X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPfamFile.java;h=e696609d7cb303d254fa316919951af6eb338847;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=223e7a468d0a924bc6d16b11e64825bf09df720f;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 223e7a4..e696609 100755
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,28 +1,34 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
  * 
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
  * 
  * You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA  02110-1301, USA
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import java.io.*;
-import java.util.*;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.util.Format;
+import jalview.util.MessageManager;
 
-import jalview.datamodel.*;
-import jalview.util.*;
+import java.io.IOException;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+import java.util.Vector;
 
 public class PfamFile extends AlignFile
 {
@@ -60,6 +66,8 @@ public class PfamFile extends AlignFile
       {
         if (line.indexOf("#") != 0)
         {
+          // TODO: verify pfam format requires spaces and not tab characters -
+          // if not upgrade to use stevesoft regex and look for whitespace.
           StringTokenizer str = new StringTokenizer(line, " ");
           String id = "";
 
@@ -83,8 +91,10 @@ public class PfamFile extends AlignFile
             {
               headers.addElement(id);
             }
-
-            tempseq.append(str.nextToken());
+            if (str.hasMoreTokens())
+            {
+              tempseq.append(str.nextToken());
+            }
           }
         }
       }
@@ -94,7 +104,8 @@ public class PfamFile extends AlignFile
 
     if (noSeqs < 1)
     {
-      throw new IOException("No sequences found (PFAM input)");
+      throw new IOException(
+              MessageManager.getString("exception.pfam_no_sequences_found"));
     }
 
     for (i = 0; i < headers.size(); i++)
@@ -157,11 +168,12 @@ public class PfamFile extends AlignFile
     {
       out.append(new Format("%-" + maxid + "s").form(printId(s[j]) + " "));
 
-      out.append(s[j].getSequenceAsString() + "\n");
+      out.append(s[j].getSequenceAsString());
+      out.append(newline);
       j++;
     }
 
-    out.append("\n");
+    out.append(newline);
 
     return out.toString();
   }