JAL-2189 format tests

[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 2ea0b80..fb092f6 100644 (file)
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -86,8 +86,11 @@ public class JmolParserTest
   @BeforeMethod(alwaysRun = true)
   public void setUp()
   {
+    Cache.loadProperties("test/jalview/io/testProps.jvprops");
     Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
             Boolean.TRUE.toString());
+    Cache.applicationProperties.setProperty("ADD_TEMPFACT_ANN",
+            Boolean.FALSE.toString());
     Cache.applicationProperties.setProperty("ADD_SS_ANN",
             Boolean.TRUE.toString());
     StructureImportSettings.setDefaultStructureFileFormat("PDB");
@@ -110,13 +113,11 @@ 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,
               AppletFormatAdapter.FILE);
-      JmolParser jtest = new JmolParser(false, false, false, pdbStr,
-              jalview.io.AppletFormatAdapter.FILE);
+      JmolParser jtest = new JmolParser(pdbStr, AppletFormatAdapter.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
       assertTrue(
@@ -134,30 +135,7 @@ 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)
@@ -187,7 +165,8 @@ public class JmolParserTest
 
   private void checkFirstAAIsAssoc(SequenceI sq)
   {
-    assertTrue("No secondary structure assigned for protein sequence.",
+    assertTrue("No secondary structure assigned for protein sequence for "
+            + sq.getName(),
             sq.getAnnotation() != null && sq.getAnnotation().length >= 1
                     && sq.getAnnotation()[0].hasIcons);
     assertTrue(
@@ -204,15 +183,9 @@ public class JmolParserTest
   public void testParse_missingResidues() throws Exception
   {
     PDBfile mctest = new PDBfile(false, false, false,
-            pastePDBDataWithChainBreak,
+            pastePDBDataWithChainBreak, AppletFormatAdapter.PASTE);
+    JmolParser jtest = new JmolParser(pastePDBDataWithChainBreak,
             AppletFormatAdapter.PASTE);
-    boolean annotFromStructure = false;
-    boolean localSecondaryStruct = false;
-    boolean serviceSecondaryStruct = false;
-    JmolParser jtest = new JmolParser(annotFromStructure,
-            localSecondaryStruct, serviceSecondaryStruct,
-            pastePDBDataWithChainBreak,
-            jalview.io.AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
 
@@ -234,15 +207,11 @@ public class JmolParserTest
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
             AppletFormatAdapter.PASTE);
-    boolean annotFromStructure = false;
-    boolean localSecondaryStruct = false;
-    boolean serviceSecondaryStruct = false;
-    JmolParser jtest = new JmolParser(annotFromStructure,
-            localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
-            jalview.io.AppletFormatAdapter.PASTE);
+    JmolParser jtest = new JmolParser(pdbWithAltLoc,
+            AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
-  
+
     assertEquals("Failed to find 1 sequence\n", 1, seqs.size());
     assertEquals("Failed to find 1 sequence\n", 1, mcseqs.size());
     assertEquals("ALC", seqs.get(0).getSequenceAsString());