X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FPDBFileWithJmolTest.java;h=fa3922b3c78c7d7be3bddc37a3a9dabd0d95e90b;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=d561acb704f6a9517606d51a23c8cbbddc2e0b50;hpb=09da3ad08ff2e25e67e3f4a08ae4644660eebd72;p=jalview.git

diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
index d561acb..fa3922b 100644
--- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java
+++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
@@ -1,6 +1,6 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,10 @@
  */
 package jalview.ext.jmol;
 
-import static org.junit.Assert.*;
-
-import java.util.Vector;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertTrue;
 
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -31,7 +31,12 @@ import jalview.gui.AlignFrame;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileLoader;
 
-import org.junit.Test;
+import java.util.Vector;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import MCview.PDBfile;
 
 /**
  * @author jimp
@@ -39,13 +44,22 @@ import org.junit.Test;
  */
 public class PDBFileWithJmolTest
 {
-  String[] testFile = new String[]
-  { "./examples/1GAQ.txt" }; // ,
+  String[] testFile = new String[] { "./examples/1GAQ.txt",
+      "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
 
   // "./examples/DNMT1_MOUSE.pdb"
   // };
 
-  @Test
+  @BeforeMethod(alwaysRun = true)
+  public void setUp()
+  {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+  }
+
+  @Test(groups = { "Functional" })
   public void testAlignmentLoader() throws Exception
   {
     for (String f : testFile)
@@ -57,14 +71,16 @@ public class PDBFileWithJmolTest
     }
   }
 
-  @Test
+  @Test(groups = { "Functional" })
   public void testFileParser() throws Exception
   {
     for (String pdbStr : testFile)
     {
+      PDBfile mctest = new PDBfile(false, false, false, pdbStr,
+              AppletFormatAdapter.FILE);
       PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
               jalview.io.AppletFormatAdapter.FILE);
-      Vector<SequenceI> seqs = jtest.getSeqs();
+      Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
       assertTrue(
               "No sequences extracted from testfile\n"
@@ -73,8 +89,11 @@ public class PDBFileWithJmolTest
                       && seqs.size() > 0);
       for (SequenceI sq : seqs)
       {
-        AlignmentI al = new Alignment(new SequenceI[]
-        { sq });
+        assertEquals("JMol didn't process " + pdbStr
+                + " to the same sequence as MCView",
+                sq.getSequenceAsString(), mcseqs.remove(0)
+                        .getSequenceAsString());
+        AlignmentI al = new Alignment(new SequenceI[] { sq });
         validateSecStrRows(al);
       }
     }