*/
package jalview.schemes;
+import jalview.api.AlignViewportI;
import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.AnnotatedCollectionI;
+import jalview.util.ColorUtils;
import java.awt.Color;
import java.util.Hashtable;
+import java.util.Map;
/**
* Became RNAHelicesColour.java. Placeholder for true covariation color scheme
*/
public class CovariationColourScheme extends ResidueColourScheme
{
- public Hashtable helixcolorhash = new Hashtable();
+ public Map<String, Color> helixcolorhash = new Hashtable<>();
- public Hashtable positionsToHelix = new Hashtable();
+ public Map<Integer, String> positionsToHelix = new Hashtable<>();
int numHelix = 0;
public AlignmentAnnotation annotation;
/**
+ * Returns a new instance of this colour scheme with which the given data may
+ * be coloured
+ */
+ @Override
+ public ColourSchemeI getInstance(AlignViewportI view,
+ AnnotatedCollectionI coll)
+ {
+ return new CovariationColourScheme(coll.getAlignmentAnnotation()[0]);
+ }
+
+ /**
* Creates a new CovariationColourScheme object.
*/
public CovariationColourScheme(AlignmentAnnotation annotation)
positionsToHelix.put(this.annotation._rnasecstr[x].getEnd(),
this.annotation._rnasecstr[x].getFeatureGroup());
- if (Integer.parseInt(this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
+ if (Integer.parseInt(
+ this.annotation._rnasecstr[x].getFeatureGroup()) > numHelix)
{
- numHelix = Integer.parseInt(this.annotation._rnasecstr[x]
- .getFeatureGroup());
+ numHelix = Integer
+ .parseInt(this.annotation._rnasecstr[x].getFeatureGroup());
}
}
for (int j = 0; j <= numHelix; j++)
{
- helixcolorhash.put(Integer.toString(j),
- jalview.util.ColorUtils.generateRandomColor(Color.white));
+ helixcolorhash.put(String.valueOf(j),
+ ColorUtils.generateRandomColor(Color.white));
}
}
Color currentColour = Color.white;
String currentHelix = null;
// System.out.println(c + " " + j);
- currentHelix = (String) positionsToHelix.get(j);
+ currentHelix = positionsToHelix.get(j);
// System.out.println(positionsToHelix.get(j));
if (currentHelix != null)
{
- currentColour = (Color) helixcolorhash.get(currentHelix);
+ currentColour = helixcolorhash.get(currentHelix);
}
// System.out.println(c + " " + j + " helix " + currentHelix + " " +
{
return "Covariation";
}
+
+ @Override
+ public boolean isSimple()
+ {
+ return false;
+ }
}