sequence is char []

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

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 9b4dfef..d0c5869 100755 (executable)
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -106,7 +106,7 @@ public class AlignSeq
      */\r
     public AlignSeq(SequenceI s1, SequenceI s2, String type)\r
     {\r
-        SeqInit(s1, s1.getSequence(), s2,  s2.getSequence(), type);\r
+        SeqInit(s1, s1.getSequenceAsString(), s2,  s2.getSequenceAsString(), type);\r
     }\r
 \r
     /**\r
@@ -751,17 +751,24 @@ public class AlignSeq
 \r
         for (int i = 0; i < s.length(); i++)\r
         {\r
-            String ss = s.substring(i, i + 1).toUpperCase();\r
+           // String ss = s.substring(i, i + 1).toUpperCase();\r
+            char c = s.charAt(i);\r
+            if ('a' <= c && c <= 'z')\r
+            {\r
+              // TO UPPERCASE !!!\r
+              c -= ('a' - 'A');\r
+            }\r
+\r
 \r
             try\r
             {\r
                 if (type.equals("pep"))\r
                 {\r
-                    seq1[i] = ((Integer) ResidueProperties.aaHash.get(ss)).intValue();\r
+                    seq1[i] = ResidueProperties.aaIndex[c];\r
                 }\r
                 else if (type.equals("dna"))\r
                 {\r
-                    seq1[i] = ((Integer) dnaHash.get(ss)).intValue();\r
+                    seq1[i] = ResidueProperties.nucleotideIndex[c];\r
                 }\r
 \r
                 if (seq1[i] > 23)\r