import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
+import javax.swing.JOptionPane;
import javax.swing.table.DefaultTableModel;
.getStructureSummaryFields();
discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
PDBRestRequest pdbRequest = new PDBRestRequest();
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq.getName());
pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ PDBRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errors.add(e.getMessage());
+ continue;
+ }
lastPdbRequest = pdbRequest;
if (resultList.getSearchSummary() != null
&& !resultList.getSearchSummary().isEmpty())
{
discoveredStructuresSet.addAll(resultList.getSearchSummary());
- updateSequenceDbRef(seq, resultList.getSearchSummary());
+ updateSequencePDBEntries(seq, resultList.getSearchSummary());
}
}
int noOfStructuresFound = 0;
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
+ mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
+ + " Found (" + totalTime + ")");
+ }
+ else
+ {
+ mainFrame
+.setTitle("Structure Chooser - Manual association");
+ if (errors.size() > 0)
+ {
+ StringBuilder errorMsg = new StringBuilder(
+ "Operation was unsucessful due to the following: \n");
+ for (String error : errors)
+ {
+ errorMsg.append(error).append("\n");
+ }
+ JOptionPane.showMessageDialog(this, errorMsg.toString(),
+ "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ }
}
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
- mainFrame.setTitle("Structure Chooser - " + noOfStructuresFound
- + " Found (" + totalTime + ")");
}
public void loadLocalCachedPDBEntries()
{
for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
{
+
String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
.getChainCode();
String[] pdbEntryRowData = new String[]
chain,
pdbEntry.getType(),
pdbEntry.getFile() };
- tableModel.addRow(pdbEntryRowData);
- cachedEntryMap.put(seq.getDisplayId(false) + pdbEntry.getId(),
+ if (pdbEntry.getFile() != null)
+ {
+ tableModel.addRow(pdbEntryRowData);
+ }
+ cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
pdbEntry);
}
}
}
/**
- * Update the DBRef entry for a given sequence with values retrieved from
+ * Update the PDBEntry for a given sequence with values retrieved from
* PDBResponseSummary
*
* @param seq
* @param responseSummaries
* a collection of PDBResponseSummary
*/
- public void updateSequenceDbRef(SequenceI seq,
+ public void updateSequencePDBEntries(SequenceI seq,
Collection<PDBResponseSummary> responseSummaries)
{
for (PDBResponseSummary response : responseSummaries)
{
- PDBEntry newEntry = new PDBEntry();
- newEntry.setId(response.getPdbId());
- newEntry.setType(PDBEntry.Type.PDB);
- seq.getDatasetSequence().addPDBId(newEntry);
+ String pdbIdStr = response.getPdbId();
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
+ seq.getDatasetSequence().addPDBId(pdbEntry);
}
}
public void run()
{
long startTime = System.currentTimeMillis();
- try
+ lbl_loading.setVisible(true);
+ Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
+ .getStructureSummaryFields();
+ Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ HashSet<String> errors = new HashSet<String>();
+ for (SequenceI seq : selectedSequences)
{
- lbl_loading.setVisible(true);
-
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
- .getStructureSummaryFields();
- Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
- for (SequenceI seq : selectedSequences)
+ PDBRestRequest pdbRequest = new PDBRestRequest();
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(text:");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRestCleint = new PDBRestClient();
+ PDBRestResponse resultList;
+ try
{
- PDBRestRequest pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(text:");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq.getName());
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint
- .executeRequest(pdbRequest);
- lastPdbRequest = pdbRequest;
- if (resultList.getSearchSummary() != null
- && !resultList.getSearchSummary().isEmpty())
- {
- filteredResponse.addAll(resultList.getSearchSummary());
- }
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ errors.add(e.getMessage());
+ continue;
}
-
- if (!filteredResponse.isEmpty())
+ lastPdbRequest = pdbRequest;
+ if (resultList.getSearchSummary() != null
+ && !resultList.getSearchSummary().isEmpty())
{
- final int filterResponseCount = filteredResponse.size();
- Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
- reorderedStructuresSet.addAll(filteredResponse);
- reorderedStructuresSet.addAll(discoveredStructuresSet);
- tbl_summary.setModel(PDBRestResponse.getTableModel(
- lastPdbRequest, reorderedStructuresSet));
+ filteredResponse.addAll(resultList.getSearchSummary());
+ }
+ }
- // Update table selection model here
- tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
+ String totalTime = (System.currentTimeMillis() - startTime)
+ + " milli secs";
+ if (!filteredResponse.isEmpty())
+ {
+ final int filterResponseCount = filteredResponse.size();
+ Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ reorderedStructuresSet.addAll(filteredResponse);
+ reorderedStructuresSet.addAll(discoveredStructuresSet);
+ tbl_summary.setModel(PDBRestResponse.getTableModel(
+ lastPdbRequest, reorderedStructuresSet));
- }
+ // Update table selection model here
+ tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
- lbl_loading.setVisible(false);
- String totalTime = (System.currentTimeMillis() - startTime)
- + " milli secs";
mainFrame.setTitle("Structure Chooser - Filter time ("
+ totalTime + ")");
-
- validateSelections();
- } catch (Exception e)
+ }
+ else
{
- e.printStackTrace();
+ mainFrame.setTitle("Structure Chooser - Filter time ("
+ + totalTime + ")");
+ if (errors.size() > 0)
+ {
+ StringBuilder errorMsg = new StringBuilder(
+ "Operation unsucessful due to the following: \n");
+ for (String error : errors)
+ {
+ errorMsg.append(error).append("\n");
+ }
+ JOptionPane.showMessageDialog(null, errorMsg.toString(),
+ "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ }
}
+
+ lbl_loading.setVisible(false);
+
+ validateSelections();
}
});
filterThread.start();
else if (selectedFilterOpt.getView() == VIEWS_ENTER_ID
|| selectedFilterOpt.getView() == VIEWS_FROM_FILE)
{
+ mainFrame.setTitle(filterTitle);
idInputAssSeqPanel.loadCmbAssSeq();
fileChooserAssSeqPanel.loadCmbAssSeq();
}
{
String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
.toString();
- PDBEntry pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType(PDBEntry.Type.PDB);
+
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
pdbEntriesToView[count++] = pdbEntry;
}
-
launchStructureViewer(ap.getStructureSelectionManager(),
pdbEntriesToView, ap, selectedSequences);
}
int count = 0;
for (int row : selectedRows)
{
- String entryKey = tbl_local_pdb.getValueAt(row, 0).toString() + tbl_local_pdb.getValueAt(row, 1).toString();
+ String entryKey = tbl_local_pdb.getValueAt(row, 1).toString()
+ .toLowerCase();
pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
}
launchStructureViewer(ap.getStructureSelectionManager(),
{
selectedSequence = userSelectedSeq;
}
- PDBEntry pdbEntry = new PDBEntry();
- pdbEntry.setId(txt_search.getText());
- pdbEntry.setType(PDBEntry.Type.PDB);
+
+ String pdbIdStr = txt_search.getText();
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(txt_search.getText());
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
+
selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
PDBEntry[] pdbEntriesToView = new PDBEntry[]
{ pdbEntry };
pdbRequest.setSearchTerm(txt_search.getText() + ")");
pdbRequest.setAssociatedSequence(selectedSequence.getName());
pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ PDBRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ JOptionPane.showMessageDialog(this, e.getMessage(),
+ "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
+ return;
+ } finally
+ {
+ System.out.println(">>>>> executing finally block");
+ validateSelections();
+ }
if (resultList.getSearchSummary() != null
&& resultList.getSearchSummary().size() > 0)
{
}
}
+
}
git://source.jalview.org / jalview.git / blobdiff