JAL-1213 test to ensure JMol extracted sequences are same as MCView

[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 8070ee1..79e3eae 100644 (file)
--- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java
+++ b/test/jalview/ext/jmol/PDBFileWithJmolTest.java
@@ -20,6 +20,7 @@
  */
 package jalview.ext.jmol;
 
+import static org.junit.Assert.assertEquals;
 import static org.junit.Assert.assertTrue;
 import jalview.datamodel.Alignment;
 import jalview.datamodel.AlignmentI;
@@ -32,6 +33,8 @@ import java.util.Vector;
 
 import org.junit.Test;
 
+import MCview.PDBfile;
+
 /**
  * @author jimp
  * 
@@ -39,7 +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"
   // };
@@ -61,9 +64,11 @@ public class PDBFileWithJmolTest
   {
     for (String pdbStr : testFile)
     {
+      PDBfile mctest = new PDBfile(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"
@@ -72,6 +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);