X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=99c6e89a894ef4db0ec3c113ce4a3b064d673ba2;hb=0f0886fe3a3070bcb7fad7f11145ada140eb92ba;hp=63f791c55289ed1afb826c8b456ef7181e41d621;hpb=e905bf509cf285c9b73ee6d89be1a038c4e41e2c;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 63f791c..99c6e89 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -100,7 +100,7 @@ public class Conservation
 
         if ((i > -1) && (i < sSize))
         {
-            sq = sequences[i].getSequence();
+            sq = sequences[i].getSequenceAsString();
 
             if (seqNums.size() <= i)
             {
@@ -187,12 +187,12 @@ public class Conservation
 
             //loop over all the found residues
             resultHash = new Hashtable();
-            for (int v = '-'; v < 'Z'; v++)
+            for (char v = '-'; v < 'Z'; v++)
             {
 
                 if (values[v] > thresh)
                 {
-                  res =  String.valueOf( (char) v);
+                  res =  String.valueOf( v );
 
                     //Now loop over the properties
                     enumeration2 = propHash.keys();
@@ -295,6 +295,12 @@ public class Conservation
         Hashtable resultHash ;
         Enumeration enumeration;
 
+        //NOTE THIS SHOULD CHECK IF THE CONSEQUENCE ALREADY
+        //EXISTS AND NOT OVERWRITE WITH '-', BUT THIS CASE
+        //DOES NOT EXIST IN JALVIEW 2.1.2
+        for(int i=0; i<start; i++)
+          consString.append('-');
+
 
         for (int i = start; i <= end; i++)
         {
@@ -343,7 +349,7 @@ public class Conservation
             }
             else
             {
-                consString.append("-");
+                consString.append('-');
             }
         }