X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=0aa980534ccd40e78a229de2a828564bf8415469;hb=9f95d8f9e281436450419985ab58be83022859b4;hp=b9b68cec25198d3bf1a175cf0efb7e1d09818bff;hpb=83b55697263efc7b0c660eba6ea7091f6904257d;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index b9b68ce..0aa9805 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -145,7 +145,9 @@ public class Conservation
     {
       Hashtable resultHash, residueHash, ht;
       int count, thresh, j, jSize = sequences.size();
-      String sequence, res, type;
+      String type, res=null;
+      SequenceI sequence;
+      char c;
       Enumeration enumeration, enumeration2;
 
       for (int i = start; i <= end; i++)
@@ -157,13 +159,25 @@ public class Conservation
             {
                 // JBPNote - have to make sure elements of the sequences vector
                 //  are tested like this everywhere...
-                if (sequences.elementAt(j) instanceof Sequence)
-                {
-                    sequence = ((Sequence) sequences.elementAt(j)).getSequence();
+                    sequence = (Sequence) sequences.elementAt(j);
 
-                    if (sequence.length() > i)
+                    if (sequence.getLength() > i)
                     {
-                        res = String.valueOf(Character.toUpperCase(sequence.charAt(i)));
+                        c = sequence.getCharAt(i);
+
+                        // No need to check if its a '-'
+                        if(c == '.' || c==' ')
+                          c = '-';
+
+                        if ('a' <= c && c <= 'z')
+                        {
+                          // TO UPPERCASE !!!
+                          //Faster than toUpperCase
+                          c -= ('a' - 'A') ;
+                        }
+
+                        res = String.valueOf( c );
+
 
                         if (residueHash.containsKey(res))
                         {
@@ -189,7 +203,6 @@ public class Conservation
                             residueHash.put("-", new Integer(1));
                         }
                     }
-                }
             }
 
             //What is the count threshold to count the residues in residueHash()