*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
-import java.awt.Color;
import java.util.Map;
/**
*/
public NucleotideColourScheme()
{
- super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide,
- 0);
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public Color findColour(char c)
- {
- // System.out.println("called"); log.debug
- return colors[ResidueProperties.nucleotideIndex[c]];
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- * @param j
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
- @Override
- public Color findColour(char c, int j, SequenceI seq)
- {
- Color currentColour;
- if ((threshold == 0) || aboveThreshold(c, j))
- {
- try
- {
- currentColour = colors[ResidueProperties.nucleotideIndex[c]];
- } catch (Exception ex)
- {
- return Color.white;
- }
- }
- else
- {
- return Color.white;
- }
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ super(ResidueProperties.nucleotideIndex, ResidueProperties.nucleotide);
}
@Override
* be coloured
*/
@Override
- public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll,
Map<SequenceI, SequenceCollectionI> hrs)
{
return new NucleotideColourScheme();