*/
package jalview.schemes;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
import java.awt.Color;
+import java.util.Map;
public class RNAInteractionColourScheme extends ResidueColourScheme
{
public Color findColour(char c, int j, SequenceI seq)
{
// FIXME this is just a copy of NucleotideColourScheme
- Color currentColour;
- if ((threshold == 0) || aboveThreshold(c, j))
+ Color currentColour = Color.white;
+ try
{
- try
- {
- currentColour = colors[ResidueProperties.nucleotideIndex[c]];
- } catch (Exception ex)
- {
- return Color.white;
- }
- }
- else
- {
- return Color.white;
- }
-
- if (conservationColouring)
+ currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+ } catch (Exception ex)
{
- currentColour = applyConservation(currentColour, j);
}
return currentColour;
{
return "RNA Interaction type";
}
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new RNAInteractionColourScheme();
+ }
}