- MsaWS msaservice = null;
- for (Services service : registry.getSupportedServices()) {
- if (service.equals(Services.ClustalOWS)) {
- msaservice = (MsaWS) Jws2Client.connect(url, service);
- if (msaservice != null) {
- break;
- }
- }
- }
- if (msaservice == null) {
- Assert.fail("couldn't find a clustalO service on the public registry");
- }
- FastaSequence fsq = new FastaSequence("seqA",
- "SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
- List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
- for (int i = 0; i < 9; i++) {
- iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
- + fsq.getSequence().substring(i + 3, i + 3 + i)));
- }
+ /**
+ * simple test for the benefit of JAL-1338
+ *
+ * @throws Exception
+ */
+ @SuppressWarnings("rawtypes")
+ @Test(groups = { "Network" })
+ public void msaTest() throws Exception
+ {
+ String url;
+ RegistryWS registry = Jws2Client
+ .connectToRegistry(url = "http://www.compbio.dundee.ac.uk/jabaws");
+ if (registry != null)
+ {
+
+ MsaWS msaservice = null;
+ for (Services service : registry.getSupportedServices())
+ {
+ if (service == null)
+ {
+ // the 'unsupported service'
+ continue;
+ }
+ if (service.equals(Services.ClustalOWS))
+ {
+ msaservice = (MsaWS) Jws2Client.connect(url, service);
+ if (msaservice != null)
+ {
+ break;
+ }
+ }
+ }
+ if (msaservice == null)
+ {
+ Assert.fail("couldn't find a clustalO service on the public registry");
+ }
+ FastaSequence fsq = new FastaSequence("seqA",
+ "SESESESESESESESSESESSESESESESESESESESESEEEEEESSESESESESSSSESESESESESESE");
+ List<FastaSequence> iseqs = new ArrayList<FastaSequence>();
+ for (int i = 0; i < 9; i++)
+ {
+ iseqs.add(new FastaSequence(fsq.getId() + i, fsq.getSequence()
+ + fsq.getSequence().substring(i + 3, i + 3 + i)));
+ }