86,6 +62,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
}
}
+ @Override
public void sendConsoleMessage(String strStatus)
{
if (console != null && strStatus != null)
@@ -115,6 +92,7 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
// appJmolWindow.repaint();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
appJmolWindow.updateTitleAndMenus();
@@ -123,17 +101,22 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
});
}
+ @Override
public void updateColours(Object source)
{
- AlignmentPanel ap = (AlignmentPanel) source,topap;
+ AlignmentPanel ap = (AlignmentPanel) source;
// ignore events from panels not used to colour this view
if (!appJmolWindow.isUsedforcolourby(ap))
+ {
return;
- if (!isLoadingFromArchive()) {
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ }
+ if (!isLoadingFromArchive())
+ {
+ colourBySequence(ap);
}
}
+ @Override
public void notifyScriptTermination(String strStatus, int msWalltime)
{
// todo - script termination doesn't happen ?
@@ -142,60 +125,43 @@ 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)
+ public void newJmolPopup(String menuName)
{
-
- jmolpopup = new JmolPopup();
- jmolpopup.initialize(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
}
+ @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);
- }
- }
- }
-
@Override
- protected JmolAppConsoleInterface createJmolConsole(JmolViewer viewer2,
+ protected JmolAppConsoleInterface createJmolConsole(
Container consolePanel, String buttonsToShow)
{
+ viewer.setJmolCallbackListener(this);
return new AppConsole(viewer, consolePanel, buttonsToShow);
}
@@ -203,28 +169,42 @@ public class AppJmolBinding extends jalview.ext.jmol.JalviewJmolBinding
protected void releaseUIResources()
{
appJmolWindow = null;
- if (console != null)
+ closeConsole();
+ }
+
+ @Override
+ public void releaseReferences(Object svl)
+ {
+ if (svl instanceof SeqPanel)
{
- try
- {
- console.setVisible(false);
- } catch (Error e)
- {
- } catch (Exception x)
- {
- }
- ;
- console = null;
+ appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
}
+ }
+ @Override
+ public Map getJSpecViewProperty(String arg0)
+ {
+ // TODO Auto-generated method stub
+ return null;
}
@Override
- public void releaseReferences(Object svl)
+ public JalviewStructureDisplayI getViewer()
{
- if (svl instanceof SeqPanel) {
- appJmolWindow.removeAlignmentPanel(((SeqPanel) svl).ap);
-
- };
+ 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;
}
}