*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
*/
public class CovariationColourScheme extends ResidueColourScheme
{
- public Map<String, Color> helixcolorhash = new Hashtable<String, Color>();
+ public Map<String, Color> helixcolorhash = new Hashtable<>();
- public Map<Integer, String> positionsToHelix = new Hashtable<Integer, String>();
+ public Map<Integer, String> positionsToHelix = new Hashtable<>();
int numHelix = 0;
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll,
Map<SequenceI, SequenceCollectionI> hrs)
{
return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
this.annotation._rnasecstr[x].getFeatureGroup());
- if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
+ if (Integer.parseInt(
+ this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
{
- numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup());
+ numHelix = Integer
+ .parseInt(this.annotation._rnasecstr[x].getFeatureGroup());
}
}
{
return "Covariation";
}
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}