X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fanalysis%2FConservation.java;h=b914108dbeb4428eb7eebf2f9d6263feaba02b17;hb=6fc9aca27f606f6e3a0121597896e1a5dae35c36;hp=d814abb4d5ed7d494510d572f6d54d1ad1ea63dd;hpb=3c3dff5249fee03952b293a4d79ea1c792aa0f60;p=jalview.git

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index d814abb..b914108 100755
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -123,8 +123,8 @@ public class Conservation
 
                 for (j = 1; j <= len; j++)
                 {
-                    sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(new String(
-                                sq.substring(j - 1, j)))).intValue(); // yuk
+                    sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(String.valueOf(
+                                sq.charAt(j - 1)))).intValue(); // yuk - JBPNote - case taken care of in aaHash
                 }
 
                 seqNums.setElementAt(sqnum, i);
@@ -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 +159,24 @@ 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 = sequence.substring(i, i + 1);
+                        c = sequence.getCharAt(i);
+
+                        if(jalview.util.Comparison.isGap(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 +202,6 @@ public class Conservation
                             residueHash.put("-", new Integer(1));
                         }
                     }
-                }
             }
 
             //What is the count threshold to count the residues in residueHash()
@@ -260,7 +272,7 @@ public class Conservation
                 continue;
             }
 
-            c = ((Sequence) sequences.elementAt(i)).getCharAt(j);
+            c = ((Sequence) sequences.elementAt(i)).getCharAt(j); // gaps do not have upper/lower case
 
             if (jalview.util.Comparison.isGap((c)))
             {