/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
public static final int COVARIATION = 14;
public static final int TCOFFEE = 15;
-
+
public static final int RNAHELIX = 16;
public static final int RNAINTERACTION = 17;
ret = "T-Coffee Scores";
break;
-
+
case RNAINTERACTION:
- ret = "RNA Interaction type";
+ ret = "RNA Interaction type";
- break;
+ break;
case RNAHELIX:
ret = "RNA Helices";
case TCOFFEE:
cs = new TCoffeeColourScheme(coll);
break;
-
+
case RNAHELIX:
cs = new RNAHelicesColour(coll);
break;
-
- // case COVARIATION:
- // cs = new CovariationColourScheme(annotation);
+
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
// break;
case USER_DEFINED:
return col;
}
+
+ public static Color rnaHelices[] = null;
+
+ public static void initRnaHelicesShading(int n)
+ {
+ int j = 0;
+ if (rnaHelices == null)
+ {
+ rnaHelices = new Color[n + 1];
+ }
+ else if (rnaHelices != null && rnaHelices.length <= n)
+ {
+ Color[] t = new Color[n + 1];
+ System.arraycopy(rnaHelices, 0, t, 0, rnaHelices.length);
+ j = rnaHelices.length;
+ rnaHelices = t;
+ }
+ else
+ {
+ return;
+ }
+ // Generate random colors and store
+ for (; j <= n; j++)
+ {
+ rnaHelices[j] = jalview.util.ColorUtils
+ .generateRandomColor(Color.white);
+ }
+ }
+
+ /**
+ * delete the existing cached RNA helces colours
+ */
+ public static void resetRnaHelicesShading()
+ {
+ rnaHelices = null;
+ }
+
}