X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fext%2Fso%2FSequenceOntology.java;h=0d631e66ee3ed0c3124eb5f69f63d8a5f521f5f0;hb=3d0101179759ef157b088ea135423cd909512d9f;hp=28ddfd9aa0fc26df7ec2b475f36d799f2db27107;hpb=b4d15601e50bafd396bce2af9dded397e63cc8b8;p=jalview.git

diff --git a/src/jalview/ext/so/SequenceOntology.java b/src/jalview/ext/so/SequenceOntology.java
index 28ddfd9..0d631e6 100644
--- a/src/jalview/ext/so/SequenceOntology.java
+++ b/src/jalview/ext/so/SequenceOntology.java
@@ -1,3 +1,23 @@
+/*
+ * 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.ext.so;
 
 import jalview.io.gff.SequenceOntologyI;
@@ -82,8 +102,8 @@ public class SequenceOntology implements SequenceOntologyI
     try
     {
       String zipFile = ontologyFile + ".zip";
-      InputStream inStream = this.getClass().getResourceAsStream(
-              "/" + zipFile);
+      InputStream inStream = this.getClass()
+              .getResourceAsStream("/" + zipFile);
       zipStream = new ZipInputStream(new BufferedInputStream(inStream));
       ZipEntry entry;
       while ((entry = zipStream.getNextEntry()) != null)
@@ -131,8 +151,8 @@ public class SequenceOntology implements SequenceOntologyI
    * @throws ParseException
    * @throws IOException
    */
-  protected void loadOboFile(InputStream is) throws ParseException,
-          IOException
+  protected void loadOboFile(InputStream is)
+          throws ParseException, IOException
   {
     BufferedReader oboFile = new BufferedReader(new InputStreamReader(is));
     OboParser parser = new OboParser();
@@ -175,9 +195,9 @@ public class SequenceOntology implements SequenceOntologyI
             }
             else
             {
-            System.err.println("Warning: " + term.getName()
-                    + " has replaced " + replaced.getName()
-                    + " for lookup of '" + description + "'");
+              System.err.println("Warning: " + term.getName()
+                      + " has replaced " + replaced.getName()
+                      + " for lookup of '" + description + "'");
             }
           }
           termsByDescription.put(description, term);
@@ -200,8 +220,8 @@ public class SequenceOntology implements SequenceOntologyI
     {
       try
       {
-      if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
-      {
+        if (Boolean.TRUE.equals(ann.getProperty("is_obsolete")))
+        {
           return true;
         }
       } catch (NoSuchElementException e)