X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fschemes%2FColourSchemeProperty.java;h=385e080a1eb07c901200cb8b04ea21d3050a3bfa;hb=47168f025aefdaa044802bd5f8f510ffe43a4808;hp=4132f32d682294d83e12be38a1108c1d2a2f01f1;hpb=28787d9646cca5dd77190930f59b7ff32cf995b4;p=jalview.git
diff --git a/src/jalview/schemes/ColourSchemeProperty.java b/src/jalview/schemes/ColourSchemeProperty.java
index 4132f32..385e080 100755
--- a/src/jalview/schemes/ColourSchemeProperty.java
+++ b/src/jalview/schemes/ColourSchemeProperty.java
@@ -1,19 +1,22 @@
/*
- * 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 .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.schemes;
@@ -85,15 +88,17 @@ public class ColourSchemeProperty
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!
@@ -168,11 +173,14 @@ public class ColourSchemeProperty
{
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;
@@ -246,12 +254,10 @@ public class ColourSchemeProperty
{
index = TCOFFEE;
}
- else if (cs instanceof RNAInteractionColourScheme)
+ else if (cs instanceof RNAHelicesColour)
{
- index = RNAINTERACTION;
+ index = RNAHELIX;
}
-
-
/*
* else if (cs instanceof CovariationColourScheme) { index = COVARIATION; }
*/
@@ -351,6 +357,10 @@ public class ColourSchemeProperty
ret = "RNA Interaction type";
break;
+ case RNAHELIX:
+ ret = "RNA Helices";
+
+ break;
/*
* case COVARIATION: ret = "Covariation";
*
@@ -503,15 +513,14 @@ public class ColourSchemeProperty
case TCOFFEE:
cs = new TCoffeeColourScheme(coll);
break;
+
+ case RNAHELIX:
+ cs = new RNAHelicesColour(coll);
+ break;
- case RNAINTERACTION:
- cs = new RNAInteractionColourScheme();
- break;
-
- // case COVARIATION:
- // cs = new CovariationColourScheme(annotation);
-
- // break;
+ // case COVARIATION:
+ // cs = new CovariationColourScheme(annotation);
+ // break;
case USER_DEFINED:
Color[] col = new Color[24];