X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Futil%2FQuickSort.java;h=6901e244ca5af1f14edaddbf6cb09e39915b1eb2;hb=ce7b8a96b93ba7e22048c94ee907ca5655b72dcb;hp=c1ef153c48f4af2d7b567b7b105955bbaa784b4b;hpb=d616b0e1ac213a82591cece50ea25c5bfbfa865f;p=jalview.git

diff --git a/src/jalview/util/QuickSort.java b/src/jalview/util/QuickSort.java
index c1ef153..6901e24 100755
--- a/src/jalview/util/QuickSort.java
+++ b/src/jalview/util/QuickSort.java
@@ -51,8 +51,9 @@ public class QuickSort
     @Override
     public int compare(Integer o1, Integer o2)
     {
-      return ascending ? Float.compare(values[o1], values[o2]) : Float
-              .compare(values[o2], values[o1]);
+      return ascending
+              ? Float.compare(values[o1.intValue()], values[o2.intValue()])
+              : Float.compare(values[o2.intValue()], values[o1.intValue()]);
     }
   }
 
@@ -77,11 +78,11 @@ public class QuickSort
     {
       if (ascending)
       {
-        return Double.compare(values[o1], values[o2]);
+        return Double.compare(values[o1.intValue()], values[o2.intValue()]);
       }
       else
       {
-        return Double.compare(values[o2], values[o1]);
+        return Double.compare(values[o2.intValue()], values[o1.intValue()]);
       }
     }
   }
@@ -105,8 +106,11 @@ public class QuickSort
     @Override
     public int compare(Integer o1, Integer o2)
     {
-      return ascending ? Integer.compare(values[o1], values[o2]) : Integer
-              .compare(values[o2], values[o1]);
+      return ascending
+              ? Integer.compare(values[o1.intValue()],
+                      values[o2.intValue()])
+              : Integer.compare(values[o2.intValue()],
+                      values[o1.intValue()]);
     }
   }
 
@@ -129,8 +133,9 @@ public class QuickSort
     @Override
     public int compare(Integer o1, Integer o2)
     {
-      return ascending ? values[o1].compareTo(values[o2]) : values[o2]
-              .compareTo(values[o1]);
+      return ascending
+              ? values[o1.intValue()].compareTo(values[o2.intValue()])
+              : values[o2.intValue()].compareTo(values[o1.intValue()]);
     }
   }
 
@@ -475,10 +480,10 @@ public class QuickSort
     /*
      * Copy sorted positive values after the negatives and zeros
      */
-    System.arraycopy(nonZeroFloats, negativeCount, arr, negativeCount
-            + zerosCount, positiveCount);
-    System.arraycopy(nonZeroChars, negativeCount, s, negativeCount
-            + zerosCount, positiveCount);
+    System.arraycopy(nonZeroFloats, negativeCount, arr,
+            negativeCount + zerosCount, positiveCount);
+    System.arraycopy(nonZeroChars, negativeCount, s,
+            negativeCount + zerosCount, positiveCount);
   }
 
   /**
@@ -613,10 +618,10 @@ public class QuickSort
     /*
      * Copy sorted positive values after the negatives and zeros
      */
-    System.arraycopy(nonZeroInts, negativeCount, arr, negativeCount
-            + zerosCount, positiveCount);
-    System.arraycopy(nonZeroChars, negativeCount, s, negativeCount
-            + zerosCount, positiveCount);
+    System.arraycopy(nonZeroInts, negativeCount, arr,
+            negativeCount + zerosCount, positiveCount);
+    System.arraycopy(nonZeroChars, negativeCount, s,
+            negativeCount + zerosCount, positiveCount);
   }
 
   /**
@@ -670,7 +675,7 @@ public class QuickSort
     final int length = arr.length;
     Integer[] indices = makeIndexArray(length);
     Arrays.sort(indices, new IntComparator(arr, ascending));
-  
+
     /*
      * Copy the array values as per the sorted indices
      */
@@ -681,7 +686,7 @@ public class QuickSort
       sortedInts[i] = arr[indices[i]];
       sortedObjects[i] = s[indices[i]];
     }
-  
+
     /*
      * And copy the sorted values back into the arrays
      */
@@ -707,7 +712,7 @@ public class QuickSort
     final int length = arr.length;
     Integer[] indices = makeIndexArray(length);
     Arrays.sort(indices, new ExternalComparator(arr, ascending));
-  
+
     /*
      * Copy the array values as per the sorted indices
      */
@@ -718,7 +723,7 @@ public class QuickSort
       sortedStrings[i] = arr[indices[i]];
       sortedObjects[i] = s[indices[i]];
     }
-  
+
     /*
      * And copy the sorted values back into the arrays
      */
@@ -743,7 +748,7 @@ public class QuickSort
     final int length = arr.length;
     Integer[] indices = makeIndexArray(length);
     Arrays.sort(indices, new DoubleComparator(arr, ascending));
-  
+
     /*
      * Copy the array values as per the sorted indices
      */
@@ -754,7 +759,7 @@ public class QuickSort
       sortedDoubles[i] = arr[indices[i]];
       sortedObjects[i] = s[indices[i]];
     }
-  
+
     /*
      * And copy the sorted values back into the arrays
      */