Sequence is char []

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

diff --git a/src/jalview/io/FastaFile.java b/src/jalview/io/FastaFile.java
index 6e3ced8..f257c6c 100755 (executable)
--- a/src/jalview/io/FastaFile.java
+++ b/src/jalview/io/FastaFile.java
@@ -73,7 +73,7 @@ public class FastaFile extends AlignFile
                 {\r
                     if (count != 0)\r
                     {\r
-                      if (!isValidProteinSequence(sb.toString()))\r
+                      if (!isValidProteinSequence(sb.toString().toCharArray()))\r
                       {\r
                         throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
                                               +" : "+seq.getName()\r
@@ -98,7 +98,7 @@ public class FastaFile extends AlignFile
 \r
         if (count > 0)\r
         {\r
-            if (!isValidProteinSequence(sb.toString()))\r
+            if (!isValidProteinSequence(sb.toString().toCharArray()))\r
             {\r
                 throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS\r
                                       +" : "+seq.getName()\r
@@ -144,11 +144,11 @@ public class FastaFile extends AlignFile
 \r
                 if (end < s[i].getLength())\r
                 {\r
-                    out.append(s[i].getSequence(start, end) + "\n");\r
+                    out.append(s[i].getSequenceAsString(start, end) + "\n");\r
                 }\r
                 else if (start < s[i].getLength())\r
                 {\r
-                    out.append(s[i].getSequence(start, s[i].getLength()) + "\n");\r
+                    out.append(s[i].getSequenceAsString(start, s[i].getLength()) + "\n");\r
                 }\r
             }\r
 \r