JAL-1912 added documentation

[jalview.git] / src / jalview / io / JSONFile.java

diff --git a/src/jalview/io/JSONFile.java b/src/jalview/io/JSONFile.java
index b778b83..9e94d91 100644 (file)
--- a/src/jalview/io/JSONFile.java
+++ b/src/jalview/io/JSONFile.java
@@ -558,11 +558,14 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
                     .get("secondaryStructure").toString().charAt(0);
             String displayChar = annot.get("displayCharacter") == null ? ""
                     : annot.get("displayCharacter").toString();
-            Color color = annot.get("colour") == null ? Color.white
-                    : UserColourScheme.getColourFromString(annot.get(
-                    "colour").toString());
-            annotations[count] = new Annotation(displayChar, desc, ss, val,
-                    color);
+
+            annotations[count] = new Annotation(displayChar, desc, ss, val);
+            if (annot.get("colour") != null)
+            {
+              Color color = UserColourScheme.getColourFromString(annot.get(
+                      "colour").toString());
+              annotations[count].colour = color;
+            }
           }
           ++count;
         }
@@ -626,7 +629,7 @@ public class JSONFile extends AlignFile implements ComplexAlignFile
             alignAnnot.adjustForAlignment();
           }
         }
-        // alignAnnot.validateRangeAndDisplay();
+        alignAnnot.validateRangeAndDisplay();
         this.annotations.add(alignAnnot);
 
       }