1 package jalview.schemes;
3 import jalview.datamodel.SequenceI;
8 public class RNAInteractionColourScheme extends ResidueColourScheme{
9 public RNAInteractionColourScheme()
20 * @return DOCUMENT ME!
23 public Color findColour(char c)
25 // System.out.println("called"); log.debug
26 return colors[ResidueProperties.nucleotideIndex[c]];
37 * @return DOCUMENT ME!
40 public Color findColour(char c, int j, SequenceI seq)
43 if ((threshold == 0) || aboveThreshold(c, j))
47 currentColour = colors[ResidueProperties.nucleotideIndex[c]];
48 } catch (Exception ex)
58 if (conservationColouring)
60 currentColour = applyConservation(currentColour, j);