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spike branch updated from latest features/JAL-2446
[jalview.git]
/
src
/
jalview
/
ext
/
rbvi
/
chimera
/
ChimeraCommands.java
diff --git
a/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
b/src/jalview/ext/rbvi/chimera/ChimeraCommands.java
index
95757fd
..
e9ce49b
100644
(file)
--- a/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
+++ b/
src/jalview/ext/rbvi/chimera/ChimeraCommands.java
@@
-25,7
+25,7
@@
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.renderer.seqfeatures.FeatureColourFinder;
@@
-194,7
+194,7
@@
public class ChimeraCommands
FeatureRenderer fr = viewPanel.getFeatureRenderer();
FeatureColourFinder finder = new FeatureColourFinder(fr);
AlignViewportI viewport = viewPanel.getAlignViewport();
FeatureRenderer fr = viewPanel.getFeatureRenderer();
FeatureColourFinder finder = new FeatureColourFinder(fr);
AlignViewportI viewport = viewPanel.getAlignViewport();
- ColumnSelection cs = viewport.getColumnSelection();
+ HiddenColumns cs = viewport.getAlignment().getHiddenColumns();
AlignmentI al = viewport.getAlignment();
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
Color lastColour = null;
AlignmentI al = viewport.getAlignment();
Map<Object, AtomSpecModel> colourMap = new LinkedHashMap<Object, AtomSpecModel>();
Color lastColour = null;
@@
-411,12
+411,8
@@
public class ChimeraCommands
StructureMapping mapping, SequenceI seq,
Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
StructureMapping mapping, SequenceI seq,
Map<String, Map<Object, AtomSpecModel>> theMap, int modelNumber)
{
- SequenceFeature[] sfs = seq.getSequenceFeatures();
- if (sfs == null)
- {
- return;
- }
-
+ List<SequenceFeature> sfs = seq.getFeatures().getPositionalFeatures(
+ visibleFeatures.toArray(new String[visibleFeatures.size()]));
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
for (SequenceFeature sf : sfs)
{
String type = sf.getType();
@@
-427,7
+423,7
@@
public class ChimeraCommands
*/
boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
.equals(sf.getFeatureGroup());
*/
boolean isFromViewer = JalviewChimeraBinding.CHIMERA_FEATURE_GROUP
.equals(sf.getFeatureGroup());
- if (isFromViewer || !visibleFeatures.contains(type))
+ if (isFromViewer)
{
continue;
}
{
continue;
}