X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=1342e93fb1abfb57c4ee0d4b7ddadc5855501ec9;hb=7504b4be0f02232f3a73b42fe177564546bb7547;hp=0af0689ed58027c8e83ddd30269c8f615859b6f9;hpb=b70a873b1f44dd388a1fda4c8cd9c30460e6679b;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index 0af0689..1342e93 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -131,7 +131,7 @@ public class Conservation
                 seqNums.setElementAt(sqnum, i);
             }
             else
-              System.out.println("NEVER THE EXCEPTION");
+              System.out.println("SEQUENCE HAS BEEN DELETED!!!");
         }
         else
         {
@@ -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('-');
             }
         }