JAL-3210 Improvements to eclipse detection. New src tree and SwingJS updated from...

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

diff --git a/src/jalview/io/AnnotationFile.java b/src/jalview/io/AnnotationFile.java
index 6b02022..02667c5 100755 (executable)
--- a/src/jalview/io/AnnotationFile.java
+++ b/src/jalview/io/AnnotationFile.java
@@ -684,7 +684,7 @@ public class AnnotationFile
     {
       if (sourceType == DataSourceType.FILE)
       {
-        in = FileLoader.getBuffereReader(file);
+        in = FileLoader.getBufferedReader(file);
       }
       else if (sourceType == DataSourceType.URL)
       {
@@ -1617,8 +1617,10 @@ public class AnnotationFile
         }
         else if (key.equalsIgnoreCase("colour"))
         {
+          // TODO need to notify colourscheme of view reference once it is
+          // available
           sg.cs.setColourScheme(
-                  ColourSchemeProperty.getColourScheme(al, value));
+                  ColourSchemeProperty.getColourScheme(null, al, value));
         }
         else if (key.equalsIgnoreCase("pidThreshold"))
         {