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JAL-1807 explicit imports (jalview.ws.*)
[jalview.git]
/
src
/
jalview
/
gui
/
JalviewChimeraBindingModel.java
diff --git
a/src/jalview/gui/JalviewChimeraBindingModel.java
b/src/jalview/gui/JalviewChimeraBindingModel.java
index
f7c4878
..
a5af244
100644
(file)
--- a/
src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/
src/jalview/gui/JalviewChimeraBindingModel.java
@@
-10,6
+10,8
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
{
private ChimeraViewFrame cvf;
{
private ChimeraViewFrame cvf;
+ private FeatureRenderer fr = null;
+
public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
SequenceI[][] sequenceIs, String[][] chains, String protocol)
public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
SequenceI[][] sequenceIs, String[][] chains, String protocol)
@@
-18,19
+20,17
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
cvf = chimeraViewFrame;
}
cvf = chimeraViewFrame;
}
- FeatureRenderer fr = null;
-
@Override
@Override
- public jalview.api.FeatureRenderer getFeatureRenderer(
+ public FeatureRenderer getFeatureRenderer(
AlignmentViewPanel alignment)
{
AlignmentViewPanel alignment)
{
- AlignmentPanel ap = (alignment == null) ? cvf.ap
+ AlignmentPanel ap = (alignment == null) ? cvf.getAlignmentPanel()
: (AlignmentPanel) alignment;
: (AlignmentPanel) alignment;
- if (ap.av.showSequenceFeatures)
+ if (ap.av.isShowSequenceFeatures())
{
if (fr == null)
{
{
if (fr == null)
{
- fr = ap.cloneFeatureRenderer();
+ fr = (jalview.gui.FeatureRenderer) ap.cloneFeatureRenderer();
}
else
{
}
else
{
@@
-47,10
+47,10
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
{
return new SequenceRenderer(((AlignmentPanel) alignment).av);
}
+
@Override
public void refreshGUI()
{
@Override
public void refreshGUI()
{
- // appJmolWindow.repaint();
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
@@
-63,40
+63,57
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
public void updateColours(Object source)
{
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 (!cvf.isUsedforcolourby(ap))
// ignore events from panels not used to colour this view
if (!cvf.isUsedforcolourby(ap))
+ {
return;
return;
+ }
if (!isLoadingFromArchive())
{
if (!isLoadingFromArchive())
{
- colourBySequence(ap.av.getShowSequenceFeatures(), ap);
+ colourBySequence(ap.av.isShowSequenceFeatures(), ap);
}
}
}
}
+
@Override
public void releaseReferences(Object svl)
{
@Override
public void releaseReferences(Object svl)
{
- // TODO Auto-generated method stub
-
}
@Override
protected void releaseUIResources()
{
}
@Override
protected void releaseUIResources()
{
- // TODO Auto-generated method stub
-
}
@Override
public void refreshPdbEntries()
{
}
@Override
public void refreshPdbEntries()
{
- // TODO Auto-generated method stub
-
}
}
- @Override
- public void showUrl(String url, String target)
+ /**
+ * Send an asynchronous command to Chimera, in a new thread, optionally with
+ * an 'in progress' message in a progress bar somewhere
+ */
+ protected void sendAsynchronousCommand(final String command,
+ final String progressMsg)
{
{
- // TODO Auto-generated method stub
+ Thread thread = new Thread(new Runnable()
+ {
+
+ @Override
+ public void run()
+ {
+ long stm = cvf.startProgressBar(progressMsg);
+ try
+ {
+ sendChimeraCommand(command, false);
+ } finally
+ {
+ cvf.stopProgressBar(null, stm);
+ }
+ }
+ });
+ thread.start();
}
}
}
}