Sequence is char []

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

diff --git a/src/jalview/io/PileUpfile.java b/src/jalview/io/PileUpfile.java
index fa77802..be16169 100755 (executable)
--- a/src/jalview/io/PileUpfile.java
+++ b/src/jalview/io/PileUpfile.java
@@ -80,21 +80,21 @@ public class PileUpfile  extends MSFfile
     int[] checksums = new int[s.length];\r
     while (i < s.length)\r
     {\r
-      checksums[i] = checkSum(s[i].getSequence());\r
+      checksums[i] = checkSum(s[i].getSequenceAsString());\r
       bigChecksum += checksums[i];\r
       i++;\r
     }\r
 \r
-    out.append("   MSF: " + s[0].getSequence().length() +\r
+    out.append("   MSF: " + s[0].getSequence().length +\r
                "   Type: P    Check:  " + bigChecksum%10000 + "   ..\n\n\n");\r
 \r
     i=0;\r
     while ( (i < s.length) && (s[i] != null))\r
     {\r
-      String seq = s[i].getSequence();\r
+      String seq = s[i].getSequenceAsString();\r
       out.append(" Name: " + printId(s[i]) +\r
                  " oo  Len:  " +\r
-                 s[i].getSequence().length() + "  Check:  " + checksums[i] +\r
+                 seq.length() + "  Check:  " + checksums[i] +\r
                  "  Weight:  1.00\n");\r
 \r
       if (seq.length() > max)\r
@@ -142,10 +142,10 @@ public class PileUpfile  extends MSFfile
           int start = (i * 50) + (k * 10);\r
           int end = start + 10;\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].getSequence(start, end));\r
 \r
             if (k < 4)\r
             {\r
@@ -158,9 +158,9 @@ public class PileUpfile  extends MSFfile
           }\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
               out.append("\n");\r
             }\r
             else\r