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JAL-2385 more tests/bug fixes mostly for gui.SliderPanel and some
[jalview.git]
/
src
/
jalview
/
gui
/
JalviewChimeraBindingModel.java
diff --git
a/src/jalview/gui/JalviewChimeraBindingModel.java
b/src/jalview/gui/JalviewChimeraBindingModel.java
index
d0a69cf
..
a797872
100644
(file)
--- a/
src/jalview/gui/JalviewChimeraBindingModel.java
+++ b/
src/jalview/gui/JalviewChimeraBindingModel.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2)
- * Copyright (C) 2015 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-21,9
+21,11
@@
package jalview.gui;
import jalview.api.AlignmentViewPanel;
package jalview.gui;
import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
+import jalview.io.DataSourceType;
import jalview.structure.StructureSelectionManager;
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
import jalview.structure.StructureSelectionManager;
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
@@
-32,11
+34,12
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
private FeatureRenderer fr = null;
private FeatureRenderer fr = null;
+
public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
public JalviewChimeraBindingModel(ChimeraViewFrame chimeraViewFrame,
StructureSelectionManager ssm, PDBEntry[] pdbentry,
- SequenceI[][] sequenceIs, String[][] chains, String protocol)
+ SequenceI[][] sequenceIs, DataSourceType protocol)
{
{
- super(ssm, pdbentry, sequenceIs, chains, protocol);
+ super(ssm, pdbentry, sequenceIs, protocol);
cvf = chimeraViewFrame;
}
cvf = chimeraViewFrame;
}
@@
-72,6
+75,7
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
cvf.updateTitleAndMenus();
public void run()
{
cvf.updateTitleAndMenus();
@@
-80,6
+84,7
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
});
}
});
}
+ @Override
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
public void updateColours(Object source)
{
AlignmentPanel ap = (AlignmentPanel) source;
@@
-90,7
+95,7
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
}
if (!isLoadingFromArchive())
{
}
if (!isLoadingFromArchive())
{
- colourBySequence(ap.av.isShowSequenceFeatures(), ap);
+ colourBySequence(ap);
}
}
}
}
@@
-113,6
+118,7
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
* Send an asynchronous command to Chimera, in a new thread, optionally with
* an 'in progress' message in a progress bar somewhere
*/
* Send an asynchronous command to Chimera, in a new thread, optionally with
* an 'in progress' message in a progress bar somewhere
*/
+ @Override
protected void sendAsynchronousCommand(final String command,
final String progressMsg)
{
protected void sendAsynchronousCommand(final String command,
final String progressMsg)
{
@@
-135,4
+141,10
@@
public class JalviewChimeraBindingModel extends JalviewChimeraBinding
thread.start();
}
thread.start();
}
+
+ @Override
+ public JalviewStructureDisplayI getViewer()
+ {
+ return cvf;
+ }
}
}