/**
* @author jimp
- *
+ *
*/
public class PDBFileWithJmolTest
{
@Test
public void test() throws Exception
{
- PDBFileWithJmol jtest=new PDBFileWithJmol("./examples/1GAQ.txt", 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)
+ PDBFileWithJmol jtest = new PDBFileWithJmol("./examples/1GAQ.txt",
+ 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});
+ AlignmentI al = new Alignment(new SequenceI[]
+ { sq });
if (!al.isNucleotide())
{
- assertTrue("No secondary structure assigned for protein sequence.",sq.getAnnotation()!=null && sq.getAnnotation().length>=1 && sq.getAnnotation()[0].hasIcons);
+ assertTrue(
+ "No secondary structure assigned for protein sequence.",
+ sq.getAnnotation() != null
+ && sq.getAnnotation().length >= 1
+ && sq.getAnnotation()[0].hasIcons);
}
}
}