package jalview.schemes;
import jalview.api.AlignViewportI;
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
import jalview.datamodel.AnnotatedCollectionI;
import jalview.datamodel.SequenceCollectionI;
import jalview.datamodel.SequenceI;
+import jalview.util.ColorUtils;
+import java.awt.Color;
import java.util.LinkedHashMap;
import java.util.Map;
-public class ColourSchemes
+public class ColourSchemes implements ApplicationSingletonI
{
- /*
- * singleton instance of this class
- */
- private static ColourSchemes instance = new ColourSchemes();
-
- /*
- * a map from scheme name (lower-cased) to an instance of it
- */
- private Map<String, ColourSchemeI> schemes;
/**
* Returns the singleton instance of this class
*/
public static ColourSchemes getInstance()
{
- return instance;
+ return (ColourSchemes) ApplicationSingletonProvider
+ .getInstance(ColourSchemes.class);
}
private ColourSchemes()
}
/**
+ * ColourSchemeProperty "static"
+ */
+ public Color[] rnaHelices = null;
+
+ /**
+ * delete the existing cached RNA helices colours
+ */
+ public static void resetRnaHelicesShading()
+ {
+ getInstance().rnaHelices = null;
+ }
+
+ public static void initRnaHelicesShading(int n)
+ {
+ int i = 0;
+ ColourSchemes j = getInstance();
+
+ if (j.rnaHelices == null)
+ {
+ j.rnaHelices = new Color[n + 1];
+ }
+ else if (j.rnaHelices != null && j.rnaHelices.length <= n)
+ {
+ Color[] t = new Color[n + 1];
+ System.arraycopy(j.rnaHelices, 0, t, 0, j.rnaHelices.length);
+ i = j.rnaHelices.length;
+ j.rnaHelices = t;
+ }
+ else
+ {
+ return;
+ }
+ // Generate random colors and store
+ for (; i <= n; i++)
+ {
+ j.rnaHelices[i] = ColorUtils.generateRandomColor(Color.white);
+ }
+ }
+
+ /**
+ * a map from scheme name (lower-cased) to an instance of it
+ */
+ private Map<String, ColourSchemeI> schemes;
+
+ /**
* Loads an instance of each standard or user-defined colour scheme
*
* @return
{
try
{
- registerColourScheme(cs.getSchemeClass().newInstance());
+ registerColourScheme(
+ cs.getSchemeClass().getDeclaredConstructor().newInstance());
} catch (InstantiationException | IllegalAccessException e)
{
System.err.println("Error instantiating colour scheme for "
+ cs.toString() + " " + e.getMessage());
e.printStackTrace();
+ } catch (ReflectiveOperationException roe)
+ {
+ roe.printStackTrace();
}
}
}
}
ColourSchemeI cs = schemes.get(name.toLowerCase());
return cs == null ? null
- : cs.getInstance(viewport, forData, hiddenRepSequences);
+ : cs.getInstance(viewport, forData);
}
/**