*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.AnnotatedCollectionI;
// assume only one set of TCOFFEE scores - but could have more than one
// potentially.
- List<AlignmentAnnotation> annots = new ArrayList<AlignmentAnnotation>();
+ List<AlignmentAnnotation> annots = new ArrayList<>();
// Search alignment to get all tcoffee annotation and pick one set of
// annotation to use to colour seqs.
- seqMap = new IdentityHashMap<SequenceI, Color[]>();
- AnnotatedCollectionI alcontext = alignment instanceof AlignmentI ? alignment
+ seqMap = new IdentityHashMap<>();
+ AnnotatedCollectionI alcontext = alignment instanceof AlignmentI
+ ? alignment
: alignment.getContext();
if (alcontext == null)
{
}
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences)
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI sg)
{
return new TCoffeeColourScheme(sg);
}
@Override
public boolean isApplicableTo(AnnotatedCollectionI ac)
{
- AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac : ac
- .getContext();
+ AnnotatedCollectionI alcontext = ac instanceof AlignmentI ? ac
+ : ac.getContext();
if (alcontext == null)
{
return false;