*/
package jalview.ext.rbvi.chimera;
-import java.awt.Color;
-import java.net.BindException;
-import java.util.ArrayList;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
+import java.awt.Color;
+import java.net.BindException;
+import java.util.ArrayList;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
+
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
{
// Chimera clause to exclude alternate locations in atom selection
* if colourBySequence is enabled.
*/
public void colourBySequence(boolean showFeatures,
- jalview.api.AlignmentViewPanel alignmentv)
+ AlignmentViewPanel alignmentv)
{
if (!colourBySequence || !loadingFinished)
{
}
AlignmentI alignment = alignmentv.getAlignment();
- for (jalview.structure.StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
+ for (StructureMappingcommandSet cpdbbyseq : getColourBySequenceCommands(
files, sr, fr, alignment))
{
for (String command : cpdbbyseq.commands)