* 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
@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();
{
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();
{
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();