boolean useJDasMultiThread)
{
this.useJDASMultiThread = useJDasMultiThread;
- this.selectedSources = new ArrayList<jalviewSourceI>();
+ this.selectedSources = new ArrayList<>();
// filter both sequences and sources to eliminate duplicates
for (jalviewSourceI src : selectedSources2)
{
FeaturesClientMultipleSources fc = new FeaturesClientMultipleSources();
fc.setConnProps(sourceRegistry.getSessionHandler());
// Now sending requests one at a time to each server
- ArrayList<jalviewSourceI> srcobj = new ArrayList<jalviewSourceI>();
- ArrayList<String> src = new ArrayList<String>();
- List<List<String>> ids = new ArrayList<List<String>>();
- List<List<DBRefEntry>> idobj = new ArrayList<List<DBRefEntry>>();
- List<Map<String, SequenceI>> sqset = new ArrayList<Map<String, SequenceI>>();
+ ArrayList<jalviewSourceI> srcobj = new ArrayList<>();
+ ArrayList<String> src = new ArrayList<>();
+ List<List<String>> ids = new ArrayList<>();
+ List<List<DBRefEntry>> idobj = new ArrayList<>();
+ List<Map<String, SequenceI>> sqset = new ArrayList<>();
for (jalviewSourceI _sr : selectedSources)
{
- Map<String, SequenceI> slist = new HashMap<String, SequenceI>();
- List<DBRefEntry> idob = new ArrayList<DBRefEntry>();
- List<String> qset = new ArrayList<String>();
+ Map<String, SequenceI> slist = new HashMap<>();
+ List<DBRefEntry> idob = new ArrayList<>();
+ List<String> qset = new ArrayList<>();
for (SequenceI seq : sequences)
{
sqset.add(slist);
}
}
- Map<String, Map<List<String>, Exception>> errors = new HashMap<String, Map<List<String>, Exception>>();
- Map<String, Map<List<String>, DasGFFAdapter>> results = new HashMap<String, Map<List<String>, DasGFFAdapter>>();
+ Map<String, Map<List<String>, Exception>> errors = new HashMap<>();
+ Map<String, Map<List<String>, DasGFFAdapter>> results = new HashMap<>();
if (!useJDASMultiThread)
{
Iterator<String> sources = src.iterator();
if (ers == null)
{
results.put(source,
- ers = new HashMap<List<String>, DasGFFAdapter>());
+ ers = new HashMap<>());
}
ers.put(qid, dga);
} catch (Exception ex)
if (ers == null)
{
errors.put(source,
- ers = new HashMap<List<String>, Exception>());
+ ers = new HashMap<>());
}
ers.put(qid, ex);
}
Map<List<String>, DasGFFAdapter> results,
Map<List<String>, Exception> errors)
{
- Set<SequenceI> sequences = new HashSet<SequenceI>();
+ Set<SequenceI> sequences = new HashSet<>();
String source = jvsource.getSourceURL();
// process features
DasGFFAdapter result = (results == null) ? null : results.get(ids);
if (seq == af.getViewport().getAlignment().getSequenceAt(index)
.getDatasetSequence())
{
- af.alignPanel.paintAlignment(true);
+ af.alignPanel.paintAlignment(true, true);
index = end;
break;
}
// TODO: minimal list of DAS queries to make by querying with untyped ID if
// distinct from any typed IDs
- List<DBRefEntry> ids = new ArrayList<DBRefEntry>();
- List<String> qstring = new ArrayList<String>();
+ List<DBRefEntry> ids = new ArrayList<>();
+ List<String> qstring = new ArrayList<>();
boolean dasCoordSysFound = false;
if (uprefs != null)