Merge branch 'develop' into features/JAL-1705_ensembl

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

diff --git a/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java b/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
new file mode 100644 (file)
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+++ b/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
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+/*
+ * 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.datamodel.AnnotatedCollectionI;
+import jalview.schemes.Blosum62ColourScheme;
+import jalview.schemes.BuriedColourScheme;
+import jalview.schemes.ClustalxColourScheme;
+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.RNAHelicesColour;
+import jalview.schemes.RNAInteractionColourScheme;
+import jalview.schemes.StrandColourScheme;
+import jalview.schemes.TCoffeeColourScheme;
+import jalview.schemes.TaylorColourScheme;
+import jalview.schemes.TurnColourScheme;
+import jalview.schemes.ZappoColourScheme;
+
+public class ColourSchemeMapper
+{
+  private static ColourSchemeI csZappo, csTaylor, csNucleotide, csPurine,
+          csHelix, csTurn, csStrand, csBuried, csHydro,
+          csRNAInteractionType, csPID, csBlosum62 = null;
+  static
+  {
+    csZappo = new ZappoColourScheme();
+    csTaylor = new TaylorColourScheme();
+    csNucleotide = new NucleotideColourScheme();
+    csPurine = new PurinePyrimidineColourScheme();
+    csHelix = new HelixColourScheme();
+    csTurn = new TurnColourScheme();
+    csStrand = new StrandColourScheme();
+    csBuried = new BuriedColourScheme();
+    csHydro = new HydrophobicColourScheme();
+    csRNAInteractionType = new RNAInteractionColourScheme();
+    csPID = new PIDColourScheme();
+    csBlosum62 = new Blosum62ColourScheme();
+  }
+
+  public static ColourSchemeI getJalviewColourScheme(
+          String colourSchemeName, AnnotatedCollectionI annotCol)
+  {
+    switch (colourSchemeName.toUpperCase())
+    {
+    case "ZAPPO":
+      return csZappo;
+    case "TAYLOR":
+      return csTaylor;
+    case "NUCLEOTIDE":
+      return csNucleotide;
+    case "PURINE":
+    case "PURINE/PYRIMIDINE":
+      return csPurine;
+    case "HELIX":
+    case "HELIX PROPENSITY":
+      return csHelix;
+    case "TURN":
+    case "TURN PROPENSITY":
+      return csTurn;
+    case "STRAND":
+    case "STRAND PROPENSITY":
+      return csStrand;
+    case "BURIED":
+    case "BURIED INDEX":
+      return csBuried;
+    case "HYDRO":
+    case "HYDROPHOBIC":
+      return csHydro;
+    case "RNA INTERACTION TYPE":
+      return csRNAInteractionType;
+    case "PID":
+    case "% IDENTITY":
+      return csPID;
+    case "BLOSUM62":
+      return csBlosum62;
+    case "T-COFFEE SCORES":
+      return (annotCol != null) ? new TCoffeeColourScheme(annotCol) : null;
+    case "RNA HELICES":
+      return (annotCol != null) ? new RNAHelicesColour(annotCol) : null;
+    case "CLUSTAL":
+      return (annotCol != null) ? new ClustalxColourScheme(annotCol, null)
+              : null;
+    case "USER DEFINED":
+      return null;
+    default:
+      return null;
+    }
+  }
+}