JAL-2148 fix to heuristically determine chain termination positions. This aids in...

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

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index 0010321..b0e0718 100644 (file)
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -109,7 +109,6 @@ public class JmolParserTest
   @Test(groups = { "Functional" })
   public void testFileParser() throws Exception
   {
-    StructureImportSettings.setProcessHETATMs(false);
     for (String pdbStr : testFile)
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
@@ -133,30 +132,7 @@ public class JmolParserTest
         validateSecStrRows(al);
       }
     }
-    StructureImportSettings.setProcessHETATMs(true);
-    for (String pdbStr : testFile)
-    {
-      PDBfile mctest = new PDBfile(false, false, false, pdbStr,
-              AppletFormatAdapter.FILE);
-      JmolParser jtest = new JmolParser(false, false, false, pdbStr,
-              jalview.io.AppletFormatAdapter.FILE);
-      Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
-      assertTrue(
-              "No sequences extracted from testfile\n"
-                      + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
-                              : "(No warnings raised)"), seqs != null
-                      && 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);
-      }
-    }
   }
 
   private void validateSecStrRows(AlignmentI al)