X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fext%2Fjmol%2FJmolParserTest.java;h=09b309de29fa3e0ba9c77612bd8e519403e7b264;hb=6d7ab37f37b09174ec61fee301aed6057ef86605;hp=2a501a7539f477930833299a3fdb3d5e357541c2;hpb=17df7bf657763e2d787fdd2d6651f2ea7f3ee07f;p=jalview.git

diff --git a/test/jalview/ext/jmol/JmolParserTest.java b/test/jalview/ext/jmol/JmolParserTest.java
index 2a501a7..09b309d 100644
--- a/test/jalview/ext/jmol/JmolParserTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -49,9 +49,9 @@ public class JmolParserTest
    * 1GAQ has been reduced to alpha carbons only
    * 1QCF is the full PDB file including headers, HETATM etc
    */
-  // String[] testFile = new String[] { "./examples/1GAQ.txt",
-  // "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
-  String[] testFile = new String[] { "./examples/testdata/1qcf.cif" }; // ,
+  String[] testFile = new String[] { "./examples/1GAQ.txt",
+      "./test/jalview/ext/jmol/1QCF.pdb" }; // ,
+  // String[] testFile = new String[] { "./examples/testdata/1qcf.cif" }; // ,
 
   //@formatter:off
   // a modified and very cut-down extract of 4UJ4
@@ -105,11 +105,15 @@ public class JmolParserTest
   @Test(groups = { "Functional" })
   public void testFileParser() throws Exception
   {
+    boolean annotFromStructure = false;
+    boolean localSecondaryStruct = false;
+    boolean serviceSecondaryStruct = false;
     for (String pdbStr : testFile)
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
               AppletFormatAdapter.FILE);
-      JmolParser jtest = new JmolParser(pdbStr,
+      JmolParser jtest = new JmolParser(annotFromStructure,
+              localSecondaryStruct, serviceSecondaryStruct, pdbStr,
               jalview.io.AppletFormatAdapter.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
@@ -175,7 +179,12 @@ public class JmolParserTest
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
             AppletFormatAdapter.PASTE);
-    JmolParser jtest = new JmolParser(pdbWithChainBreak,
+    boolean annotFromStructure = false;
+    boolean localSecondaryStruct = false;
+    boolean serviceSecondaryStruct = false;
+    JmolParser jtest = new JmolParser(annotFromStructure,
+            localSecondaryStruct, serviceSecondaryStruct,
+            pdbWithChainBreak,
             jalview.io.AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
@@ -198,7 +207,11 @@ public class JmolParserTest
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
             AppletFormatAdapter.PASTE);
-    JmolParser jtest = new JmolParser(pdbWithAltLoc,
+    boolean annotFromStructure = false;
+    boolean localSecondaryStruct = false;
+    boolean serviceSecondaryStruct = false;
+    JmolParser jtest = new JmolParser(annotFromStructure,
+            localSecondaryStruct, serviceSecondaryStruct, pdbWithAltLoc,
             jalview.io.AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();