JAL-920 compute a consensus for single sequence

diff --git a/src/jalview/analysis/AAFrequency.java b/src/jalview/analysis/AAFrequency.java
index 656cdcb..b24fff0 100755 (executable)
--- a/src/jalview/analysis/AAFrequency.java
+++ b/src/jalview/analysis/AAFrequency.java
@@ -91,7 +91,7 @@ public class AAFrequency
     Hashtable residueHash;
     int maxCount, nongap, i, j, v, jSize = sequences.length;
     String maxResidue;
-    char c;
+    char c='-';
     float percentage;
 
     int[] values = new int[255];
@@ -105,7 +105,7 @@ public class AAFrequency
       maxResidue = "";
       nongap = 0;
       values = new int[255];
-
+      
       for (j = 0; j < jSize; j++)
       {
         if (sequences[j] == null)
@@ -143,8 +143,11 @@ public class AAFrequency
           values['-']++;
         }
       }
-
-      for (v = 'A'; v < 'Z'; v++)
+      if (jSize==1)
+      {
+        maxResidue = String.valueOf(c);
+        maxCount=1;
+      } else {for (v = 'A'; v < 'Z'; v++)
       {
         if (values[v] < 2 || values[v] < maxCount)
         {
@@ -161,7 +164,7 @@ public class AAFrequency
         }
         maxCount = values[v];
       }
-
+      }
       if (maxResidue.length() == 0)
       {
         maxResidue = "-";