JAL-1517 fix copyright for 2.8.2

[jalview.git] / test / jalview / io / StockholmFileTest.java

diff --git a/test/jalview/io/StockholmFileTest.java b/test/jalview/io/StockholmFileTest.java
index d831b08..f7d6448 100644 (file)
--- a/test/jalview/io/StockholmFileTest.java
+++ b/test/jalview/io/StockholmFileTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 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 static org.junit.Assert.assertNotNull;
@@ -147,6 +167,11 @@ public class StockholmFileTest
           // compare graphGroup or graph properties - needed to verify JAL-1299
           assertTrue("Graph type not identical.",aa_original[i].graph==aa_new[i].graph);
           assertTrue("Visibility not identical.", aa_original[i].visible==aa_new[i].visible);
+          assertTrue(
+                  "Threshold line not identical.",
+                  aa_original[i].threshold == null ? aa_new[i].threshold == null
+                          : aa_original[i].threshold
+                                  .equals(aa_new[i].threshold));
           // graphGroup may differ, but pattern should be the same
           Integer o_ggrp=new Integer(aa_original[i].graphGroup+2),n_ggrp=new Integer(aa_new[i].graphGroup+2);
           BitSet orig_g=orig_groups.get(o_ggrp),new_g=new_groups.get(n_ggrp);
@@ -277,9 +302,9 @@ public class StockholmFileTest
       if (an_or != null
               && an_new!= null)
       {
-        if (!an_or.displayCharacter
-                .equals(an_new.displayCharacter)
-                || an_or.secondaryStructure != an_new.secondaryStructure
+        if (!an_or.displayCharacter.trim()
+                .equals(an_new.displayCharacter.trim())
+                || !(""+an_or.secondaryStructure).trim().equals((""+an_new.secondaryStructure).trim())
                 || (an_or.description != an_new.description && (an_or.description == null
                         || an_new.description == null || !an_or.description
                           .equals(an_new.description))))