*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
public interface ColourSchemeI
{
/**
- * Returns the colour for the given character. For use when the colour depends
- * only on the symbol.
- *
- * @param c
- * @return
- */
- Color findColour(char c);
-
- /**
* Returns the possibly context dependent colour for the given symbol at the
* aligned position in the given sequence. For example, the colour may depend
* on the symbol's relationship to the consensus residue for the column.
* new instance for each call to this method, as different instances may have
* differing shading by consensus or percentage identity applied.
*
+ * @param viewport
+ * - the parent viewport
* @param sg
- * @param hiddenRepSequences
+ * - the collection of sequences to be coloured
* @return copy of current scheme with any inherited settings transferred
*/
- ColourSchemeI getInstance(AnnotatedCollectionI sg,
- Map<SequenceI, SequenceCollectionI> hiddenRepSequences);
+ ColourSchemeI getInstance(AlignViewportI viewport,
+ AnnotatedCollectionI sg);
/**
* Answers true if the colour scheme is suitable for the given data, else
* @return
*/
boolean isSimple();
+
+ /**
+ * Answers true if the colour scheme has a colour specified for gaps.
+ *
+ * @return
+ */
+ boolean hasGapColour();
}