/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2b1)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b1)
+ * Copyright (C) 2015 The Jalview Authors
*
* This file is part of Jalview.
*
reply = JOptionPane
.showInternalConfirmDialog(
Desktop.desktop,
- MessageManager.getString("info.you_want_jalview_to_find_uniprot_accessions"),
- MessageManager.getString("label.find_uniprot_accession_ids"),
+ MessageManager
+ .getString("info.you_want_jalview_to_find_uniprot_accessions"),
+ MessageManager
+ .getString("label.find_uniprot_accession_ids"),
JOptionPane.YES_NO_OPTION,
JOptionPane.QUESTION_MESSAGE);
}
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)
{
source));
for (String id : idl)
{
- List<String> qid = Arrays.asList(new String[]
- { id });
+ List<String> qid = Arrays.asList(new String[] { id });
try
{
DasGFFAdapter dga = featuresc.fetchData(source, qid);
if (af != null)
{
- af.setProgressBar(MessageManager.getString("status.no_das_sources_active"), startTime);
+ af.setProgressBar(
+ MessageManager.getString("status.no_das_sources_active"),
+ startTime);
}
if (getFeatSettings() != null)
{
{
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)
{
- af.featureSettings.setTableData();
+ af.featureSettings.discoverAllFeatureData();
}
if (getFeatSettings() != null)
return null;
}
DBRefEntry[] uprefs = jalview.util.DBRefUtils.selectRefs(
- seq.getDBRef(), new String[]
- {
+ seq.getDBRef(), new String[] {
// jalview.datamodel.DBRefSource.PDB,
jalview.datamodel.DBRefSource.UNIPROT,
// jalview.datamodel.DBRefSource.EMBL - not tested on any EMBL coord
}
}
- return new Object[]
- { ids, qstring };
+ return new Object[] { ids, qstring };
}
/**