import javax.swing.JCheckBox;
import javax.swing.JComboBox;
import javax.swing.JLabel;
+import javax.swing.JOptionPane;
import javax.swing.table.DefaultTableModel;
public void run()
{
long startTime = System.currentTimeMillis();
- String msg = MessageManager.getString("status.fetching_db_refs");
- updateProgressIndicator(msg, startTime);
+ updateProgressIndicator(MessageManager
+ .getString("status.loading_cached_pdb_entries"), startTime);
loadLocalCachedPDBEntries();
+ updateProgressIndicator(null, startTime);
+ updateProgressIndicator(MessageManager
+ .getString("status.searching_for_pdb_structures"),
+ startTime);
fetchStructuresMetaData();
populateFilterComboBox();
updateProgressIndicator(null, startTime);
.getStructureSummaryFields();
discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
PDBRestRequest pdbRequest = new PDBRestRequest();
pdbRequest.setFieldToSearchBy("(text:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRequest.setAssociatedSequence(seq);
pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ PDBRestResponse resultList;
+ try
+ {
+ resultList = pdbRestCleint.executeRequest(pdbRequest);
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ 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 unsuccessful 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()
{
- DefaultTableModel tableModel = new DefaultTableModel();
- tableModel.addColumn("Sequence");
+ DefaultTableModel tableModel = new DefaultTableModel()
+ {
+ @Override
+ public boolean isCellEditable(int row, int column)
+ {
+ return false;
+ }
+ };
+ tableModel.addColumn("Ref Sequence");
tableModel.addColumn("PDB Id");
+ tableModel.addColumn("Chain");
tableModel.addColumn("Type");
tableModel.addColumn("File");
cachedEntryMap = new Hashtable<String, PDBEntry>();
{
for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
{
- String[] pdbEntryRowData = new String[]
- { seq.getDisplayId(false), pdbEntry.getId(), pdbEntry.getType(),
+
+ String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
+ .getChainCode();
+ Object[] pdbEntryRowData = new Object[]
+ { seq, pdbEntry.getId(),
+ 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("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);
}
}
String[] names = seqName.toLowerCase().split("\\|");
for (String name : names)
{
- System.out.println("Found name : " + name);
+ // System.out.println("Found name : " + name);
name.trim();
if (isValidSeqName(name))
{
{
for (PDBEntry entry : seq.getPDBId())
{
- seqRefs.add(entry.getId());
+ if (isValidSeqName(entry.getId()))
+ {
+ seqRefs.add(entry.getId());
+ }
}
}
int count = 0;
for (DBRefEntry dbRef : seq.getDBRef())
{
- seqRefs.add(getDBRefId(dbRef));
+ if (isValidSeqName(getDBRefId(dbRef)))
+ {
+ seqRefs.add(getDBRefId(dbRef));
+ }
++count;
if (count > 10)
{
*/
public static boolean isValidSeqName(String seqName)
{
- String ignoreList = "pdb,uniprot";
+ // System.out.println("seqName : " + seqName);
+ String ignoreList = "pdb,uniprot,swiss-prot";
if (seqName.length() < 3)
{
return false;
}
+ if (seqName.contains(":"))
+ {
+ return false;
+ }
+ seqName = seqName.toLowerCase();
for (String ignoredEntry : ignoreList.split(","))
{
- if (seqName.equalsIgnoreCase(ignoredEntry))
+ if (seqName.contains(ignoredEntry))
{
return false;
}
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);
+ 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)
+ {
+ e.printStackTrace();
+ 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();
+ 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();
}
AssociateSeqOptions assSeqOpt = (AssociateSeqOptions) idInputAssSeqPanel
.getCmb_assSeq().getSelectedItem();
lbl_pdbManualFetchStatus.setIcon(errorImage);
+ lbl_pdbManualFetchStatus.setToolTipText("");
+ if (txt_search.getText().length() > 0)
+ {
+ lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
+ true, "No PDB entry found for \'" + txt_search.getText()
+ + "\'"));
+ }
+
+ if (errorWarning.length() > 0)
+ {
+ lbl_pdbManualFetchStatus.setIcon(warningImage);
+ lbl_pdbManualFetchStatus.setToolTipText(JvSwingUtils.wrapTooltip(
+ true, errorWarning.toString()));
+ }
+
if (selectedSequences.length == 1
|| !assSeqOpt.getName().equalsIgnoreCase(
"-Select Associated Seq-"))
if (isValidPBDEntry)
{
btn_view.setEnabled(true);
+ lbl_pdbManualFetchStatus.setToolTipText("");
lbl_pdbManualFetchStatus.setIcon(goodImage);
}
}
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- int pdbIdCol = PDBRestClient.getPDBIdColumIndex(
- lastPdbRequest.getWantedFields(), true);
+ int pdbIdColIndex = tbl_summary.getColumn(
+ PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+ int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
+ .getModelIndex();
int[] selectedRows = tbl_summary.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
+ ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
for (int summaryRow : selectedRows)
{
- String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdColIndex)
.toString();
- PDBEntry pdbEntry = new PDBEntry();
- pdbEntry.setId(pdbIdStr);
- pdbEntry.setType("PDB");
+ SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(
+ summaryRow, refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ if (pdbEntry == null)
+ {
+ pdbEntry = new PDBEntry();
+ pdbEntry.setId(pdbIdStr);
+ pdbEntry.setType(PDBEntry.Type.PDB);
+ }
pdbEntriesToView[count++] = pdbEntry;
}
-
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, selectedSequences);
+ pdbEntriesToView, ap, selectedSeqs);
}
else if(currentView == VIEWS_LOCAL_PDB){
int[] selectedRows = tbl_local_pdb.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
+ int pdbIdColIndex = tbl_local_pdb.getColumn(
+ PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+ int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
+ .getModelIndex();
+ ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
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, pdbIdColIndex)
+ .toString()
+ .toLowerCase();
pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
+ SequenceI selectedSeq = (SequenceI) tbl_local_pdb.getValueAt(row,
+ refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+
}
+ SequenceI[] selectedSeqs = selectedSeqsToView
+ .toArray(new SequenceI[selectedSeqsToView.size()]);
launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, selectedSequences);
+ pdbEntriesToView, ap, selectedSeqs);
}
else if (currentView == VIEWS_ENTER_ID)
{
{
selectedSequence = userSelectedSeq;
}
- PDBEntry pdbEntry = new PDBEntry();
- pdbEntry.setId(txt_search.getText());
- pdbEntry.setType("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 };
private void launchStructureViewer(StructureSelectionManager ssm,
PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
- SequenceI[] selectedSequences)
+ SequenceI[] sequences)
{
StructureViewer sViewer = new StructureViewer(ssm);
if (pdbEntriesToView.length > 1)
{
- sViewer.viewStructures(alignPanel, pdbEntriesToView,
- alignPanel.av.collateForPDB(pdbEntriesToView));
+ ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
+ for (SequenceI seq : sequences)
+ {
+ seqsMap.add(new SequenceI[]
+ { seq });
+ }
+ SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
+ sViewer.viewStructures(pdbEntriesToView, collatedSeqs,
+ alignPanel);
+ // sViewer.viewStructures(pdbEntriesToView,
+ // alignPanel.av.collateForPDB(pdbEntriesToView),
+ // alignPanel);
}
else
{
- sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
+ sViewer.viewStructures(pdbEntriesToView[0], sequences,
alignPanel);
}
}
@Override
protected void txt_search_ActionPerformed()
{
+ errorWarning.setLength(0);
isValidPBDEntry = false;
if (txt_search.getText().length() > 0)
{
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(txt_search.getText() + ")");
- pdbRequest.setAssociatedSequence(selectedSequence.getName());
+ pdbRequest.setAssociatedSequence(selectedSequence);
pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList = pdbRestCleint.executeRequest(pdbRequest);
+ 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)
{
git://source.jalview.org / jalview.git / blobdiff