From 6ff627c729ffdea1bbf658a463e3e993aad493bb Mon Sep 17 00:00:00 2001
From: Charles Ofoegbu <tcnofoegbu@dundee.ac.uk>
Date: Fri, 23 Jan 2015 10:37:09 +0000
Subject: [PATCH] JAL-1553 fixed null pointer exception thrown in SeqCanvas
 and ScalePanel of jalview applet while attempting to redraw
 the panels when hidden columns no longer exists

---
 src/jalview/appletgui/ScalePanel.java |   33 ++++++++++++++++++++++++---------
 src/jalview/appletgui/SeqCanvas.java  |   28 ++++++++++++++++++++++------
 2 files changed, 46 insertions(+), 15 deletions(-)

diff --git a/src/jalview/appletgui/ScalePanel.java b/src/jalview/appletgui/ScalePanel.java
index 60d89aa..bc5b3e7 100755
--- a/src/jalview/appletgui/ScalePanel.java
+++ b/src/jalview/appletgui/ScalePanel.java
@@ -20,12 +20,23 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
 import jalview.util.MessageManager;
 
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.MenuItem;
+import java.awt.Panel;
+import java.awt.PopupMenu;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.InputEvent;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+
 public class ScalePanel extends Panel implements MouseMotionListener,
         MouseListener
 {
@@ -323,6 +334,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     res = av.getColumnSelection().adjustForHiddenColumns(res);
 
     reveal = null;
+    if (av.getColumnSelection().getHiddenColumns() != null)
+    {
     for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
     {
       int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
@@ -333,6 +346,7 @@ public class ScalePanel extends Panel implements MouseMotionListener,
         break;
       }
     }
+    }
 
     repaint();
   }
@@ -407,18 +421,18 @@ public class ScalePanel extends Panel implements MouseMotionListener,
         }
 
         gg.drawLine(
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
                 y + 2,
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
                 y + (fm.getDescent() * 2));
 
       }
       else
       {
         gg.drawLine(
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
                 y + fm.getDescent(),
-                (int) (((i - startx - 1) * av.charWidth) + (av.charWidth / 2)),
+                ((i - startx - 1) * av.charWidth) + (av.charWidth / 2),
                 y + (fm.getDescent() * 2));
       }
     }
@@ -427,7 +441,8 @@ public class ScalePanel extends Panel implements MouseMotionListener,
     {
       gg.setColor(Color.blue);
       int res;
-      if (av.getShowHiddenMarkers())
+      if (av.getColumnSelection().getHiddenColumns() != null
+              && av.getShowHiddenMarkers())
       {
         for (int i = 0; i < av.getColumnSelection().getHiddenColumns()
                 .size(); i++)
diff --git a/src/jalview/appletgui/SeqCanvas.java b/src/jalview/appletgui/SeqCanvas.java
index 53cca3c..4b3cd1c 100755
--- a/src/jalview/appletgui/SeqCanvas.java
+++ b/src/jalview/appletgui/SeqCanvas.java
@@ -20,9 +20,16 @@
  */
 package jalview.appletgui;
 
-import java.awt.*;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SearchResults;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
 
-import jalview.datamodel.*;
+import java.awt.Color;
+import java.awt.FontMetrics;
+import java.awt.Graphics;
+import java.awt.Image;
+import java.awt.Panel;
 
 public class SeqCanvas extends Panel
 {
@@ -510,18 +517,27 @@ public class SeqCanvas extends Panel
   void drawPanel(Graphics g1, int startRes, int endRes, int startSeq,
           int endSeq, int offset)
   {
+
+
     if (!av.hasHiddenColumns())
     {
       draw(g1, startRes, endRes, startSeq, endSeq, offset);
     }
     else
     {
-      java.util.Vector regions = av.getColumnSelection().getHiddenColumns();
+
+
 
       int screenY = 0;
       int blockStart = startRes;
       int blockEnd = endRes;
 
+      if (av.getColumnSelection() != null
+              && av.getColumnSelection().getHiddenColumns() != null)
+      {
+        java.util.Vector regions = av.getColumnSelection()
+                .getHiddenColumns();
+
       for (int i = 0; i < regions.size(); i++)
       {
         int[] region = (int[]) regions.elementAt(i);
@@ -552,7 +568,7 @@ public class SeqCanvas extends Panel
         screenY += blockEnd - blockStart + 1;
         blockStart = hideEnd + 1;
       }
-
+      }
       if (screenY <= (endRes - startRes))
       {
         blockEnd = blockStart + (endRes - startRes) - screenY;
@@ -646,7 +662,7 @@ public class SeqCanvas extends Panel
 
     if ((group == null) && (av.getAlignment().getGroups().size() > 0))
     {
-      group = (SequenceGroup) av.getAlignment().getGroups().get(0);
+      group = av.getAlignment().getGroups().get(0);
       groupIndex = 0;
     }
 
@@ -803,7 +819,7 @@ public class SeqCanvas extends Panel
           break;
         }
 
-        group = (SequenceGroup) av.getAlignment().getGroups()
+        group = av.getAlignment().getGroups()
                 .get(groupIndex);
       } while (groupIndex < av.getAlignment().getGroups().size());
 
-- 
1.7.10.2