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.DBRefFetcher;
import jalview.ws.sifts.SiftsSettings;
-import jalview.ws.uimodel.PDBRestRequest;
-import jalview.ws.uimodel.PDBRestResponse;
-import jalview.ws.uimodel.PDBRestResponse.PDBResponseSummary;
import java.awt.event.ItemEvent;
import java.util.ArrayList;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Objects;
+import java.util.Vector;
import javax.swing.JCheckBox;
import javax.swing.JComboBox;
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 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;
}
/**
- * Remove the following special characters from input string +, -, &, |, !, (,
- * ), {, }, [, ], ^, ", ~, *, ?, :, \
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
*
* @param seqName
* @return
{
Objects.requireNonNull(seqName);
return seqName.replaceAll("\\[\\d*\\]", "")
- .replaceAll("[^\\dA-Za-z ]", "").replaceAll("\\s+", "+");
+ .replaceAll("[^\\dA-Za-z|_]", "").replaceAll("\\s+", "+");
}
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();
+ FTSRestRequest pdbRequest = new FTSRestRequest();
if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
{
System.out.println(">>>>>> Filtering with uniprot coverate");
pdbRequest.setWantedFields(wantedFields);
pdbRequest.setAssociatedSequence(seq);
}
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ 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));
+ "overall_quality", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most UniProt Coverage",
- PDBDocField.UNIPROT_COVERAGE.getCode(), VIEWS_FILTER));
+ "uniprot_coverage", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Best Resolution",
- PDBDocField.RESOLUTION.getCode(), VIEWS_FILTER));
+ "resolution", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most Protein Chain",
- PDBDocField.PROTEIN_CHAIN_COUNT.getCode(), VIEWS_FILTER));
+ "number_of_protein_chains", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most Bound Molecules",
- PDBDocField.BOUND_MOLECULE_COUNT.getCode(), VIEWS_FILTER));
+ "number_of_bound_molecules", VIEWS_FILTER));
cmb_filterOption.addItem(new FilterOption("Most Polymer Residues",
- PDBDocField.POLYMER_RESIDUE_COUNT.getCode(), VIEWS_FILTER));
+ "number_of_polymer_residues", VIEWS_FILTER));
}
cmb_filterOption.addItem(new FilterOption("Enter PDB Id", "-",
VIEWS_ENTER_ID));
String currentView = selectedFilterOpt.getView();
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = tbl_summary.getColumn(
- PDBRestClient.PDBDocField.PDB_ID.getName()).getModelIndex();
- int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
+ int pdbIdColIndex = tbl_summary.getColumn("PDB Id")
+ .getModelIndex();
+ int refSeqColIndex = tbl_summary.getColumn("Ref Sequence")
.getModelIndex();
- int[] selectedRows = tbl_summary.getSelectedRows();
+ int[] selectedRows = tbl_summary.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
int count = 0;
ArrayList<SequenceI> selectedSeqsToView = new ArrayList<SequenceI>();
for (int row : selectedRows)
{
- String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
+ String pdbIdStr = tbl_summary.getValueAt(row, pdbIdColIndex)
.toString();
- SequenceI selectedSeq = (SequenceI) tbl_summary.getValueAt(row,
+ 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();
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>();
if (pdbEntry == null)
{
pdbEntry = new PDBEntry();
+ if (pdbIdStr.split(":").length > 1)
+ {
+ pdbEntry.setChainCode(pdbIdStr.split(":")[1]);
+ }
pdbEntry.setId(pdbIdStr);
pdbEntry.setType(PDBEntry.Type.PDB);
selectedSequence.getDatasetSequence().addPDBId(pdbEntry);
}).start();
}
+ 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, SequenceI[] sequences)
if (SiftsSettings.isMapWithSifts())
{
+ ArrayList<SequenceI> seqsWithoutSourceDBRef = new ArrayList<SequenceI>();
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 (seq.getDBRefs() == null)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ continue;
+ }
+ for (DBRefEntry dbRef : seq.getDBRefs())
+ {
+ if (dbRef.getSource().equalsIgnoreCase("uniprot"))
+ {
+ seq.setSourceDBRef(dbRef);
+ break;
+ }
+ }
+ for (DBRefEntry dbRef : seq.getDBRefs())
+ {
+ if (dbRef.getSource().equalsIgnoreCase("pdb"))
+ {
+ seq.setSourceDBRef(dbRef);
+ break;
+ }
+ }
+ if (seq.getSourceDBRef() == null)
+ {
+ seqsWithoutSourceDBRef.add(seq);
+ }
}
}
- }
- if (pdbEntriesToView.length > 1)
+ if (!seqsWithoutSourceDBRef.isEmpty())
+ {
+ int y = seqsWithoutSourceDBRef.size();
+ ssm.setProgressBar(null);
+ ssm.setProgressBar(">>>>> Fetching Database refs for " + y
+ + " sequence" + (y > 1 ? "s" : "")
+ + " with no valid uniprot or pdb ref for SIFTS mapping");
+ System.out.println(">>>>> Fetching Database refs for " + y
+ + " sequence" + (y > 1 ? "s" : "")
+ + " with no valid uniprot or pdb ref for SIFTS mapping");
+ SequenceI[] seqWithoutSrcDBRef = new SequenceI[y];
+ int x = 0;
+ for (SequenceI fSeq : seqsWithoutSourceDBRef)
{
- ArrayList<SequenceI[]> seqsMap = new ArrayList<SequenceI[]>();
- for (SequenceI seq : sequences)
- {
- seqsMap.add(new SequenceI[] { seq });
- }
- SequenceI[][] collatedSeqs = seqsMap.toArray(new SequenceI[0][0]);
+ seqWithoutSrcDBRef[x++] = fSeq;
+ }
+ new DBRefFetcher(seqWithoutSrcDBRef).fetchDBRefs(true);
+ }
+ }
+ 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]);
ssm.setProgressBar(null);
ssm.setProgressBar("Fetching PDB Structures for selected entries..");
- sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
- }
- else
- {
+ sViewer.viewStructures(pdbEntriesToView, collatedSeqs, alignPanel);
+ }
+ else
+ {
ssm.setProgressBar(null);
ssm.setProgressBar("Fetching PDB Structure for "
+ pdbEntriesToView[0].getId());
- sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
- }
+ sViewer.viewStructures(pdbEntriesToView[0], sequences, alignPanel);
+ }
}
/**
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();
+ String searchTerm = txt_search.getText().toLowerCase();
+ searchTerm = searchTerm.split(":")[0];
+ System.out.println(">>>>> search term : " + searchTerm);
+ 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().toLowerCase() + ")");
+.setSearchTerm(searchTerm + ")");
pdbRequest.setAssociatedSequence(selectedSequence);
- pdbRestCleint = new PDBRestClient();
- PDBRestResponse resultList;
+ pdbRestCleint = PDBFTSRestClient.getInstance();
+ wantedFields.add(pdbRestCleint.getPrimaryKeyColumn());
+ FTSRestResponse resultList;
try
{
resultList = pdbRestCleint.executeRequest(pdbRequest);
git://source.jalview.org / jalview.git / blobdiff