X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FAnnotationPanel.java;h=452f0027adf0935925dfa5a3e7d1a0947a4d11a1;hb=46406ae21c62b964714ce136c9d692985c17211d;hp=69975174670501f88833339f9f1bb15fc6e25702;hpb=1af07fa4f32bcb8c9f35be3f92565774ca35215c;p=jalview.git

diff --git a/src/jalview/gui/AnnotationPanel.java b/src/jalview/gui/AnnotationPanel.java
index 6997517..452f002 100755
--- a/src/jalview/gui/AnnotationPanel.java
+++ b/src/jalview/gui/AnnotationPanel.java
@@ -23,6 +23,7 @@ package jalview.gui;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.Annotation;
 import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.SequenceI;
 import jalview.renderer.AnnotationRenderer;
 import jalview.renderer.AwtRenderPanelI;
@@ -294,7 +295,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     {
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (av.getColumnSelection().isVisible(index))
+        if (av.getAlignment().getHiddenColumns().isVisible(index))
         {
           anot[index] = null;
         }
@@ -318,7 +319,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -341,7 +342,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -401,7 +402,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
       }
       for (int index : av.getColumnSelection().getSelected())
       {
-        if (!av.getColumnSelection().isVisible(index))
+        if (!av.getAlignment().getHiddenColumns().isVisible(index))
         {
           continue;
         }
@@ -444,6 +445,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     StringBuilder collatedInput = new StringBuilder(64);
     String last = "";
     ColumnSelection viscols = av.getColumnSelection();
+    HiddenColumns hidden = av.getAlignment().getHiddenColumns();
 
     /*
      * the selection list (read-only view) is in selection order, not
@@ -454,7 +456,7 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
     for (int index : selected)
     {
       // always check for current display state - just in case
-      if (!viscols.isVisible(index))
+      if (!hidden.isVisible(index))
       {
         continue;
       }
@@ -716,7 +718,8 @@ public class AnnotationPanel extends JPanel implements AwtRenderPanelI,
 
     if (av.hasHiddenColumns())
     {
-      column = av.getColumnSelection().adjustForHiddenColumns(column);
+      column = av.getAlignment().getHiddenColumns()
+              .adjustForHiddenColumns(column);
     }
 
     AlignmentAnnotation ann = aa[row];