JAL-2598 Sequence.getSequence return a copy of the char array

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

diff --git a/src/jalview/analysis/CrossRef.java b/src/jalview/analysis/CrossRef.java
index 103025c..b77e403 100644 (file)
--- a/src/jalview/analysis/CrossRef.java
+++ b/src/jalview/analysis/CrossRef.java
@@ -783,15 +783,15 @@ public class CrossRef
     {
       return false;
     }
-    char[] c1 = seq1.getSequence();
-    char[] c2 = seq2.getSequence();
-    if (c1.length != c2.length)
+
+    if (seq1.getLength() != seq2.getLength())
     {
       return false;
     }
-    for (int i = 0; i < c1.length; i++)
+    int length = seq1.getLength();
+    for (int i = 0; i < length; i++)
     {
-      int diff = c1[i] - c2[i];
+      int diff = seq1.getCharAt(i) - seq2.getCharAt(i);
       /*
        * same char or differ in case only ('a'-'A' == 32)
        */