Merge branch 'develop' into trialMerge

[jalview.git] / test / jalview / ext / jmol / JmolVsJalviewPDBParserEndToEndTest.java

diff --git a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
index 01b4adf..6baa1dd 100644 (file)
--- a/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.java
+++ b/test/jalview/ext/jmol/JmolVsJalviewPDBParserEndToEndTest.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.jmol;
 
 import jalview.datamodel.SequenceI;
@@ -51,10 +71,8 @@ public class JmolVsJalviewPDBParserEndToEndTest
       JmolParser jtest = null;
       try
       {
-        mctest = new PDBfile(false, false, false, testFile,
-                DataSourceType.FILE);
-        jtest = new JmolParser(false, false, false, testFile,
-                DataSourceType.FILE);
+        mctest = new PDBfile(false, false, false, testFile, DataSourceType.FILE);
+        jtest = new JmolParser(testFile, DataSourceType.FILE);
       } catch (IOException e)
       {
         System.err.println("Exception thrown while parsing : " + pdbStr);
@@ -66,15 +84,15 @@ public class JmolVsJalviewPDBParserEndToEndTest
       {
         try
         {
-        String testSeq = mcseqs.remove(0).getSequenceAsString();
+          String testSeq = mcseqs.remove(0).getSequenceAsString();
           if (!sq.getSequenceAsString().equals(testSeq))
-        {
-          ++totalFail;
+          {
+            ++totalFail;
             System.err.println("Test Failed for " + pdbStr + ". Diff:");
-          System.err.println(sq.getSequenceAsString());
-          System.err.println(testSeq);
-          failedFiles.add(pdbStr);
-        }
+            System.err.println(sq.getSequenceAsString());
+            System.err.println(testSeq);
+            failedFiles.add(pdbStr);
+          }
           ++totalSeqScanned;
         } catch (Exception e)
         {