/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
- * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 = 16;
+ public static final int RNAINTERACTION = 17;
/**
* index of first colourscheme (includes 'None')
*/
public static final int FIRST_COLOUR = NONE;
- public static final int LAST_COLOUR = NUCLEOTIDE;
+ public static final int LAST_COLOUR = RNAINTERACTION;
/**
* DOCUMENT ME!
{
ret = PURINEPYRIMIDINE;
}
-
else if (name.equalsIgnoreCase("RNA Interaction type"))
{
ret = RNAINTERACTION;
}
+ else if (name.equalsIgnoreCase("RNA Helices"))
+ {
+ ret = RNAHELIX;
+ }
// else if (name.equalsIgnoreCase("Covariation"))
// {
// ret = COVARIATION;
{
index = TCOFFEE;
}
-
-
-
+ else if (cs instanceof RNAHelicesColour)
+ {
+ index = RNAHELIX;
+ }
/*
* else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
*/
ret = "RNA Interaction type";
break;
+ case RNAHELIX:
+ ret = "RNA Helices";
+
+ break;
/*
* case COVARIATION: ret = "Covariation";
*
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: