X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;fp=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=adca17e5a81152a2a1bc5b217b487527a7bb1b61;hb=8c5cefb3ac80bd094a8dab7ce6735a11583b1772;hp=25a81f9ea6ff70f5f6957e354b0f064cc03bea45;hpb=34b682702fe2dee7a5d79f95960a1accbea17ef6;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 25a81f9..adca17e 100644
--- 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.visibleToAbsoluteColumn(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.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);
 
@@ -1147,7 +1149,8 @@ public class AnnotationRenderer
   {
     g.setColor(HELIX_COLOUR);
 
-    int sCol = (lastSSX / charWidth) + startRes;
+    int sCol = (lastSSX / charWidth)
+            + hiddenColumns.visibleToAbsoluteColumn(startRes);
     int x1 = lastSSX;
     int x2 = (x * charWidth);