*/
package jalview.schemes;
-import java.awt.Color;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceI;
+
+import java.util.Map;
/**
* Class is based off of NucleotideColourScheme
public PurinePyrimidineColourScheme()
{
super(ResidueProperties.purinepyrimidineIndex,
- ResidueProperties.purinepyrimidine, 0);
- }
-
- /**
- * Finds the corresponding color for the type of character inputed
- *
- * @param c
- * Character in sequence
- *
- * @return Color from purinepyrimidineIndex in
- * jalview.schemes.ResidueProperties
- */
- @Override
- public Color findColour(char c)
- {
- return colors[ResidueProperties.purinepyrimidineIndex[c]];
- }
-
- /**
- * Returns color based on conservation
- *
- * @param c
- * Character in sequence
- * @param j
- * Threshold
- *
- * @return Color in RGB
- */
- public Color findColour(char c, int j)
- {
- Color currentColour;
- if ((threshold == 0) || aboveThreshold(c, j))
- {
- try
- {
- currentColour = colors[ResidueProperties.purinepyrimidineIndex[c]];
- } catch (Exception ex)
- {
- return Color.white;
- }
- }
- else
- {
- return Color.white;
- }
-
- if (conservationColouring)
- {
- currentColour = applyConservation(currentColour, j);
- }
-
- return currentColour;
+ ResidueProperties.purinepyrimidine);
}
@Override
{
return JalviewColourScheme.PurinePyrimidine.toString();
}
+
+ /**
+ * 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 PurinePyrimidineColourScheme();
+ }
}