git://source.jalview.org
/
jalview.git
/ blobdiff
commit
grep
author
committer
pickaxe
?
search:
re
summary
|
shortlog
|
log
|
commit
|
commitdiff
|
tree
raw
|
inline
| side by side
JAL-3066 Fix NullPointerException thrown when showing HMMER run dialog
[jalview.git]
/
src
/
jalview
/
gui
/
AppJmolBinding.java
diff --git
a/src/jalview/gui/AppJmolBinding.java
b/src/jalview/gui/AppJmolBinding.java
index
9325172
..
75b98bc
100644
(file)
--- a/
src/jalview/gui/AppJmolBinding.java
+++ b/
src/jalview/gui/AppJmolBinding.java
@@
-28,17
+28,20
@@
import jalview.datamodel.SequenceI;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
import jalview.ext.jmol.JalviewJmolBinding;
import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
+import jalview.util.Platform;
import java.awt.Container;
import java.awt.Container;
+import java.io.File;
+import java.util.List;
import java.util.Map;
import org.jmol.api.JmolAppConsoleInterface;
import java.util.Map;
import org.jmol.api.JmolAppConsoleInterface;
-import org.jmol.java.BS;
-import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+
+import javajs.util.BS;
public class AppJmolBinding extends JalviewJmolBinding
{
public class AppJmolBinding extends JalviewJmolBinding
{
- private AppJmol appJmolWindow;
+ protected AppJmol appJmolWindow;
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
PDBEntry[] pdbentry, SequenceI[][] sequenceIs,
@@
-49,6
+52,12
@@
public class AppJmolBinding extends JalviewJmolBinding
}
@Override
}
@Override
+ protected IProgressIndicator getIProgressIndicator()
+ {
+ return appJmolWindow.progressBar;
+ }
+
+ @Override
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
public SequenceRenderer getSequenceRenderer(AlignmentViewPanel alignment)
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
@@
-97,6
+106,8
@@
public class AppJmolBinding extends JalviewJmolBinding
public void run()
{
appJmolWindow.updateTitleAndMenus();
public void run()
{
appJmolWindow.updateTitleAndMenus();
+ // initiates a colourbySequence
+ // via seqColour_ActionPerformed.
appJmolWindow.revalidate();
}
});
appJmolWindow.revalidate();
}
});
@@
-163,7
+174,7
@@
public class AppJmolBinding extends JalviewJmolBinding
Container consolePanel, String buttonsToShow)
{
viewer.setJmolCallbackListener(this);
Container consolePanel, String buttonsToShow)
{
viewer.setJmolCallbackListener(this);
- return new AppConsole(viewer, consolePanel, buttonsToShow);
+ return null;//BH can't do this yet. new AppConsole(viewer, consolePanel, buttonsToShow);
}
@Override
}
@Override
@@
-209,4
+220,17
@@
public class AppJmolBinding extends JalviewJmolBinding
return null;
}
return null;
}
+
+ @SuppressWarnings("unused")
+ public void cacheFiles(List<File> files)
+ {
+ if (files == null)
+ {
+ return;
+ }
+ for (File f : files)
+ {
+ Platform.cacheFileData(f);
+ }
+ }
}
}