JAL-1645 Version-Rel Version 2.9 Year-Rel 2015 Licensing glob

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

diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index ce65eea..656e103 100644 (file)
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -1,9 +1,25 @@
-/**
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.io;
 
-import jalview.datamodel.Alignment;
 import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceI;
 
@@ -171,13 +187,6 @@ public class PhylipFile extends AlignFile
         seqs.add(sequenceElements[i]);
       }
 
-      // create an alignment based on the sequences
-      Alignment a = new Alignment(sequenceElements);
-      // add annotations - although comments say addAnnotations
-      // is used by AppletFormatAdapter, it doesn't say other
-      // classes should/can not use it
-      addAnnotations(a);
-
     } catch (IOException e)
     {
       System.err.println("Exception parsing PHYLIP file " + e);
@@ -209,8 +218,8 @@ public class PhylipFile extends AlignFile
    */
   private String validateName(String name) throws IOException
   {
-    char[] invalidCharacters = new char[]
-    { '(', ')', '[', ']', ':', ';', ',' };
+    char[] invalidCharacters = new char[] { '(', ')', '[', ']', ':', ';',
+        ',' };
     for (char c : invalidCharacters)
     {
       if (name.indexOf(c) > -1)
@@ -317,4 +326,4 @@ public class PhylipFile extends AlignFile
 
     return sb.toString();
   }
-}
\ No newline at end of file
+}