X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=4c90bca4979caa8f967b5ee1ebb41c8f9822177f;hb=6905363d02254a557f93f66a2b69d85aa0b23696;hp=bbd441c8378190078a1b23cf352fa079cc3aa5a4;hpb=174230b4233d9ce80f94527768d2cd2f76da11ab;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index bbd441c..4c90bca 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,6 +1,6 @@
 /*
  * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Copyright (C) 2007 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
@@ -43,7 +43,8 @@ public class PfamFile
     super.initData();
   }
 
-  public void parse() throws IOException
+  public void parse()
+      throws IOException
   {
     int i = 0;
     String line;
@@ -105,17 +106,10 @@ public class PfamFile
               .length();
         }
 
-
         Sequence newSeq = parseId(headers.elementAt(i).toString());
-        newSeq.setSequence( seqhash.get(headers.elementAt(i).toString()).toString());
+        newSeq.setSequence(seqhash.get(headers.elementAt(i).toString()).
+                           toString());
         seqs.addElement(newSeq);
-
-        if (!isValidProteinSequence(newSeq.getSequence()))
-        {
-          throw new IOException(AppletFormatAdapter.INVALID_CHARACTERS
-                                +" : "+ newSeq.getName()
-                                +" : "+invalidCharacter);
-        }
       }
       else
       {
@@ -138,9 +132,9 @@ public class PfamFile
     {
       String tmp = printId(s[i]);
 
-      if (s[i].getSequence().length() > max)
+      if (s[i].getSequence().length > max)
       {
-        max = s[i].getSequence().length();
+        max = s[i].getSequence().length;
       }
 
       if (tmp.length() > maxid)
@@ -160,9 +154,9 @@ public class PfamFile
 
     while ( (j < s.length) && (s[j] != null))
     {
-      out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));
+      out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
 
-      out.append(s[j].getSequence() + "\n");
+      out.append(s[j].getSequenceAsString() + "\n");
       j++;
     }