X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FPhylipFile.java;h=8e01c8868acd011a9ac4f3f2df99b069e5305e52;hb=refs%2Fheads%2Freleases%2FRelease_2_10_0_Branch;hp=ce65eea1486deb4d83e5f4924c1866896583859e;hpb=77abb3fac2965a8966410cd77cd749c7c1dc6453;p=jalview.git

diff --git a/src/jalview/io/PhylipFile.java b/src/jalview/io/PhylipFile.java
index ce65eea..8e01c88 100644
--- a/src/jalview/io/PhylipFile.java
+++ b/src/jalview/io/PhylipFile.java
@@ -1,9 +1,25 @@
-/**
- *
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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
+}