From 1774759f889464551c244c070b7771dabbb4bad2 Mon Sep 17 00:00:00 2001
From: amwaterhouse <Andrew Waterhouse>
Date: Thu, 16 Mar 2006 15:12:26 +0000
Subject: [PATCH] Out of bounds check

---
 src/jalview/schemes/ClustalxColourScheme.java |   15 ++++++++++-----
 src/jalview/schemes/PIDColourScheme.java      |   23 +++++++++++++----------
 2 files changed, 23 insertions(+), 15 deletions(-)

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 353accf..1e38a6d 100755
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -248,6 +248,11 @@ public class ClustalxColourScheme
 
   public Color findColour(String s, int j)
   {
+
+    if(cons2.length<=j)
+      return currentColour;
+
+
     if ( (threshold != 0) && !aboveThreshold(s, j))
     {
       return Color.white;
@@ -262,13 +267,13 @@ public class ClustalxColourScheme
       return currentColour;
     }
 
-    for (int k = 0; k < ResidueColour[i].conses.length; k++)
+  for (int k = 0; k < ResidueColour[i].conses.length; k++)
+  {
+    if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
     {
-      if (ResidueColour[i].conses[k].isConserved(cons2, j, size))
-      {
-        currentColour = ResidueColour[i].c;
-      }
+      currentColour = ResidueColour[i].c;
     }
+  }
 
     if (i == 4)
     {
diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 66f180b..1575a6a 100755
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -53,24 +53,27 @@ public class PIDColourScheme
 
     double sc = 0;
 
-    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
-        consensus[j].contains(s))
-    {
-      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();
+    if(consensus.length<=j)
+      return Color.white;
 
-      if (!jalview.util.Comparison.isGap( res ))
+      if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&
+          consensus[j].contains(s))
       {
-        for (int i = 0; i < thresholds.length; i++)
+        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();
+
+        if (!jalview.util.Comparison.isGap(res))
         {
-          if (sc > thresholds[i])
+          for (int i = 0; i < thresholds.length; i++)
           {
-            currentColour = pidColours[i];
+            if (sc > thresholds[i])
+            {
+              currentColour = pidColours[i];
 
-            break;
+              break;
+            }
           }
         }
       }
-    }
 
     if(conservationColouring)
          applyConservation(j);
-- 
1.7.10.2