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];