@Override
public void ok_ActionPerformed()
{
- final long progressSessionId = System.currentTimeMillis();
final StructureSelectionManager ssm = ap.getStructureSelectionManager();
final int preferredHeight = pnl_filter.getHeight();
- ssm.setProgressIndicator(this);
- ssm.setProgressSessionId(progressSessionId);
ssm.setMappingForPhyre2Model(false);
new Thread(new Runnable()
{
selectedSequence = userSelectedSeq;
}
+
String pdbIdStr = txt_search.getText();
PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
DataSourceType.FILE,
selectedSequence, true, Desktop.instance);
- launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ launchStructureViewer(ssm,
+ new PDBEntry[] { fileEntry }, ap,
new SequenceI[] { selectedSequence });
}
else if (currentView == VIEWS_PHYRE2_PREDICTION)
final PDBEntry[] pdbEntriesToView,
final AlignmentPanel alignPanel, SequenceI[] sequences)
{
- ssm.setProgressBar(MessageManager
- .getString("status.launching_3d_structure_viewer"));
+ long progressId = sequences.hashCode();
+ setProgressBar(MessageManager
+ .getString("status.launching_3d_structure_viewer"), progressId);
final StructureViewer sViewer = new StructureViewer(ssm);
+ setProgressBar(null, progressId);
if (SiftsSettings.isMapWithSifts())
{
// TODO: skip PDBEntry:Sequence pairs where PDBEntry doesn't look like a
// real PDB ID. For moment, we can also safely do this if there is already
// a known mapping between the PDBEntry and the sequence.
+
for (SequenceI seq : sequences)
{
PDBEntry pdbe = pdbEntriesToView[p++];
if (!seqsWithoutSourceDBRef.isEmpty())
{
int y = seqsWithoutSourceDBRef.size();
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_dbrefs_for_sequences_without_valid_refs",
- y));
+ y), progressId);
SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
int x = 0;
for (SequenceI fSeq : seqsWithoutSourceDBRef)
{
seqWithoutSrcDBRef[x++] = fSeq;
}
- DBRefFetcher dbRefFetcher = new DBRefFetcher(seqWithoutSrcDBRef);
- dbRefFetcher.fetchDBRefs(true);
+ new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
+ setProgressBar("Fetch complete.", progressId); // todo i18n
}
}
if (pdbEntriesToView.length > 1)
seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager
- .getString("status.fetching_3d_structures_for_selected_entries"));
+ setProgressBar(MessageManager
+ .getString("status.fetching_3d_structures_for_selected_entries"), progressId);
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
{
- ssm.setProgressBar(null);
- ssm.setProgressBar(MessageManager.formatMessage(
+ setProgressBar(MessageManager.formatMessage(
"status.fetching_3d_structures_for",
- pdbEntriesToView[0].getId()));
+ pdbEntriesToView[0].getId()),progressId);
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
+ setProgressBar(null, progressId);
}
/**