+ public void testAlignmentLoader() throws Exception
+ {
+ for (String f:testFile) {
+ FileLoader fl = new jalview.io.FileLoader(false);
+ AlignFrame af = fl.LoadFileWaitTillLoaded(f, AppletFormatAdapter.FILE);
+ validateSecStrRows(af.getViewport().getAlignment());
+ }
+ }
+ @Test
+ public void testFileParser() throws Exception
+ {
+ for (String pdbStr : testFile)
+ {
+ PDBFileWithJmol jtest = new PDBFileWithJmol(pdbStr,
+ jalview.io.AppletFormatAdapter.FILE);
+ Vector<SequenceI> seqs = jtest.getSeqs();
+
+ assertTrue(
+ "No sequences extracted from testfile\n"
+ + (jtest.hasWarningMessage() ? jtest.getWarningMessage()
+ : "(No warnings raised)"), seqs != null
+ && seqs.size() > 0);
+ for (SequenceI sq : seqs)
+ {
+ AlignmentI al = new Alignment(new SequenceI[]
+ { sq });
+ validateSecStrRows(al);
+ }
+ }
+ }
+
+ private void validateSecStrRows(AlignmentI al)