src/jalview/schemes/RNAInteractionColourScheme.java

   1 package jalview.schemes;
   2
   3 import jalview.datamodel.SequenceI;
   4
   5 import java.awt.Color;
   6
   7
   8 public class RNAInteractionColourScheme extends ResidueColourScheme{
   9          public RNAInteractionColourScheme()
  10           {
  11             super(ResidueProperties.nucleotide, 0);
  12           }
  13
  14           /**
  15            * DOCUMENT ME!
  16            *
  17            * @param n
  18            *          DOCUMENT ME!
  19            *
  20            * @return DOCUMENT ME!
  21            */
  22           @Override
  23           public Color findColour(char c)
  24           {
  25             // System.out.println("called"); log.debug
  26             return colors[ResidueProperties.nucleotideIndex[c]];
  27           }
  28
  29           /**
  30            * DOCUMENT ME!
  31            *
  32            * @param n
  33            *          DOCUMENT ME!
  34            * @param j
  35            *          DOCUMENT ME!
  36            *
  37            * @return DOCUMENT ME!
  38            */
  39           @Override
  40           public Color findColour(char c, int j, SequenceI seq)
  41           {
  42             Color currentColour;
  43             if ((threshold == 0) || aboveThreshold(c, j))
  44             {
  45               try
  46               {
  47                 currentColour = colors[ResidueProperties.nucleotideIndex[c]];
  48               } catch (Exception ex)
  49               {
  50                 return Color.white;
  51               }
  52             }
  53             else
  54             {
  55               return Color.white;
  56             }
  57
  58             if (conservationColouring)
  59             {
  60               currentColour = applyConservation(currentColour, j);
  61             }
  62
  63             return currentColour;
  64           }
  65         }