X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=d84dc70801af742883d39b922e05d145cc7df9f2;hb=dd74fc4938723fe5ec48d4e5fdcfbe58ac42a48d;hp=8056f383763dd8e557d0084b244ebc211b947edf;hpb=8d3d3b4edf47e543b8b352c1b2c247cfc59122a4;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 8056f38..d84dc70 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) 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
@@ -32,11 +32,6 @@ public class PfamFile
   {
   }
 
-  public PfamFile(String inStr)
-  {
-    super(inStr);
-  }
-
   public PfamFile(String inFile, String type)
       throws IOException
   {
@@ -114,14 +109,7 @@ public class PfamFile
         Sequence newSeq = parseId(headers.elementAt(i).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
       {
         System.err.println("PFAM File reader: Can't find sequence for " +
@@ -143,9 +131,9 @@ 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)
@@ -167,7 +155,7 @@ public class PfamFile
     {
       out.append(new Format("%-" + maxid + "s").form( printId(s[j])+" "));
 
-      out.append(s[j].getSequence() + "\n");
+      out.append(s[j].getSequenceAsString() + "\n");
       j++;
     }