int reply = JvOptionPane.YES_OPTION;
if (promptFetchDbrefs)
{
- reply = JvOptionPane
- .showInternalConfirmDialog(
- Desktop.desktop,
- MessageManager
- .getString("info.you_want_jalview_to_find_uniprot_accessions"),
- MessageManager
- .getString("label.find_uniprot_accession_ids"),
- JvOptionPane.YES_NO_OPTION,
- JvOptionPane.QUESTION_MESSAGE);
+ reply = JvOptionPane.showInternalConfirmDialog(Desktop.desktop,
+ MessageManager.getString(
+ "info.you_want_jalview_to_find_uniprot_accessions"),
+ MessageManager
+ .getString("label.find_uniprot_accession_ids"),
+ JvOptionPane.YES_NO_OPTION, JvOptionPane.QUESTION_MESSAGE);
}
if (reply == JvOptionPane.YES_OPTION)
startTime = System.currentTimeMillis();
if (af != null)
{
- af.setProgressBar(MessageManager
- .getString("status.fetching_das_sequence_features"),
- startTime);
+ af.setProgressBar(MessageManager.getString(
+ "status.fetching_das_sequence_features"), startTime);
}
if (sourceRegistry == null)
{
{
try
{
- jalviewSourceI[] sources = sourceRegistry.getSources().toArray(
- new jalviewSourceI[0]);
+ jalviewSourceI[] sources = sourceRegistry.getSources()
+ .toArray(new jalviewSourceI[0]);
String active = Cache.getDefault("DAS_ACTIVE_SOURCE", "uniprot");
StringTokenizer st = new StringTokenizer(active, "\t");
selectedSources = new Vector();
for (List<String> idl : ids)
{
String source = sources.next();
- FeaturesClient featuresc = new FeaturesClient(sourceRegistry
- .getSessionHandler().getConnectionPropertyProviderFor(
- source));
+ FeaturesClient featuresc = new FeaturesClient(
+ sourceRegistry.getSessionHandler()
+ .getConnectionPropertyProviderFor(source));
for (String id : idl)
{
List<String> qid = Arrays.asList(new String[] { id });
}
private void processResponse(Map<String, SequenceI> sequencemap,
- jalviewSourceI jvsource, List<String> ids,
- List<DBRefEntry> idobj, Map<List<String>, DasGFFAdapter> results,
+ jalviewSourceI jvsource, List<String> ids, List<DBRefEntry> idobj,
+ Map<List<String>, DasGFFAdapter> results,
Map<List<String>, Exception> errors)
{
Set<SequenceI> sequences = new HashSet<SequenceI>();
vf = dbref.getMap().locateFeature(f);
} catch (Exception ex)
{
- Cache.log
- .warn("Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
+ Cache.log.warn(
+ "Error in 'experimental' mapping of features. Please try to reproduce and then report info to jalview-discuss@jalview.org.");
Cache.log.warn("Mapping feature from " + f.getBegin()
+ " to " + f.getEnd() + " in dbref "
+ dbref.getAccessionId() + " in "
{
if (af != null)
{
- af.setProgressBar(MessageManager
- .getString("status.das_feature_fetching_cancelled"),
- startTime);
+ af.setProgressBar(MessageManager.getString(
+ "status.das_feature_fetching_cancelled"), startTime);
}
cancelled = true;
}
if (!cancelled && af != null)
{
// only update the progress bar if we've completed the fetch normally
- af.setProgressBar(MessageManager
- .getString("status.das_feature_fetching_complete"), startTime);
+ af.setProgressBar(MessageManager.getString(
+ "status.das_feature_fetching_complete"), startTime);
}
if (af != null && af.featureSettings != null)
return null;
}
DBRefEntry[] uprefs = DBRefUtils.selectRefs(seq.getDBRefs(),
- new String[] {
- // jalview.datamodel.DBRefSource.PDB,
- DBRefSource.UNIPROT,
+ new String[]
+ {
+ // jalview.datamodel.DBRefSource.PDB,
+ DBRefSource.UNIPROT,
// jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
// sys sources
});
// - the start/end for the DBRefEntry may not be the same as the
// sequence's start/end
- System.out.println(seq.getName() + " "
- + (seq.getDatasetSequence() == null) + " "
- + csys.getUri());
+ System.out.println(
+ seq.getName() + " " + (seq.getDatasetSequence() == null)
+ + " " + csys.getUri());
dasCoordSysFound = true; // break's out of the loop
ids.add(uprefs[j]);
{
}
- SequenceFeature f = new SequenceFeature(
- getTypeString(feat.getTYPE()), desc, start, end, score,
- nickname);
+ SequenceFeature f = new SequenceFeature(getTypeString(feat.getTYPE()),
+ desc, start, end, score, nickname);
if (feat.getLINK() != null)
{