private boolean isValidPBDEntry;
-
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
{
if (seq.getDatasetSequence() != null
&& seq.getDatasetSequence().getAllPDBEntries() != null)
{
- for (PDBEntry pdbEntry : seq.getDatasetSequence().getAllPDBEntries())
+ for (PDBEntry pdbEntry : seq.getDatasetSequence()
+ .getAllPDBEntries())
{
if (pdbEntry.getFile() != null)
{
tbl_local_pdb.setModel(tableModelx);
}
-
/**
* Builds a query string for a given sequences using its DBRef entries
*
// Update table selection model here
tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_filter_time",
- totalTime));
+ "label.structure_chooser_filter_time", totalTime));
}
else
{
mainFrame.setTitle(MessageManager.formatMessage(
- "label.structure_chooser_filter_time",
- totalTime));
+ "label.structure_chooser_filter_time", totalTime));
if (errors.size() > 0)
{
StringBuilder errorMsg = new StringBuilder();
{
errorMsg.append(error).append("\n");
}
- JOptionPane.showMessageDialog(null, errorMsg.toString(),
+ JOptionPane.showMessageDialog(
+ null,
+ errorMsg.toString(),
MessageManager.getString("label.pdb_web-service_error"),
JOptionPane.ERROR_MESSAGE);
}
lbl_pdbManualFetchStatus.setToolTipText("");
if (txt_search.getText().length() > 0)
{
- lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
- true, MessageManager.formatMessage(
- "info.no_pdb_entry_found_for",
+ lbl_pdbManualFetchStatus
+ .setToolTipText(JvSwingUtils.wrapTooltip(true, MessageManager
+ .formatMessage("info.no_pdb_entry_found_for",
txt_search.getText())));
}
selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
}
- PDBEntry[] pdbEntriesToView = new PDBEntry[]
- { pdbEntry };
+ PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, new SequenceI[]
- { selectedSequence });
+ pdbEntriesToView, ap, new SequenceI[] { selectedSequence });
}
else if (currentView == VIEWS_FROM_FILE)
{
selectedSequence, true, Desktop.instance);
launchStructureViewer(ap.getStructureSelectionManager(),
- new PDBEntry[]
- { fileEntry }, ap, new SequenceI[]
- { selectedSequence });
+ new PDBEntry[] { fileEntry }, ap,
+ new SequenceI[] { selectedSequence });
}
mainFrame.dispose();
}
ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
for (SequenceI seq : sequences)
{
- seqsMap.add(new SequenceI[]
- { seq });
+ seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
{
public void run()
{
- errorWarning.setLength(0);
- isValidPBDEntry = false;
- if (txt_search.getText().length() > 0)
- {
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.PDB_ID);
- PDBRestRequest pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(pdb_id:");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(txt_search.getText() + ")");
- pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
- try
- {
- resultList = pdbRestCleint.executeRequest(pdbRequest);
- } catch (Exception e)
- {
- errorWarning.append(e.getMessage());
- return;
- } finally
- {
+ errorWarning.setLength(0);
+ isValidPBDEntry = false;
+ if (txt_search.getText().length() > 0)
+ {
+ List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
+ wantedFields.add(PDBDocField.PDB_ID);
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(pdb_id:");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setSearchTerm(txt_search.getText() + ")");
+ pdbRequest.setAssociatedSequence(selectedSequence);
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errorWarning.append(e.getMessage());
+ return;
+ } finally
+ {
+ validateSelections();
+ }
+ if (resultList.getSearchSummary() != null
+ && resultList.getSearchSummary().size() > 0)
+ {
+ isValidPBDEntry = true;
+ }
+ }
validateSelections();
}
- if (resultList.getSearchSummary() != null
- && resultList.getSearchSummary().size() > 0)
- {
- isValidPBDEntry = true;
- }
- }
- validateSelections();
- }
}.start();
}
public class PDBEntryTableModel extends AbstractTableModel
{
- String[] columns =
- { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
+ String[] columns = { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
private List<CachedPDB> pdbEntries;