Merge branch 'develop' into features/JAL-2360colourSchemeApplicability

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index f80adef..ae34f6b 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -32,7 +32,6 @@ import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.UserColourScheme;
 import jalview.util.ColorUtils;
 
 import java.awt.Color;
@@ -1430,7 +1429,7 @@ public class AnnotationFile
       value = Float.valueOf(nextToken);
     } catch (NumberFormatException e)
     {
-      System.err.println("Threshold '" + nextToken
+      System.err.println("line " + nlinesread + ": Threshold '" + nextToken
               + "' invalid, setting to zero");
     }
     String label = st.hasMoreTokens() ? st.nextToken() : null;
@@ -1677,9 +1676,8 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("idColour"))
         {
-          // consider warning if colour doesn't resolve to a real colour
-          def = new UserColourScheme(value);
-          sg.setIdColour(def.findColour());
+          Color idColour = ColorUtils.parseColourString(value);
+          sg.setIdColour(idColour == null ? Color.black : idColour);
         }
         else if (key.equalsIgnoreCase("hide"))
         {