JAL-1919 basic support for importing and viewing mmCIF files - mapping support not...

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

diff --git a/test/jalview/ext/jmol/PDBFileWithJmolTest.java b/test/jalview/ext/jmol/JmolParserTest.java
similarity index 95%
rename from test/jalview/ext/jmol/PDBFileWithJmolTest.java
rename to test/jalview/ext/jmol/JmolParserTest.java
index 4dc7095..2a501a7 100644 (file)
--- a/test/jalview/ext/jmol/PDBFileWithJmolTest.java
+++ b/test/jalview/ext/jmol/JmolParserTest.java
@@ -43,14 +43,15 @@ import MCview.PDBfile;
  * @author jimp
  * 
  */
-public class PDBFileWithJmolTest
+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/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
@@ -108,7 +109,7 @@ public class PDBFileWithJmolTest
     {
       PDBfile mctest = new PDBfile(false, false, false, pdbStr,
               AppletFormatAdapter.FILE);
-      PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
+      JmolParser jtest = new JmolParser(pdbStr,
               jalview.io.AppletFormatAdapter.FILE);
       Vector<SequenceI> seqs = jtest.getSeqs(), mcseqs = mctest.getSeqs();
 
@@ -174,7 +175,7 @@ public class PDBFileWithJmolTest
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithChainBreak,
             AppletFormatAdapter.PASTE);
-    PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithChainBreak,
+    JmolParser jtest = new JmolParser(pdbWithChainBreak,
             jalview.io.AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
@@ -197,7 +198,7 @@ public class PDBFileWithJmolTest
   {
     PDBfile mctest = new PDBfile(false, false, false, pdbWithAltLoc,
             AppletFormatAdapter.PASTE);
-    PDBFileWithJmol jtest = new PDBFileWithJmol(pdbWithAltLoc,
+    JmolParser jtest = new JmolParser(pdbWithAltLoc,
             jalview.io.AppletFormatAdapter.PASTE);
     Vector<SequenceI> seqs = jtest.getSeqs();
     Vector<SequenceI> mcseqs = mctest.getSeqs();
@@ -211,7 +212,7 @@ public class PDBFileWithJmolTest
   @Test(groups = "Functional")
   public void testSetSecondaryStructure()
   {
-    PDBFileWithJmol testee = new PDBFileWithJmol();
+    JmolParser testee = new JmolParser();
     char[] struct = new char[10];
     char[] structCode = new char[10];
     struct[0] = '1';