X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=bae4342276b8a701109efd851b0ca3593c14a3f7;hb=72baa5e02d3f71f1c0259072fdbd0b2bf8250e6c;hp=8082ee319f5b22f276925b61aa15436d21e8ca66;hpb=f24dacb1da56fccf05d684e2f4899facec2aecf7;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 8082ee3..bae4342 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -70,7 +70,7 @@ public class MSFfile extends AlignFile
     /**
      * DOCUMENT ME!
      */
-    public void parse()
+    public void parse() throws IOException
     {
         int i = 0;
         boolean seqFlag = false;
@@ -147,38 +147,25 @@ public class MSFfile extends AlignFile
                 String head = headers.elementAt(i).toString();
                 String seq = seqhash.get(head).toString();
 
-                int start = -1;
-                int end =  -1;
-
                 if (maxLength < head.length())
                 {
                     maxLength = head.length();
                 }
 
-                if (head.indexOf("/") > 0)
+                // Replace ~ with a sensible gap character
+                seq = seq.replace('~', '-');
+                if (!isValidProteinSequence(seq))
                 {
-                    StringTokenizer st = new StringTokenizer(head, "/");
-
-                    if (st.countTokens() == 2)
-                    {
-                        head = st.nextToken();
-
-                        String tmp = st.nextToken();
-                        st = new StringTokenizer(tmp, "-");
-
-                        if (st.countTokens() == 2)
-                        {
-                            start = Integer.valueOf(st.nextToken()).intValue();
-                            end = Integer.valueOf(st.nextToken()).intValue();
-                        }
-                    }
+                    throw new IOException(AppletFormatAdapter.
+                                          INVALID_CHARACTERS
+                                          + " : " + head
+                                          + " : " + invalidCharacter);
                 }
 
 
-                // Replace ~ with a sensible gap character
-                seq = seq.replace('~', '-');
+                Sequence newSeq = parseId(head);
 
-                Sequence newSeq = new Sequence(head, seq, start, end);
+                newSeq.setSequence(seq);
 
                 seqs.addElement(newSeq);
             }
@@ -197,7 +184,7 @@ public class MSFfile extends AlignFile
      *
      * @return DOCUMENT ME!
      */
-    public static int checkSum(String seq)
+    public int checkSum(String seq)
     {
         int check = 0;
         String sequence = seq.toUpperCase();
@@ -223,17 +210,6 @@ public class MSFfile extends AlignFile
         return check % 10000;
     }
 
-    /**
-     * DOCUMENT ME!
-     *
-     * @param s DOCUMENT ME!
-     *
-     * @return DOCUMENT ME!
-     */
-    public static String print(SequenceI[] s)
-    {
-        return print(s, false);
-    }
 
     /**
      * DOCUMENT ME!
@@ -243,9 +219,11 @@ public class MSFfile extends AlignFile
      *
      * @return DOCUMENT ME!
      */
-    public static String print(SequenceI[] seqs, boolean is_NA)
+    public String print(SequenceI[] seqs)
     {
 
+      boolean is_NA = jalview.util.Comparison.isNucleotide(seqs);
+
       SequenceI [] s = new SequenceI[seqs.length];
 
         StringBuffer out = new StringBuffer("!!" + (is_NA ? "NA" : "AA") +
@@ -265,7 +243,7 @@ public class MSFfile extends AlignFile
           {
             if (sb.charAt(ii) == '.')
             {
-              sb.replace(ii, ii + 1, "~");
+              sb.setCharAt(ii, '~');
             }
             else
               break;
@@ -275,7 +253,7 @@ public class MSFfile extends AlignFile
           {
             if (sb.charAt(ii) == '.')
             {
-              sb.replace(ii, ii + 1, "~");
+              sb.setCharAt(ii,'~');
             }
             else
               break;
@@ -316,7 +294,9 @@ public class MSFfile extends AlignFile
         i=0;
         while ((i < s.length) && (s[i] != null))
         {
-            nameBlock[i] = new String("  Name: " + s[i].getName() + " ");
+
+            nameBlock[i] = new String("  Name: " + printId(s[i])+" ");
+
             idBlock[i] = new String("Len: " +
                     maxLenpad.form(s[i].getSequence().length()) + "  Check: " +
                     maxChkpad.form(checksums[i]) + "  Weight: 1.00\n");
@@ -369,8 +349,10 @@ public class MSFfile extends AlignFile
 
             while ((j < s.length) && (s[j] != null))
             {
-                String name = s[j].getName();
-                out.append(new Format("%-" + maxid + "s").form(name)+ " ");
+                String name = printId( s[j] );
+
+                out.append(new Format("%-" + maxid + "s").form(name+" "));
+
 
                 for (int k = 0; k < 5; k++)
                 {