JAL-1896 bugfix to enabled Jalview restore clustal, RNA Helices and T-Coffee colour...

[jalview.git] / src / jalview / json / binding / biojson / v1 / JalviewBioJsColorSchemeMapper.java

diff --git a/src/jalview/json/binding/biojson/v1/JalviewBioJsColorSchemeMapper.java b/src/jalview/json/binding/biojson/v1/JalviewBioJsColorSchemeMapper.java
deleted file mode 100644 (file)
index e7a302e..0000000
--- a/src/jalview/json/binding/biojson/v1/JalviewBioJsColorSchemeMapper.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
- * Copyright (C) $$Year-Rel$$ 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.
- *  
- * 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/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.json.binding.biojson.v1;
-
-import jalview.schemes.Blosum62ColourScheme;
-import jalview.schemes.BuriedColourScheme;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.HelixColourScheme;
-import jalview.schemes.HydrophobicColourScheme;
-import jalview.schemes.NucleotideColourScheme;
-import jalview.schemes.PIDColourScheme;
-import jalview.schemes.PurinePyrimidineColourScheme;
-import jalview.schemes.RNAInteractionColourScheme;
-import jalview.schemes.StrandColourScheme;
-import jalview.schemes.TaylorColourScheme;
-import jalview.schemes.TurnColourScheme;
-import jalview.schemes.ZappoColourScheme;
-
-public enum JalviewBioJsColorSchemeMapper
-{
-
-  USER_DEFINED("User Defined", "user defined", null), NONE("None", "foo",
-          null), CLUSTAL("Clustal", "clustal", null), ZAPPO("Zappo",
-          "zappo", new ZappoColourScheme()), TAYLOR("Taylor", "taylor",
-          new TaylorColourScheme()), NUCLEOTIDE("Nucleotide", "nucleotide",
-          new NucleotideColourScheme()), PURINE_PYRIMIDINE(
-          "Purine/Pyrimidine", "purine", new PurinePyrimidineColourScheme()), HELIX_PROPENSITY(
-          "Helix Propensity", "helix", new HelixColourScheme()), TURN_PROPENSITY(
-          "Turn Propensity", "turn", new TurnColourScheme()), STRAND_PROPENSITY(
-          "Strand Propensity", "strand", new StrandColourScheme()), BURIED_INDEX(
-          "Buried Index", "buried", new BuriedColourScheme()), HYDROPHOBIC(
-          "Hydrophobic", "hydro", new HydrophobicColourScheme()),
-
-  // The color types below are not yet supported by BioJs MSA viewer
-  T_COFFE_SCORES("T-Coffee Scores", "T-Coffee Scores", null), RNA_INT_TYPE(
-          "RNA Interaction type", "RNA Interaction type",
-          new RNAInteractionColourScheme()), BLOSUM62("Blosum62",
-          "Blosum62", new Blosum62ColourScheme()), RNA_HELICES(
-          "RNA Helices", "RNA Helices", null), PERCENTAGE_IDENTITY(
-          "% Identity", "pid", new PIDColourScheme());
-
-  private String jalviewName;
-
-  private String bioJsName;
-
-  private ColourSchemeI jvColourScheme;
-
-  private JalviewBioJsColorSchemeMapper(String jalviewName,
-          String bioJsName, ColourSchemeI jvColourScheme)
-  {
-    this.jalviewName = jalviewName;
-    this.bioJsName = bioJsName;
-    this.setJvColourScheme(jvColourScheme);
-  }
-
-  public String getJalviewName()
-  {
-    return jalviewName;
-  }
-
-  public String getBioJsName()
-  {
-    return bioJsName;
-  }
-
-  public ColourSchemeI getJvColourScheme()
-  {
-    return jvColourScheme;
-  }
-
-  public void setJvColourScheme(ColourSchemeI jvColourScheme)
-  {
-    this.jvColourScheme = jvColourScheme;
-  }
-
-}