JAL-1517 update copyright to version 2.8.2

[jalview.git] / src / jalview / io / PfamFile.java

diff --git a/src/jalview/io/PfamFile.java b/src/jalview/io/PfamFile.java
index 223e7a4..5758ea2 100755 (executable)
--- a/src/jalview/io/PfamFile.java
+++ b/src/jalview/io/PfamFile.java
@@ -1,26 +1,27 @@
 /*
- * 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 2.8.2)
+ * Copyright (C) 2014 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
+ * You should have received a copy of the GNU General Public License 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.*;
 import jalview.util.*;
 
@@ -60,6 +61,8 @@ 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 +86,10 @@ public class PfamFile extends AlignFile
             {
               headers.addElement(id);
             }
-
-            tempseq.append(str.nextToken());
+            if (str.hasMoreTokens())
+            {
+              tempseq.append(str.nextToken());
+            }
           }
         }
       }
@@ -157,11 +162,12 @@ 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();
   }