Merge branch 'develop' into features/JAL-2094_colourInterface

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 8b3aa98..ad3b630 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -30,6 +30,7 @@ import jalview.datamodel.GraphLine;
 import jalview.datamodel.HiddenSequences;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
+import jalview.schemes.Colour;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
 import jalview.schemes.ResidueProperties;
@@ -1670,11 +1671,13 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("textCol1"))
         {
-          sg.textColour = new UserColourScheme(value).findColour('A');
+          sg.textColour = new Colour(
+                  new UserColourScheme(value).findColour('A'));
         }
         else if (key.equalsIgnoreCase("textCol2"))
         {
-          sg.textColour2 = new UserColourScheme(value).findColour('A');
+          sg.textColour2 = new Colour(
+                  new UserColourScheme(value).findColour('A'));
         }
         else if (key.equalsIgnoreCase("textColThreshold"))
         {
@@ -1760,6 +1763,10 @@ public class AnnotationFile
    */
   public String printCSVAnnotations(AlignmentAnnotation[] annotations)
   {
+    if (annotations == null)
+    {
+      return "";
+    }
     StringBuffer sp = new StringBuffer();
     for (int i = 0; i < annotations.length; i++)
     {