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JAL-1752 structure highlight scoped to only its mapped sequences
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 5 Jun 2015 15:26:15 +0000
(16:26 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 5 Jun 2015 15:26:15 +0000
(16:26 +0100)
src/MCview/AppletPDBCanvas.java
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src/MCview/PDBCanvas.java
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src/jalview/gui/AppVarnaBinding.java
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src/jalview/javascript/MouseOverStructureListener.java
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src/jalview/structure/StructureListener.java
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src/jalview/structure/StructureSelectionManager.java
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src/jalview/structures/models/AAStructureBindingModel.java
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diff --git
a/src/MCview/AppletPDBCanvas.java
b/src/MCview/AppletPDBCanvas.java
index
c1c4b2f
..
dc69f43
100644
(file)
--- a/
src/MCview/AppletPDBCanvas.java
+++ b/
src/MCview/AppletPDBCanvas.java
@@
-1227,4
+1227,20
@@
public class AppletPDBCanvas extends Panel implements MouseListener,
// TODO Auto-generated method stub
}
// TODO Auto-generated method stub
}
+
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ if (sequence != null)
+ {
+ for (SequenceI s : sequence)
+ {
+ if (s == seq)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
}
}
diff --git
a/src/MCview/PDBCanvas.java
b/src/MCview/PDBCanvas.java
index
76bf59b
..
406d9f1
100644
(file)
--- a/
src/MCview/PDBCanvas.java
+++ b/
src/MCview/PDBCanvas.java
@@
-1185,4
+1185,20
@@
public class PDBCanvas extends JPanel implements MouseListener,
// TODO Auto-generated method stub
}
// TODO Auto-generated method stub
}
+
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ if (sequence != null)
+ {
+ for (SequenceI s : sequence)
+ {
+ if (s == seq)
+ {
+ return true;
+ }
+ }
+ }
+ return false;
+ }
}
}
diff --git
a/src/jalview/gui/AppVarnaBinding.java
b/src/jalview/gui/AppVarnaBinding.java
index
7894ee2
..
38385f0
100644
(file)
--- a/
src/jalview/gui/AppVarnaBinding.java
+++ b/
src/jalview/gui/AppVarnaBinding.java
@@
-20,9
+20,6
@@
*/
package jalview.gui;
*/
package jalview.gui;
-import jalview.structure.AtomSpec;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Component;
@@
-72,6
+69,10
@@
import fr.orsay.lri.varna.models.VARNAConfig;
import fr.orsay.lri.varna.models.rna.Mapping;
import fr.orsay.lri.varna.models.rna.RNA;
import fr.orsay.lri.varna.models.rna.Mapping;
import fr.orsay.lri.varna.models.rna.RNA;
+import jalview.datamodel.SequenceI;
+import jalview.structure.AtomSpec;
+import jalview.util.MessageManager;
+
public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
implements DropTargetListener, InterfaceVARNAListener,
MouseListener
public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
implements DropTargetListener, InterfaceVARNAListener,
MouseListener
@@
-920,4
+921,10
@@
public class AppVarnaBinding extends jalview.ext.varna.JalviewVarnaBinding
public void highlightAtoms(List<AtomSpec> atoms)
{
}
public void highlightAtoms(List<AtomSpec> atoms)
{
}
+
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ return true;
+ }
}
}
diff --git
a/src/jalview/javascript/MouseOverStructureListener.java
b/src/jalview/javascript/MouseOverStructureListener.java
index
f46cd90
..
4b1c9ce
100644
(file)
--- a/
src/jalview/javascript/MouseOverStructureListener.java
+++ b/
src/jalview/javascript/MouseOverStructureListener.java
@@
-20,6
+20,9
@@
*/
package jalview.javascript;
*/
package jalview.javascript;
+import java.util.ArrayList;
+import java.util.List;
+
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
@@
-33,9
+36,6
@@
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
-import java.util.ArrayList;
-import java.util.List;
-
/**
* Propagate events involving PDB structures associated with sequences to a
* javascript function. Generally, the javascript handler is called with a
/**
* Propagate events involving PDB structures associated with sequences to a
* javascript function. Generally, the javascript handler is called with a
@@
-312,4
+312,10
@@
public class MouseOverStructureListener extends JSFunctionExec implements
}
}
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ return true;
+ }
+
}
}
diff --git
a/src/jalview/structure/StructureListener.java
b/src/jalview/structure/StructureListener.java
index
69658bf
..
2364549
100644
(file)
--- a/
src/jalview/structure/StructureListener.java
+++ b/
src/jalview/structure/StructureListener.java
@@
-22,6
+22,8
@@
package jalview.structure;
import java.util.List;
import java.util.List;
+import jalview.datamodel.SequenceI;
+
public interface StructureListener
{
/**
public interface StructureListener
{
/**
@@
-56,4
+58,12
@@
public interface StructureListener
* @param svl
*/
public void releaseReferences(Object svl);
* @param svl
*/
public void releaseReferences(Object svl);
+
+ /**
+ * Answers true if this listener is interested in the given sequence
+ *
+ * @param seq
+ * @return
+ */
+ public boolean isListeningFor(SequenceI seq);
}
}
diff --git
a/src/jalview/structure/StructureSelectionManager.java
b/src/jalview/structure/StructureSelectionManager.java
index
ef4a7a5
..
0253a7e
100644
(file)
--- a/
src/jalview/structure/StructureSelectionManager.java
+++ b/
src/jalview/structure/StructureSelectionManager.java
@@
-756,6
+756,10
@@
public class StructureSelectionManager
protected void highlightStructure(StructureListener sl, SequenceI seq,
int index)
{
protected void highlightStructure(StructureListener sl, SequenceI seq,
int index)
{
+ if (!sl.isListeningFor(seq))
+ {
+ return;
+ }
int atomNo;
List<AtomSpec> atoms = new ArrayList<AtomSpec>();
for (StructureMapping sm : mappings)
int atomNo;
List<AtomSpec> atoms = new ArrayList<AtomSpec>();
for (StructureMapping sm : mappings)
diff --git
a/src/jalview/structures/models/AAStructureBindingModel.java
b/src/jalview/structures/models/AAStructureBindingModel.java
index
86c9a21
..
e77a23c
100644
(file)
--- a/
src/jalview/structures/models/AAStructureBindingModel.java
+++ b/
src/jalview/structures/models/AAStructureBindingModel.java
@@
-601,4
+601,26
@@
public abstract class AAStructureBindingModel extends
}
return true;
}
}
return true;
}
+
+ @Override
+ public boolean isListeningFor(SequenceI seq)
+ {
+ if (sequence != null)
+ {
+ for (SequenceI[] seqs : sequence)
+ {
+ if (seqs != null)
+ {
+ for (SequenceI s : seqs)
+ {
+ if (s == seq)
+ {
+ return true;
+ }
+ }
+ }
+ }
+ }
+ return false;
+ }
}
\ No newline at end of file
}
\ No newline at end of file