@Test(groups = { "Functional" })
public void testFileParser() throws Exception
{
- StructureImportSettings.setProcessHETATMs(false);
for (String pdbStr : testFile)
{
PDBfile mctest = new PDBfile(false, false, false, pdbStr,
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)