JAL-2827 related fixes for stem and non-canonical annotation

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 683ca78..8a80d41 100644 (file)
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -162,7 +162,8 @@ public class AnnotationRenderer
           boolean validRes, boolean validEnd)
   {
     g.setColor(STEM_COLOUR);
-    int sCol = (lastSSX / charWidth) + startRes;
+    int sCol = (lastSSX / charWidth)
+            + hiddenColumns.adjustForHiddenColumns(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -228,7 +229,8 @@ public class AnnotationRenderer
     // System.out.println(nonCanColor);
 
     g.setColor(nonCanColor);
-    int sCol = (lastSSX / charWidth) + startRes;
+    int sCol = (lastSSX / charWidth)
+            + hiddenColumns.adjustForHiddenColumns(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);