{
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();
@Test(groups = { "Network" }, enabled = true)
public void testRnaSeqRetrieve() throws Exception
{
- Cache.applicationProperties.setProperty("PDB_DOWNLOAD_FORMAT", "PDB");
+ Cache.setPropertyNoSave("PDB_DOWNLOAD_FORMAT", "PDB");
List<DbSourceProxy> sps = sf.getSourceProxy("PDB");
AlignmentI response = sps.get(0).getSequenceRecords("2GIS");
assertTrue(response != null);
// chains in structure have a mapping to data in the structure
List<SequenceFeature> prev = null;
int lastp = -1;
- for (int col = 1; col <= sq.getLength(); col++)
+ for (int col = 1, ns = sq.getLength(); col <= ns; col++)
{
List<SequenceFeature> sf = sq.findFeatures(col, col, "RESNUM");
if (sf.size() != 1)