JAL-674 make temperature factor, local secondary structure and service based secondar...

[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..7bcf902 100644 (file)
--- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java
+++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
@@ -20,10 +20,8 @@
  */
 package jalview.ext.jmol;
 
-import static org.junit.Assert.*;
-
-import java.util.Vector;
-
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.SequenceI;
@@ -31,8 +29,12 @@ import jalview.gui.AlignFrame;
 import jalview.io.AppletFormatAdapter;
 import jalview.io.FileLoader;
 
+import java.util.Vector;
+
 import org.junit.Test;
 
+import MCview.PDBfile;
+
 /**
  * @author jimp
  * 
@@ -40,7 +42,7 @@ 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"
   // };
@@ -62,9 +64,11 @@ 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 +77,10 @@ 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 +88,7 @@ public class PDBFileWithJmolTest
     }
   }
 
+
   private void validateSecStrRows(AlignmentI al)
   {
     if (!al.isNucleotide())