Merge branch 'features/JAL-1541_BioJsMSA' into develop

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

diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
index d561acb..ae50bdf 100644 (file)
--- 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 ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
  * This file is part of Jalview.
  * 
@@ -20,10 +20,17 @@
  */
 package jalview.ext.jmol;
 
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 
 import java.util.Vector;
 
+import org.junit.Before;
+import org.junit.Test;
+
+import MCview.PDBfile;
+
+import jalview.bin.Cache;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -31,8 +38,6 @@ import jalview.gui.AlignFrame;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileLoader;
 
-import org.junit.Test;
-
 /**
  * @author jimp
  * 
@@ -40,11 +45,20 @@ import org.junit.Test;
 public class PDBFileWithJmolTest
 {
   String[] testFile = new String[]
-  { "./examples/1GAQ.txt" }; // ,
+  { "./examples/1GAQ.txt", "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
 
   // "./examples/DNMT1_MOUSE.pdb"
   // };
 
+  @Before
+  public void setUp()
+  {
+    Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+            Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_SS_ANN",
+            Boolean.TRUE.toString());
+  }
+
   @Test
   public void testAlignmentLoader() throws Exception
   {
@@ -62,9 +76,11 @@ public class PDBFileWithJmolTest
   {
     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"
@@ -73,6 +89,10 @@ public class PDBFileWithJmolTest
                       && seqs.size() > 0);
       for (SequenceI sq : seqs)
       {
+        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);
@@ -80,6 +100,7 @@ public class PDBFileWithJmolTest
     }
   }
 
+
   private void validateSecStrRows(AlignmentI al)
   {
     if (!al.isNucleotide())