X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=61b3528fff048fa3e262cd024272de6b1149273f;hb=141ad7e898f94594bacb1c77eabbcd837505409c;hp=7d9c07cf09a17a6eaa931ec49bd9f198a3a674f1;hpb=04011072920c5e2587a8d549869ee47e28ad7d81;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 7d9c07c..61b3528 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -1,6 +1,6 @@
 /*
 * Jalview - A Sequence Alignment Editor and Viewer
-* Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
 *
 * This program is free software; you can redistribute it and/or
 * modify it under the terms of the GNU General Public License
@@ -145,7 +145,7 @@ public class MSFfile extends AlignFile
 
                 // Replace ~ with a sensible gap character
                 seq = seq.replace('~', '-');
-                if (!isValidProteinSequence(seq))
+                if (!isValidProteinSequence(seq.toCharArray()))
                 {
                     throw new IOException(AppletFormatAdapter.
                                           INVALID_CHARACTERS
@@ -227,9 +227,11 @@ public class MSFfile extends AlignFile
         while ((i < seqs.length) && (seqs[i] != null))
         {
           // Replace all internal gaps with . and external spaces with ~
-          s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequence().replace('-', '.'));
+          s[i] =new Sequence(seqs[i].getName(),seqs[i].getSequenceAsString().replace('-', '.'));
+
+          StringBuffer sb = new StringBuffer();
+          sb.append(s[i].getSequence());
 
-          StringBuffer sb = new StringBuffer(s[i].getSequence());
           for (int ii = 0; ii < sb.length(); ii++)
           {
             if (sb.charAt(ii) == '.')
@@ -252,9 +254,9 @@ public class MSFfile extends AlignFile
 
             s[i].setSequence(sb.toString());
 
-            if (s[i].getSequence().length() > max)
+            if (s[i].getSequence().length > max)
             {
-                max = s[i].getSequence().length();
+                max = s[i].getSequence().length;
             }
 
             i++;
@@ -270,13 +272,13 @@ public class MSFfile extends AlignFile
         int [] checksums = new int[s.length];
         while ( i < s.length )
         {
-          checksums[i] = checkSum(s[i].getSequence());
+          checksums[i] = checkSum(s[i].getSequenceAsString());
           bigChecksum += checksums[i];
           i++;
         }
 
         long maxNB = 0;
-        out.append("   MSF: " + s[0].getSequence().length() + "   Type: " +
+        out.append("   MSF: " + s[0].getSequence().length + "   Type: " +
             (is_NA ? "N" : "P") + "    Check:  " + (bigChecksum%10000) + "   ..\n\n\n");
 
         String[] nameBlock = new String[s.length];
@@ -289,7 +291,7 @@ public class MSFfile extends AlignFile
             nameBlock[i] = new String("  Name: " + printId(s[i])+" ");
 
             idBlock[i] = new String("Len: " +
-                    maxLenpad.form(s[i].getSequence().length()) + "  Check: " +
+                    maxLenpad.form(s[i].getSequence().length) + "  Check: " +
                     maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
 
             if (s[i].getName().length() > maxid)
@@ -350,10 +352,10 @@ public class MSFfile extends AlignFile
                     int start = (i * 50) + (k * 10);
                     int end = start + 10;
 
-                    if ((end < s[j].getSequence().length()) &&
-                            (start < s[j].getSequence().length()))
+                    if ((end < s[j].getSequence().length) &&
+                            (start < s[j].getSequence().length))
                     {
-                        out.append(s[j].getSequence().substring(start, end));
+                        out.append(s[j].getSequence(start, end));
 
                         if (k < 4)
                         {
@@ -366,9 +368,9 @@ public class MSFfile extends AlignFile
                     }
                     else
                     {
-                        if (start < s[j].getSequence().length())
+                        if (start < s[j].getSequence().length)
                         {
-                            out.append(s[j].getSequence().substring(start));
+                            out.append(s[j].getSequenceAsString().substring(start));
                             out.append("\n");
                         }
                         else