X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Frenderer%2FAnnotationRenderer.java;h=518c17924b7fea6fba291c2cefbc052e544c44c7;hb=48e7970c595ea8dbaa11e2244ac1b67d6c40d4aa;hp=3a27c7d05340f287d087991aa4699bde5e2aae61;hpb=97b26ba418dec7a6e926378205d25470bf098633;p=jalview.git

diff --git a/src/jalview/renderer/AnnotationRenderer.java b/src/jalview/renderer/AnnotationRenderer.java
index 3a27c7d..518c179 100644
--- a/src/jalview/renderer/AnnotationRenderer.java
+++ b/src/jalview/renderer/AnnotationRenderer.java
@@ -28,6 +28,7 @@ import jalview.api.AlignViewportI;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.ProfilesI;
 import jalview.schemes.ColourSchemeI;
 import jalview.schemes.NucleotideColourScheme;
@@ -75,6 +76,8 @@ public class AnnotationRenderer
   ResidueShaderI profcolour = null;
 
   private ColumnSelection columnSelection;
+  
+  private HiddenColumns hiddenColumns;
 
   private ProfilesI hconsensus;
 
@@ -327,6 +330,7 @@ public class AnnotationRenderer
       profcolour = new ResidueShader(col);
     }
     columnSelection = av.getColumnSelection();
+    hiddenColumns = av.getAlignment().getHiddenColumns();
     hconsensus = av.getSequenceConsensusHash();
     complementConsensus = av.getComplementConsensusHash();
     hStrucConsensus = av.getRnaStructureConsensusHash();
@@ -589,7 +593,7 @@ hconsensus.get(column),
         {
           if (hasHiddenColumns)
           {
-            column = columnSelection.adjustForHiddenColumns(startRes + x);
+            column = hiddenColumns.adjustForHiddenColumns(startRes + x);
             if (column > row_annotations.length - 1)
             {
               break;
@@ -1231,7 +1235,7 @@ hconsensus.get(column),
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)
@@ -1310,7 +1314,7 @@ hconsensus.get(column),
       column = sRes + x;
       if (hasHiddenColumns)
       {
-        column = columnSelection.adjustForHiddenColumns(column);
+        column = hiddenColumns.adjustForHiddenColumns(column);
       }
 
       if (column > aaMax)