package jalview.gui;
+import jalview.bin.Jalview;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.DBRefSource;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.fts.api.FTSData;
+import jalview.fts.api.FTSDataColumnI;
+import jalview.fts.api.FTSRestClientI;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.jbgui.GStructureChooser;
-import jalview.jbgui.PDBDocFieldPreferences;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
-import jalview.ws.dbsources.PDBRestClient;
-import jalview.ws.dbsources.PDBRestClient.PDBDocField;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
+import jalview.ws.sifts.SiftsSettings;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
+import java.util.Objects;
+import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
*
*/
@SuppressWarnings("serial")
-public class StructureChooser extends GStructureChooser
+public class StructureChooser extends GStructureChooser implements
+ IProgressIndicator
{
private boolean structuresDiscovered = false;
private IProgressIndicator progressIndicator;
- private Collection<PDBResponseSummary> discoveredStructuresSet;
+ private Collection<FTSData> discoveredStructuresSet;
- private PDBRestRequest lastPdbRequest;
+ private FTSRestRequest lastPdbRequest;
- private PDBRestClient pdbRestCleint;
+ private FTSRestClientI pdbRestCleint;
private String selectedPdbFileName;
*/
public void init()
{
+ if (!Jalview.isHeadlessMode())
+ {
+ progressBar = new ProgressBar(this.statusPanel, this.statusBar);
+ }
+
Thread discoverPDBStructuresThread = new Thread(new Runnable()
{
@Override
public void fetchStructuresMetaData()
{
long startTime = System.currentTimeMillis();
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
- .getStructureSummaryFields();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ Collection<FTSDataColumnI> wantedFields = pdbRestCleint
+ .getAllDefaulDisplayedDataColumns();
- discoveredStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ discoveredStructuresSet = new LinkedHashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
for (SequenceI seq : selectedSequences)
{
- PDBRestRequest pdbRequest = new PDBRestRequest();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(500);
pdbRequest.setFieldToSearchBy("(");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setSearchTerm(buildQuery(seq) + ")");
pdbRequest.setAssociatedSequence(seq);
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
if (discoveredStructuresSet != null
&& !discoveredStructuresSet.isEmpty())
{
- tbl_summary.setModel(PDBRestResponse.getTableModel(lastPdbRequest,
+ tbl_summary.setModel(FTSRestResponse.getTableModel(lastPdbRequest,
discoveredStructuresSet));
structuresDiscovered = true;
noOfStructuresFound = discoveredStructuresSet.size();
{
if (isValidSeqName(entry.getId()))
{
- queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode())
+ queryBuilder.append("pdb_id")
.append(":")
.append(entry.getId().toLowerCase())
.append(" OR ");
if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
{
queryBuilder
- .append(PDBRestClient.PDBDocField.UNIPROT_ACCESSION
- .getCode()).append(":")
+.append("uniprot_accession").append(":")
.append(getDBRefId(dbRef))
.append(" OR ");
queryBuilder
- .append(PDBRestClient.PDBDocField.UNIPROT_ID.getCode())
+.append("uniprot_id")
.append(":")
.append(getDBRefId(dbRef)).append(" OR ");
isUniProtRefsFound = true;
else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
{
- queryBuilder.append(PDBRestClient.PDBDocField.PDB_ID.getCode())
+ queryBuilder.append("pdb_id")
.append(":").append(getDBRefId(dbRef).toLowerCase())
.append(" OR ");
isPDBRefsFound = true;
if (!isPDBRefsFound && !isUniProtRefsFound)
{
String seqName = seq.getName();
+ seqName = sanitizeSeqName(seqName);
String[] names = seqName.toLowerCase().split("\\|");
for (String name : names)
{
}
/**
+ * Remove the following special characters from input string +, -, &, |, !, (,
+ * ), {, }, [, ], ^, ", ~, *, ?, :, \
+ *
+ * @param seqName
+ * @return
+ */
+ private static String sanitizeSeqName(String seqName)
+ {
+ Objects.requireNonNull(seqName);
+ return seqName.replaceAll("\\[\\d*\\]", "")
+ .replaceAll("[^\\dA-Za-z|]", "").replaceAll("\\s+", "+");
+ }
+
+
+ /**
* Ensures sequence ref names are not less than 3 characters and does not
* contain a database name
*
public void run()
{
long startTime = System.currentTimeMillis();
+ pdbRestCleint = PDBFTSRestClient.getInstance();
lbl_loading.setVisible(true);
- Collection<PDBDocField> wantedFields = PDBDocFieldPreferences
- .getStructureSummaryFields();
- Collection<PDBResponseSummary> filteredResponse = new HashSet<PDBResponseSummary>();
+ Collection<FTSDataColumnI> wantedFields = pdbRestCleint
+ .getAllDefaulDisplayedDataColumns();
+ Collection<FTSData> filteredResponse = new HashSet<FTSData>();
HashSet<String> errors = new HashSet<String>();
+
for (SequenceI seq : selectedSequences)
{
- PDBRestRequest pdbRequest = new PDBRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(1);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setFieldToSortBy(fieldToFilterBy,
- !chk_invertFilter.isSelected());
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ FTSRestRequest pdbRequest = new FTSRestRequest();
+ if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
+ {
+ System.out.println(">>>>>> Filtering with uniprot coverate");
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ pdbRequest.setFacet(true);
+ pdbRequest.setFacetPivot(fieldToFilterBy + ",entry_entity");
+ pdbRequest.setFacetPivotMinCount(1);
+ }
+ else
+ {
+ pdbRequest.setAllowEmptySeq(false);
+ pdbRequest.setResponseSize(1);
+ pdbRequest.setFieldToSearchBy("(");
+ pdbRequest.setFieldToSortBy(fieldToFilterBy,
+ !chk_invertFilter.isSelected());
+ pdbRequest.setSearchTerm(buildQuery(seq) + ")");
+ pdbRequest.setWantedFields(wantedFields);
+ pdbRequest.setAssociatedSequence(seq);
+ }
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
if (!filteredResponse.isEmpty())
{
final int filterResponseCount = filteredResponse.size();
- Collection<PDBResponseSummary> reorderedStructuresSet = new LinkedHashSet<PDBResponseSummary>();
+ Collection<FTSData> reorderedStructuresSet = new LinkedHashSet<FTSData>();
reorderedStructuresSet.addAll(filteredResponse);
reorderedStructuresSet.addAll(discoveredStructuresSet);
- tbl_summary.setModel(PDBRestResponse.getTableModel(
+ tbl_summary.setModel(FTSRestResponse.getTableModel(
lastPdbRequest, reorderedStructuresSet));
+ FTSRestResponse.configureTableColumn(tbl_summary, wantedFields);
+ tbl_summary.getColumn("Ref Sequence").setPreferredWidth(120);
+ tbl_summary.getColumn("Ref Sequence").setMinWidth(100);
+ tbl_summary.getColumn("Ref Sequence").setMaxWidth(200);
// Update table selection model here
tbl_summary.addRowSelectionInterval(0, filterResponseCount - 1);
mainFrame.setTitle(MessageManager.formatMessage(
if (isStructuresDiscovered())
{
cmb_filterOption.addItem(new FilterOption("Best Quality",
- PDBDocField.OVERALL_QUALITY.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Best UniProt Coverage",
- PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Resolution",
- PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Protein Chain",
- PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Bound Molecules",
- PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
- cmb_filterOption.addItem(new FilterOption("Highest Polymer Residues",
- PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
+ "overall_quality", VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage",
+ "uniprot_coverage", VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Best Resolution",
+ "resolution", VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
+ "number_of_protein_chains", VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
+ "number_of_bound_molecules", VIEWS_FILTER));
+ cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
+ "number_of_polymer_residues", VIEWS_FILTER));
}
cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
VIEWS_ENTER_ID));
@Override
public void ok_ActionPerformed()
{
+ final long progressSessionId = System.currentTimeMillis();
+ final StructureSelectionManager ssm = ap.getStructureSelectionManager();
+ ssm.setProgressIndicator(this);
+ ssm.setProgressSessionId(progressSessionId);
+ new Thread(new Runnable()
+ {
+ @Override
+ public void run()
+ {
FilterOption selectedFilterOpt = ((FilterOption) cmb_filterOption
.getSelectedItem());
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = tbl_summary.getColumn(
- PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
+ int pdbIdColIndex = tbl_summary.getColumn("PDB Id")
+ .getModelIndex();
int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
.getModelIndex();
int[] selectedRows = tbl_summary.getSelectedRows();
SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
refSeqColIndex);
selectedSeqsToView.add(selectedSeq);
- PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+ PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
+ if (pdbEntry == null)
+ {
+ pdbEntry = getFindEntry(pdbIdStr,
+ selectedSeq.getAllPDBEntries());
+ }
if (pdbEntry == null)
{
pdbEntry = new PDBEntry();
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, selectedSeqs);
+ launchStructureViewer(ssm, 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 pdbIdColIndex = tbl_local_pdb.getColumn("PDB Id")
+ .getModelIndex();
int refSeqColIndex = tbl_local_pdb.getColumn("Ref Sequence")
.getModelIndex();
ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
}
SequenceI[] selectedSeqs = selectedSeqsToView
.toArray(new SequenceI[selectedSeqsToView.size()]);
- launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, selectedSeqs);
+ launchStructureViewer(ssm, pdbEntriesToView, ap, selectedSeqs);
}
else if (currentView == VIEWS_ENTER_ID)
{
}
PDBEntry[] pdbEntriesToView = new PDBEntry[] { pdbEntry };
- launchStructureViewer(ap.getStructureSelectionManager(),
- pdbEntriesToView, ap, new SequenceI[] { selectedSequence });
+ launchStructureViewer(ssm, pdbEntriesToView, ap,
+ new SequenceI[] { selectedSequence });
}
else if (currentView == VIEWS_FROM_FILE)
{
jalview.io.AppletFormatAdapter.FILE,
selectedSequence, true, Desktop.instance);
- launchStructureViewer(ap.getStructureSelectionManager(),
- new PDBEntry[] { fileEntry }, ap,
- new SequenceI[] { selectedSequence });
+ launchStructureViewer(ssm, new PDBEntry[] { fileEntry }, ap,
+ new SequenceI[] { selectedSequence });
}
mainFrame.dispose();
+ }
+ }).start();
}
- private void launchStructureViewer(final StructureSelectionManager ssm,
+ private PDBEntry getFindEntry(String id, Vector<PDBEntry> pdbEntries)
+ {
+ Objects.requireNonNull(id);
+ Objects.requireNonNull(pdbEntries);
+ PDBEntry foundEntry = null;
+ for (PDBEntry entry : pdbEntries)
+ {
+ if (entry.getId().equalsIgnoreCase(id))
+ {
+ return entry;
+ }
+ }
+ return foundEntry;
+ }
+
+ private void launchStructureViewer(StructureSelectionManager ssm,
final PDBEntry[] pdbEntriesToView,
- final AlignmentPanel alignPanel, final SequenceI[] sequences)
+ final AlignmentPanel alignPanel, SequenceI[] sequences)
{
+ ssm.setProgressBar("Launching PDB structure viewer..");
final StructureViewer sViewer = new StructureViewer(ssm);
- new jalview.ws.DBRefFetcher(sequences, null, null, null, false)
- .fetchDBRefs(true);
- new Thread(new Runnable()
+ if (SiftsSettings.isMapWithSifts())
{
- @Override
- public void run()
+ for (SequenceI seq : sequences)
{
+ if (seq.getSourceDBRef() == null)
+ {
+ ssm.setProgressBar(null);
+ ssm.setProgressBar("Fetching Database refs..");
+ new jalview.ws.DBRefFetcher(sequences, null, null, null, false)
+ .fetchDBRefs(true);
+ break;
+ }
+ }
+ }
if (pdbEntriesToView.length > 1)
{
ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
seqsMap.add(new SequenceI[] { seq });
}
SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
+ ssm.setProgressBar(null);
+ ssm.setProgressBar("Fetching PDB Structures for selected entries..");
sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
}
else
{
+ ssm.setProgressBar(null);
+ ssm.setProgressBar("Fetching PDB Structure for "
+ + pdbEntriesToView[0].getId());
sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
}
- }
- }).start();
}
/**
this.structuresDiscovered = structuresDiscovered;
}
- public Collection<PDBResponseSummary> getDiscoveredStructuresSet()
+ public Collection<FTSData> getDiscoveredStructuresSet()
{
return discoveredStructuresSet;
}
isValidPBDEntry = false;
if (txt_search.getText().length() > 0)
{
- List<PDBDocField> wantedFields = new ArrayList<PDBDocField>();
- wantedFields.add(PDBDocField.PDB_ID);
- PDBRestRequest pdbRequest = new PDBRestRequest();
+ List<FTSDataColumnI> wantedFields = new ArrayList<FTSDataColumnI>();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
pdbRequest.setAllowEmptySeq(false);
pdbRequest.setResponseSize(1);
pdbRequest.setFieldToSearchBy("(pdb_id:");
pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(txt_search.getText() + ")");
+ pdbRequest
+ .setSearchTerm(txt_search.getText().toLowerCase() + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
}
}
+
+ private IProgressIndicator progressBar;
+
+ @Override
+ public void setProgressBar(String message, long id)
+ {
+ progressBar.setProgressBar(message, id);
+ }
+
+ @Override
+ public void registerHandler(long id, IProgressIndicatorHandler handler)
+ {
+ progressBar.registerHandler(id, handler);
+ }
+
+ @Override
+ public boolean operationInProgress()
+ {
+ return progressBar.operationInProgress();
+ }
}
git://source.jalview.org / jalview.git / blobdiff