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

diff --git a/src/jalview/analysis/Conservation.java b/src/jalview/analysis/Conservation.java
index d814abb..b914108 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(String.valueOf(\r
+                                sq.charAt(j - 1)))).intValue(); // yuk - JBPNote - case taken care of in aaHash\r
                 }\r
 \r
                 seqNums.setElementAt(sqnum, i);\r
@@ -145,7 +145,9 @@ public class Conservation
     {\r
       Hashtable resultHash, residueHash, ht;\r
       int count, thresh, j, jSize = sequences.size();\r
-      String sequence, res, type;\r
+      String type, res=null;\r
+      SequenceI sequence;\r
+      char c;\r
       Enumeration enumeration, enumeration2;\r
 \r
       for (int i = start; i <= end; i++)\r
@@ -157,13 +159,24 @@ public class Conservation
             {\r
                 // JBPNote - have to make sure elements of the sequences vector\r
                 //  are tested like this everywhere...\r
-                if (sequences.elementAt(j) instanceof Sequence)\r
-                {\r
-                    sequence = ((Sequence) sequences.elementAt(j)).getSequence();\r
+                    sequence = (Sequence) sequences.elementAt(j);\r
 \r
-                    if (sequence.length() > i)\r
+                    if (sequence.getLength() > i)\r
                     {\r
-                        res = sequence.substring(i, i + 1);\r
+                        c = sequence.getCharAt(i);\r
+\r
+                        if(jalview.util.Comparison.isGap(c))\r
+                          c = '-';\r
+\r
+                        if ('a' <= c && c <= 'z')\r
+                        {\r
+                          // TO UPPERCASE !!!\r
+                          //Faster than toUpperCase\r
+                          c -= ('a' - 'A') ;\r
+                        }\r
+\r
+                        res = String.valueOf( c );\r
+\r
 \r
                         if (residueHash.containsKey(res))\r
                         {\r
@@ -189,7 +202,6 @@ public class Conservation
                             residueHash.put("-", new Integer(1));\r
                         }\r
                     }\r
-                }\r
             }\r
 \r
             //What is the count threshold to count the residues in residueHash()\r
@@ -260,7 +272,7 @@ 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