*/
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 class RNAInteractionColourScheme extends ResidueColourScheme
{
super();
}
- /**
- * DOCUMENT ME!
- *
- * @param n
- * DOCUMENT ME!
- *
- * @return DOCUMENT ME!
- */
@Override
public Color findColour(char c)
{
- // System.out.println("called"); log.debug
+ // FIXME this is just a copy of NucleotideColourScheme
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))
+ // FIXME this is just a copy of NucleotideColourScheme
+ Color currentColour = Color.white;
+ try
{
- try
- {
- currentColour = colors[ResidueProperties.nucleotideIndex[c]];
- } catch (Exception ex)
- {
- return Color.white;
- }
- }
- else
+ currentColour = colors[ResidueProperties.nucleotideIndex[c]];
+ } catch (Exception ex)
{
- return Color.white;
- }
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
}
return currentColour;
}
+
+ @Override
+ public boolean isNucleotideSpecific()
+ {
+ return true;
+ }
+
+ @Override
+ public String getSchemeName()
+ {
+ return "RNA Interaction type";
+ }
+
+ /**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll,
+ Map<SequenceI, SequenceCollectionI> hrs)
+ {
+ return new RNAInteractionColourScheme();
+ }
}