Sequence is char []

[jalview.git] / src / jalview / io / ClustalFile.java

diff --git a/src/jalview/io/ClustalFile.java b/src/jalview/io/ClustalFile.java
index e3f83ee..b43e3ea 100755 (executable)
--- a/src/jalview/io/ClustalFile.java
+++ b/src/jalview/io/ClustalFile.java
@@ -164,9 +164,9 @@ public class ClustalFile
     {\r
       String tmp = printId(s[i]);\r
 \r
-      if (s[i].getSequence().length() > max)\r
+      if (s[i].getSequence().length > max)\r
       {\r
-        max = s[i].getSequence().length();\r
+        max = s[i].getSequence().length;\r
       }\r
 \r
       if (tmp.length() > maxid)\r
@@ -198,16 +198,16 @@ public class ClustalFile
         int start = i * len;\r
         int end = start + len;\r
 \r
-        if ( (end < s[j].getSequence().length()) &&\r
-            (start < s[j].getSequence().length()))\r
+        if ( (end < s[j].getSequence().length) &&\r
+            (start < s[j].getSequence().length))\r
         {\r
-          out.append(s[j].getSequence().substring(start, end));\r
+          out.append(s[j].getSequenceAsString(start, end));\r
         }\r
         else\r
         {\r
-          if (start < s[j].getSequence().length())\r
+          if (start < s[j].getSequence().length)\r
           {\r
-            out.append(s[j].getSequence().substring(start));\r
+            out.append(s[j].getSequenceAsString().substring(start));\r
           }\r
         }\r
 \r