X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FMSFfile.java;h=179204e44a677d305ca68830775fa87704c69d4f;hb=55e2e9b22b133db8b9ff0979b0338a33081fc8fd;hp=2cef0fe98490e2a8052428c5ea30da157749d06f;hpb=87fc98c92b4d1083db30212139b1137b508a0c86;p=jalview.git

diff --git a/src/jalview/io/MSFfile.java b/src/jalview/io/MSFfile.java
index 2cef0fe..179204e 100755
--- a/src/jalview/io/MSFfile.java
+++ b/src/jalview/io/MSFfile.java
@@ -155,30 +155,11 @@ public class MSFfile extends AlignFile
                     maxLength = head.length();
                 }
 
-                if (head.indexOf("/") > 0)
-                {
-                    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();
-                        }
-                    }
-                }
-
-
                 // Replace ~ with a sensible gap character
                 seq = seq.replace('~', '-');
 
-                Sequence newSeq = new Sequence(head, seq, start, end);
+                Sequence newSeq = parseId(head);
+                newSeq.setSequence(seq);
 
                 seqs.addElement(newSeq);
             }
@@ -197,7 +178,7 @@ 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 +204,6 @@ 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 +213,11 @@ 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 +237,7 @@ public class MSFfile extends AlignFile
           {
             if (sb.charAt(ii) == '.')
             {
-              sb.replace(ii, ii + 1, "~");
+              sb.setCharAt(ii, '~');
             }
             else
               break;
@@ -275,7 +247,7 @@ public class MSFfile extends AlignFile
           {
             if (sb.charAt(ii) == '.')
             {
-              sb.replace(ii, ii + 1, "~");
+              sb.setCharAt(ii,'~');
             }
             else
               break;
@@ -317,9 +289,7 @@ public class MSFfile extends AlignFile
         while ((i < s.length) && (s[i] != null))
         {
 
-            nameBlock[i] = new String("  Name: " + s[i].getName()
-                                      + "/" + s[i].getStart() + "-" + s[i].getEnd()
-                                      +" ");
+            nameBlock[i] = new String("  Name: " + printId(s[i])+" ");
 
             idBlock[i] = new String("Len: " +
                     maxLenpad.form(s[i].getSequence().length()) + "  Check: " +
@@ -373,11 +343,9 @@ 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
-                   + "/" + s[j].getStart() + "-" + s[j].getEnd()) + " ");
+                out.append(new Format("%-" + maxid + "s").form(name+" "));
 
 
                 for (int k = 0; k < 5; k++)