From d7ab9290294941178265fbd3da9c71ac9f969f05 Mon Sep 17 00:00:00 2001
From: gmungoc <g.m.carstairs@dundee.ac.uk>
Date: Wed, 24 Aug 2016 14:07:26 +0100
Subject: [PATCH] JAL-2151 port fix to applet

---
 src/jalview/appletgui/ScalePanel.java |   39 ++++++++++++++++++++-------------
 1 file changed, 24 insertions(+), 15 deletions(-)

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 0f71818..d2c1693 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -409,22 +409,33 @@ public class ScalePanel extends Panel implements MouseMotionListener,
 
     // Fill the selected columns
     ColumnSelection cs = av.getColumnSelection();
-    gg.setColor(new Color(220, 0, 0));
     int avCharWidth = av.getCharWidth();
     int avcharHeight = av.getCharHeight();
-    for (int sel : cs.getSelected())
+    if (cs != null)
     {
-      // TODO: JAL-2001 - provide a fast method to list visible selected in a
-      // given range
-      if (av.hasHiddenColumns())
+      gg.setColor(new Color(220, 0, 0));
+      boolean hasHiddenColumns = cs.hasHiddenColumns();
+      for (int sel : cs.getSelected())
       {
-        sel = av.getColumnSelection().findColumnPosition(sel);
-      }
+        // TODO: JAL-2001 - provide a fast method to list visible selected in a
+        // given range
+        if (hasHiddenColumns)
+        {
+          if (cs.isVisible(sel))
+          {
+            sel = cs.findColumnPosition(sel);
+          }
+          else
+          {
+            continue;
+          }
+        }
 
-      if ((sel >= startx) && (sel <= endx))
-      {
-        gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
-                getSize().height);
+        if ((sel >= startx) && (sel <= endx))
+        {
+          gg.fillRect((sel - startx) * avCharWidth, 0, avCharWidth,
+                  getSize().height);
+        }
       }
     }
 
@@ -471,12 +482,10 @@ public class ScalePanel extends Panel implements MouseMotionListener,
       if (av.getShowHiddenMarkers())
       {
         int widthx = 1 + endx - startx;
-        for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
-                .size(); i++)
+        for (int i = 0; i < cs.getHiddenColumns().size(); i++)
         {
 
-          res = av.getColumnSelection().findHiddenRegionPosition(i)
-                  - startx;
+          res = cs.findHiddenRegionPosition(i) - startx;
 
           if (res < 0 || res > widthx)
           {
-- 
1.7.10.2