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

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index 0c0f395..717ab8b 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -28,6 +28,7 @@ import jalview.api.ComplexAlignFile;
 import jalview.api.FeatureRenderer;
 import jalview.api.FeaturesDisplayedI;
 import jalview.bin.BuildDetails;
+import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
@@ -40,7 +41,7 @@ import jalview.datamodel.SequenceI;
 import jalview.json.binding.biojson.v1.AlignmentAnnotationPojo;
 import jalview.json.binding.biojson.v1.AlignmentPojo;
 import jalview.json.binding.biojson.v1.AnnotationPojo;
-import jalview.json.binding.biojson.v1.JalviewBioJsColorSchemeMapper;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.json.binding.biojson.v1.SequenceFeaturesPojo;
 import jalview.json.binding.biojson.v1.SequenceGrpPojo;
 import jalview.json.binding.biojson.v1.SequencePojo;
@@ -388,6 +389,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
   @SuppressWarnings("unchecked")
   public JSONFile parse(Reader jsonAlignmentString)
   {
+    String jsColourScheme = null;
     try
     {
       JSONParser jsonParser = new JSONParser();
@@ -405,11 +407,10 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
 
       if (jvSettingsJsonObj != null)
       {
-        String jsColourScheme = (String) jvSettingsJsonObj
+        jsColourScheme = (String) jvSettingsJsonObj
                 .get("globalColorScheme");
         Boolean showFeatures = Boolean.valueOf(jvSettingsJsonObj.get(
                 "showSeqFeatures").toString());
-        setColourScheme(getJalviewColorScheme(jsColourScheme));
         setShowSeqFeatures(showFeatures);
         parseHiddenSeqRefsAsList(jvSettingsJsonObj);
         parseHiddenCols(jvSettingsJsonObj);
@@ -435,6 +436,13 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
         seqs.add(seq);
         seqMap.put(seqUniqueId, seq);
       }
+
+      if (jsColourScheme != null)
+      {
+        setColourScheme(ColourSchemeMapper.getJalviewColourScheme(
+                jsColourScheme,
+                new Alignment(seqs.toArray(new SequenceI[0]))));
+      }
       parseFeatures(jsonSeqArray);
 
       for (Iterator<JSONObject> seqGrpIter = seqGrpJsonArray.iterator(); seqGrpIter
@@ -472,10 +480,11 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             }
           }
         }
-        ColourSchemeI grpColourScheme = getJalviewColorScheme(colourScheme);
-        SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName,
-                grpColourScheme, displayBoxes, displayText, colourText,
+        SequenceGroup seqGrp = new SequenceGroup(grpSeqs, grpName, null,
+                displayBoxes, displayText, colourText,
                 startRes, endRes);
+        seqGrp.cs = ColourSchemeMapper.getJalviewColourScheme(colourScheme,
+                seqGrp);
         seqGrp.setShowNonconserved(showNonconserved);
         seqGrp.setDescription(description);
         this.seqGroups.add(seqGrp);
@@ -600,24 +609,6 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
     }
   }
 
-  public static ColourSchemeI getJalviewColorScheme(
-          String bioJsColourSchemeName)
-  {
-    ColourSchemeI jalviewColor = null;
-    for (JalviewBioJsColorSchemeMapper cs : JalviewBioJsColorSchemeMapper
-            .values())
-    {
-      if (cs.getBioJsName().equalsIgnoreCase(bioJsColourSchemeName)
-              || cs.getJalviewName()
-                      .equalsIgnoreCase(bioJsColourSchemeName))
-      {
-        jalviewColor = cs.getJvColourScheme();
-        break;
-      }
-    }
-    return jalviewColor;
-  }
-
   public String getGlobalColorScheme()
   {
     return globalColorScheme;

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)
index 0000000..de4ba8d
--- /dev/null
+++ b/src/jalview/json/binding/biojson/v1/ColourSchemeMapper.java
@@ -0,0 +1,92 @@
+/*
+ * 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
+{
+  public static ColourSchemeI getJalviewColourScheme(
+          String colourSchemeName, AnnotatedCollectionI annotCol)
+  {
+    switch (colourSchemeName.toUpperCase())
+    {
+    case "ZAPPO":
+      return new ZappoColourScheme();
+    case "TAYLOR":
+      return new TaylorColourScheme();
+    case "NUCLEOTIDE":
+      return new NucleotideColourScheme();
+    case "PURINE":
+    case "PURINE/PYRIMIDINE":
+      return new PurinePyrimidineColourScheme();
+    case "HELIX":
+    case "HELIX PROPENSITY":
+      return new HelixColourScheme();
+    case "TURN":
+    case "TURN PROPENSITY":
+      return new TurnColourScheme();
+    case "STRAND":
+    case "STRAND PROPENSITY":
+      return new StrandColourScheme();
+    case "BURIED":
+    case "BURIED INDEX":
+      return new BuriedColourScheme();
+    case "HYDRO":
+    case "HYDROPHOBIC":
+      return new HydrophobicColourScheme();
+    case "RNA INTERACTION TYPE":
+      return new RNAInteractionColourScheme();
+    case "PID":
+    case "% IDENTITY":
+      return new PIDColourScheme();
+    case "BLOSUM62":
+      return new Blosum62ColourScheme();
+    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;
+    }
+  }
+}

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;
-  }
-
-}

diff --git a/test/jalview/io/JSONFileTest.java b/test/jalview/io/JSONFileTest.java
index da2e64e..4371ff9 100644 (file)
--- a/test/jalview/io/JSONFileTest.java
+++ b/test/jalview/io/JSONFileTest.java
@@ -33,6 +33,7 @@ import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.gui.AlignFrame;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ZappoColourScheme;
 
@@ -124,9 +125,11 @@ public class JSONFileTest
     grpSeqs.add(seqs[2]);
     grpSeqs.add(seqs[3]);
     grpSeqs.add(seqs[4]);
-    ColourSchemeI scheme = JSONFile.getJalviewColorScheme("zappo");
     SequenceGroup seqGrp = new SequenceGroup(grpSeqs, "JGroup:1883305585",
-            scheme, true, true, false, 21, 29);
+            null, true, true, false, 21, 29);
+    ColourSchemeI scheme = ColourSchemeMapper.getJalviewColourScheme(
+            "zappo", seqGrp);
+    seqGrp.cs = scheme;
     seqGrp.setShowNonconserved(false);
     seqGrp.setDescription(null);
 
@@ -419,13 +422,14 @@ public class JSONFileTest
             + actualGrp.getStartRes());
     System.out.println(expectedGrp.getEndRes() + " | "
             + actualGrp.getEndRes());
+    System.out.println(expectedGrp.cs + " | " + actualGrp.cs);
 
     if (expectedGrp.getName().equals(actualGrp.getName())
             && expectedGrp.getColourText() == actualGrp.getColourText()
             && expectedGrp.getDisplayBoxes() == actualGrp.getDisplayBoxes()
             && expectedGrp.getIgnoreGapsConsensus() == actualGrp
                     .getIgnoreGapsConsensus()
-            && expectedGrp.cs.equals(actualGrp.cs)
+            && (expectedGrp.cs.getClass().equals(actualGrp.cs.getClass()))
             && expectedGrp.getSequences().size() == actualGrp
                     .getSequences().size()
             && expectedGrp.getStartRes() == actualGrp.getStartRes()