Out of bounds check

diff --git a/src/jalview/schemes/ClustalxColourScheme.java b/src/jalview/schemes/ClustalxColourScheme.java
index 353accf..1e38a6d 100755 (executable)
--- a/src/jalview/schemes/ClustalxColourScheme.java
+++ b/src/jalview/schemes/ClustalxColourScheme.java
@@ -248,6 +248,11 @@ public class ClustalxColourScheme
 \r
   public Color findColour(String s, int j)\r
   {\r
+\r
+    if(cons2.length<=j)\r
+      return currentColour;\r
+\r
+\r
     if ( (threshold != 0) && !aboveThreshold(s, j))\r
     {\r
       return Color.white;\r
@@ -262,13 +267,13 @@ public class ClustalxColourScheme
       return currentColour;\r
     }\r
 \r
-    for (int k = 0; k < ResidueColour[i].conses.length; k++)\r
+  for (int k = 0; k < ResidueColour[i].conses.length; k++)\r
+  {\r
+    if (ResidueColour[i].conses[k].isConserved(cons2, j, size))\r
     {\r
-      if (ResidueColour[i].conses[k].isConserved(cons2, j, size))\r
-      {\r
-        currentColour = ResidueColour[i].c;\r
-      }\r
+      currentColour = ResidueColour[i].c;\r
     }\r
+  }\r
 \r
     if (i == 4)\r
     {\r

diff --git a/src/jalview/schemes/PIDColourScheme.java b/src/jalview/schemes/PIDColourScheme.java
index 66f180b..1575a6a 100755 (executable)
--- a/src/jalview/schemes/PIDColourScheme.java
+++ b/src/jalview/schemes/PIDColourScheme.java
@@ -53,24 +53,27 @@ public class PIDColourScheme
 \r
     double sc = 0;\r
 \r
-    if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&\r
-        consensus[j].contains(s))\r
-    {\r
-      sc = ((Float)consensus[j].get(ignoreGaps)).floatValue();\r
+    if(consensus.length<=j)\r
+      return Color.white;\r
 \r
-      if (!jalview.util.Comparison.isGap( res ))\r
+      if ( (Integer.parseInt(consensus[j].get("maxCount").toString()) != -1) &&\r
+          consensus[j].contains(s))\r
       {\r
-        for (int i = 0; i < thresholds.length; i++)\r
+        sc = ( (Float) consensus[j].get(ignoreGaps)).floatValue();\r
+\r
+        if (!jalview.util.Comparison.isGap(res))\r
         {\r
-          if (sc > thresholds[i])\r
+          for (int i = 0; i < thresholds.length; i++)\r
           {\r
-            currentColour = pidColours[i];\r
+            if (sc > thresholds[i])\r
+            {\r
+              currentColour = pidColours[i];\r
 \r
-            break;\r
+              break;\r
+            }\r
           }\r
         }\r
       }\r
-    }\r
 \r
     if(conservationColouring)\r
          applyConservation(j);\r