import java.util.ArrayList;
import java.util.Collection;
import java.util.HashSet;
-import java.util.Hashtable;
import java.util.LinkedHashSet;
import java.util.List;
import javax.swing.JComboBox;
import javax.swing.JLabel;
import javax.swing.JOptionPane;
-import javax.swing.table.DefaultTableModel;
-
+import javax.swing.table.AbstractTableModel;
/**
* Provides the behaviors for the Structure chooser Panel
private boolean isValidPBDEntry;
- private static Hashtable<String, PDBEntry> cachedEntryMap;
public StructureChooser(SequenceI[] selectedSeqs, SequenceI selectedSeq,
AlignmentPanel ap)
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);
pdbRequest.setFieldToSearchBy("(text:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRequest.setAssociatedSequence(seq);
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList;
try
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
+ e.printStackTrace();
errors.add(e.getMessage());
continue;
}
&& !resultList.getSearchSummary().isEmpty())
{
discoveredStructuresSet.addAll(resultList.getSearchSummary());
- updateSequencePDBEntries(seq, resultList.getSearchSummary());
}
}
}
else
{
- mainFrame
-.setTitle("Structure Chooser - Manual association");
+ 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");
public void loadLocalCachedPDBEntries()
{
- DefaultTableModel tableModel = new DefaultTableModel();
- tableModel.addColumn("Sequence");
- tableModel.addColumn("PDB Id");
- tableModel.addColumn("Chain");
- tableModel.addColumn("Type");
- tableModel.addColumn("File");
- cachedEntryMap = new Hashtable<String, PDBEntry>();
+ ArrayList<CachedPDB> entries = new ArrayList<CachedPDB>();
for (SequenceI seq : selectedSequences)
{
if (seq.getDatasetSequence() != null
- && seq.getDatasetSequence().getPDBId() != null)
+ && seq.getDatasetSequence().getAllPDBEntries() != null)
{
- for (PDBEntry pdbEntry : seq.getDatasetSequence().getPDBId())
+ for (PDBEntry pdbEntry : seq.getDatasetSequence().getAllPDBEntries())
{
-
- String chain = pdbEntry.getChainCode() == null ? "_" : pdbEntry
- .getChainCode();
- String[] pdbEntryRowData = new String[]
- { seq.getDisplayId(false), pdbEntry.getId(),
- chain,
- pdbEntry.getType(),
- pdbEntry.getFile() };
if (pdbEntry.getFile() != null)
{
- tableModel.addRow(pdbEntryRowData);
+ entries.add(new CachedPDB(seq, pdbEntry));
}
- cachedEntryMap.put(pdbEntry.getId().toLowerCase(),
- pdbEntry);
}
}
}
- tbl_local_pdb.setModel(tableModel);
- }
- /**
- * Update the PDBEntry for a given sequence with values retrieved from
- * PDBResponseSummary
- *
- * @param seq
- * the Sequence to update its DBRef entry
- * @param responseSummaries
- * a collection of PDBResponseSummary
- */
- public void updateSequencePDBEntries(SequenceI seq,
- Collection<PDBResponseSummary> responseSummaries)
- {
- for (PDBResponseSummary response : responseSummaries)
- {
- 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);
- }
+ PDBEntryTableModel tableModelx = new PDBEntryTableModel(entries);
+ tbl_local_pdb.setModel(tableModelx);
}
+
/**
* Builds a query string for a given sequences using its DBRef entries
*
}
}
- if (seq.getPDBId() != null)
+ if (seq.getAllPDBEntries() != null)
{
- for (PDBEntry entry : seq.getPDBId())
+ for (PDBEntry entry : seq.getAllPDBEntries())
{
- 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;
}
!chk_invertFilter.isSelected());
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq.getName());
+ pdbRequest.setAssociatedSequence(seq);
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList;
try
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
+ e.printStackTrace();
errors.add(e.getMessage());
continue;
}
+ totalTime + ")");
if (errors.size() > 0)
{
- StringBuilder errorMsg = new StringBuilder(
- "Operation unsucessful due to the following: \n");
+ StringBuilder errorMsg = new StringBuilder();
for (String error : errors)
{
errorMsg.append(error).append("\n");
filterThread.start();
}
-
/**
* Handles action event for btn_pdbFromFile
*/
.getCmb_assSeq().getSelectedItem();
lbl_fromFileStatus.setIcon(errorImage);
if (selectedSequences.length == 1
- || (assSeqOpt != null
- && !assSeqOpt.getName().equalsIgnoreCase(
+ || (assSeqOpt != null && !assSeqOpt.getName().equalsIgnoreCase(
"-Select Associated Seq-")))
{
btn_pdbFromFile.setEnabled(true);
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;
- for (int summaryRow : selectedRows)
+ ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
+ for (int row : selectedRows)
{
- String pdbIdStr = tbl_summary.getValueAt(summaryRow, pdbIdCol)
+ String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
.toString();
-
- PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
+ refSeqColIndex);
+ selectedSeqsToView.add(selectedSeq);
+ PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
pdbEntry = new PDBEntry();
pdbEntry.setId(pdbIdStr);
pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
}
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){
+ 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, 1).toString()
- .toLowerCase();
- pdbEntriesToView[count++] = cachedEntryMap.get(entryKey);
+ PDBEntry pdbEntry = (PDBEntry) tbl_local_pdb.getValueAt(row,
+ pdbIdColIndex);
+ pdbEntriesToView[count++] = pdbEntry;
+ 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)
{
}
String pdbIdStr = txt_search.getText();
- PDBEntry pdbEntry = cachedEntryMap.get(pdbIdStr.toLowerCase());
+ PDBEntry pdbEntry = selectedSequence.getPDBEntry(pdbIdStr);
if (pdbEntry == null)
{
pdbEntry = new PDBEntry();
- pdbEntry.setId(txt_search.getText());
+ pdbEntry.setId(pdbIdStr);
pdbEntry.setType(PDBEntry.Type.PDB);
+ selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
}
- selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
PDBEntry[] pdbEntriesToView = new PDBEntry[]
{ pdbEntry };
launchStructureViewer(ap.getStructureSelectionManager(),
selectedSequence = userSelectedSeq;
}
PDBEntry fileEntry = new AssociatePdbFileWithSeq()
- .associatePdbWithSeq(
- selectedPdbFileName, jalview.io.AppletFormatAdapter.FILE,
- selectedSequence, true, Desktop.instance);
+ .associatePdbWithSeq(selectedPdbFileName,
+ jalview.io.AppletFormatAdapter.FILE,
+ selectedSequence, true, Desktop.instance);
launchStructureViewer(ap.getStructureSelectionManager(),
new PDBEntry[]
mainFrame.dispose();
}
- private void launchStructureViewer(StructureSelectionManager ssm,
- PDBEntry[] pdbEntriesToView, AlignmentPanel alignPanel,
- SequenceI[] selectedSequences)
+ private void launchStructureViewer(final StructureSelectionManager ssm,
+ final PDBEntry[] pdbEntriesToView,
+ final AlignmentPanel alignPanel, final SequenceI[] sequences)
{
- StructureViewer sViewer = new StructureViewer(ssm);
- if (pdbEntriesToView.length > 1)
- {
- sViewer.viewStructures(alignPanel, pdbEntriesToView,
- alignPanel.av.collateForPDB(pdbEntriesToView));
- }
- else
+ final StructureViewer sViewer = new StructureViewer(ssm);
+ new Thread(new Runnable()
{
- sViewer.viewStructures(pdbEntriesToView[0], selectedSequences, null,
- alignPanel);
- }
+ public void run()
+ {
+ if (pdbEntriesToView.length > 1)
+ {
+ 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);
+ }
+ else
+ {
+ sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ }
+ }
+ }).start();
}
/**
cmb_assSeq.removeAllItems();
cmb_assSeq.addItem(new AssociateSeqOptions("-Select Associated Seq-",
null));
- // cmb_assSeq.addItem(new AssociateSeqOptions("Auto Detect", null));
lbl_associateSeq.setVisible(false);
if (selectedSequences.length > 1)
{
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(txt_search.getText() + ")");
- pdbRequest.setAssociatedSequence(selectedSequence.getName());
+ pdbRequest.setAssociatedSequence(selectedSequence);
pdbRestCleint = new PDBRestClient();
PDBRestResponse resultList;
try
resultList = pdbRestCleint.executeRequest(pdbRequest);
} catch (Exception e)
{
- // JOptionPane.showMessageDialog(this, e.getMessage(),
- // "PDB Web-service Error", JOptionPane.ERROR_MESSAGE);
errorWarning.append(e.getMessage());
return;
} finally
{
- // System.out.println(">>>>> executing finally block");
validateSelections();
}
if (resultList.getSearchSummary() != null
}
}
+ public class PDBEntryTableModel extends AbstractTableModel
+ {
+ String[] columns =
+ { "Ref Sequence", "PDB Id", "Chain", "Type", "File" };
+
+ private List<CachedPDB> pdbEntries;
+
+ public PDBEntryTableModel(List<CachedPDB> pdbEntries)
+ {
+ this.pdbEntries = new ArrayList<CachedPDB>(pdbEntries);
+ }
+
+ @Override
+ public String getColumnName(int columnIndex)
+ {
+ return columns[columnIndex];
+ }
+
+ @Override
+ public int getRowCount()
+ {
+ return pdbEntries.size();
+ }
+
+ @Override
+ public int getColumnCount()
+ {
+ return columns.length;
+ }
+
+ @Override
+ public boolean isCellEditable(int row, int column)
+ {
+ return false;
+ }
+
+ @Override
+ public Object getValueAt(int rowIndex, int columnIndex)
+ {
+ Object value = "??";
+ CachedPDB entry = pdbEntries.get(rowIndex);
+ switch (columnIndex)
+ {
+ case 0:
+ value = entry.getSequence();
+ break;
+ case 1:
+ value = entry.getPdbEntry();
+ break;
+ case 2:
+ value = entry.getPdbEntry().getChainCode() == null ? "_" : entry
+ .getPdbEntry().getChainCode();
+ break;
+ case 3:
+ value = entry.getPdbEntry().getType();
+ break;
+ case 4:
+ value = entry.getPdbEntry().getFile();
+ break;
+ }
+ return value;
+ }
+
+ @Override
+ public Class<?> getColumnClass(int columnIndex)
+ {
+ return columnIndex == 0 ? SequenceI.class : PDBEntry.class;
+ }
+
+ public CachedPDB getPDBEntryAt(int row)
+ {
+ return pdbEntries.get(row);
+ }
+
+ }
+
+ private class CachedPDB
+ {
+ private SequenceI sequence;
+
+ private PDBEntry pdbEntry;
+
+ public CachedPDB(SequenceI sequence, PDBEntry pdbEntry)
+ {
+ this.sequence = sequence;
+ this.pdbEntry = pdbEntry;
+ }
+
+ public SequenceI getSequence()
+ {
+ return sequence;
+ }
+
+ public PDBEntry getPdbEntry()
+ {
+ return pdbEntry;
+ }
+
+ }
}
git://source.jalview.org / jalview.git / blobdiff