{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
// ensure 'add annotation from structure' is selected
- Cache.applicationProperties.setProperty("STRUCT_FROM_PDB",
+ Cache.setPropertyNoSave("STRUCT_FROM_PDB",
Boolean.TRUE.toString());
- Cache.applicationProperties.setProperty("ADD_SS_ANN",
+ Cache.setPropertyNoSave("ADD_SS_ANN",
Boolean.TRUE.toString());
- sf = new SequenceFetcher(false);
+ sf = SequenceFetcher.getInstance();
}
@DataProvider(name = "AccessionData")
SequenceI sq = al.getSequenceAt(0);
// suppress this check as only Uniprot and PDB acquire PDB refs
// assertTrue(sq.getAllPDBEntries().size() > 0, "No PDBEntry on sequence.");
- assertTrue(sq.getDBRefs().length > 0, "No DBRef on sequence.");
+ assertTrue(sq.getDBRefs().size() > 0, "No DBRef on sequence.");
// suppress this test as only certain databases provide 'primary' dbrefs
// assertFalse(sq.getPrimaryDBRefs().isEmpty());
int length = AlignSeq.extractGaps("-. ", sq.getSequenceAsString())
@Test(groups = { "Network" })
public void testUniprotFreeTextSearch() throws Exception
{
- List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ List<FTSDataColumnI> wantedFields = new ArrayList<>();
FTSRestClientI client = UniProtFTSRestClient.getInstance();
wantedFields.add(client.getDataColumnByNameOrCode("id"));
wantedFields.add(client.getDataColumnByNameOrCode("entry name"));