JAL-2089 patch broken merge to master for Release 2.10.0b1

[jalview.git] / src / jalview / analysis / Conservation.java

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 19a6514..75dec63 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -251,8 +251,7 @@ public class Conservation
           // Now loop over the properties
           for (String type : ResidueProperties.propHash.keySet())
           {
-            Hashtable<String, Integer> ht = (Hashtable<String, Integer>) ResidueProperties.propHash
-                    .get(type);
+            Map<String, Integer> ht = ResidueProperties.propHash.get(type);
 
             // Have we ticked this before?
             if (!resultHash.containsKey(type))
@@ -559,8 +558,10 @@ public class Conservation
       {
         tot = 0;
         xx = new double[24];
-        seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1]
-                : 23; // Sequence, or gap at the end
+        seqNum = (j < lengths[k]) ? seqNums.elementAt(k)[j + 1] : 23; // Sequence,
+                                                                      // or gap
+                                                                      // at the
+                                                                      // end
 
         // This is a loop over r
         for (i = 0; i < 23; i++)
@@ -742,12 +743,12 @@ public class Conservation
     Conservation cons = new Conservation(name, threshold, seqs, start, end);
     cons.calculate();
     cons.verdict(posOrNeg, consPercGaps);
-    
+
     if (calcQuality)
     {
       cons.findQuality();
     }
-    
+
     return cons;
   }
 }