various case sensitivity bugs fixed in residue comparison functions.

[jalview.git] / src / jalview / analysis / Conservation.java

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index d814abb..0bfb636 100755 (executable)
--- a/src/jalview/analysis/Conservation.java
+++ b/src/jalview/analysis/Conservation.java
@@ -123,8 +123,8 @@ public class Conservation
 \r
                 for (j = 1; j <= len; j++)\r
                 {\r
-                    sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(new String(\r
-                                sq.substring(j - 1, j)))).intValue(); // yuk\r
+                    sqnum[j] = ((Integer) jalview.schemes.ResidueProperties.aaHash.get(Character.toString(\r
+                                sq.charAt(j - 1)))).intValue(); // yuk - JBPNote - case taken care of in aaHash\r
                 }\r
 \r
                 seqNums.setElementAt(sqnum, i);\r
@@ -163,7 +163,7 @@ public class Conservation
 \r
                     if (sequence.length() > i)\r
                     {\r
-                        res = sequence.substring(i, i + 1);\r
+                        res = Character.toString(Character.toUpperCase(sequence.charAt(i)));\r
 \r
                         if (residueHash.containsKey(res))\r
                         {\r
@@ -260,7 +260,7 @@ public class Conservation
                 continue;\r
             }\r
 \r
-            c = ((Sequence) sequences.elementAt(i)).getCharAt(j);\r
+            c = ((Sequence) sequences.elementAt(i)).getCharAt(j); // gaps do not have upper/lower case\r
 \r
             if (jalview.util.Comparison.isGap((c)))\r
             {\r