}
return true;
}
+
+
+ /**
+ * Permanent URI for retrieving the original structure data
+ * @param urlStr
+ */
+ public void setRetrievalUrl(String urlStr)
+ {
+ setProperty("RETRIEVE_FROM", urlStr);
+ }
+ /**
+ * get the Permanent URI for retrieving the original structure data
+ */
+ public String getRetrievalUrl()
+ {
+ return (String) getProperty("RETRIEVE_FROM");
+ }
}
package jalview.fts.api;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
* @return the default response page size
*/
public int getDefaultResponsePageSize();
+
+ public String[] getPreferencesColumnsFor(PreferenceSource source);
}
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.api.StructureFTSRestClientI;
import jalview.fts.service.pdb.PDBFTSRestClient;
import java.util.ArrayList;
if (source.equals(PreferenceSource.STRUCTURE_CHOOSER)
|| source.equals(PreferenceSource.PREFERENCES))
{
- structSummaryColumns = ((PDBFTSRestClient) ftsRestClient)
+ structSummaryColumns = ((StructureFTSRestClientI) ftsRestClient)
.getAllDefaultDisplayedStructureDataColumns();
}
allFTSDataColumns.addAll(ftsRestClient.getAllFTSDataColumns());
this.getViewport().add(tbl_FTSDataColumnPrefs);
this.currentSource = source;
- String[] columnNames = null;
- switch (source)
- {
- case SEARCH_SUMMARY:
- columnNames = new String[] { "", "Display", "Group" };
- break;
- case STRUCTURE_CHOOSER:
- columnNames = new String[] { "", "Display", "Group" };
- break;
- case PREFERENCES:
- columnNames = new String[] { "PDB Field", "Show in search summary",
- "Show in structure summary" };
- break;
- default:
- break;
- }
+ String[] columnNames = ftsRestClient.getPreferencesColumnsFor(source);
Object[][] data = new Object[allFTSDataColumns.size()][3];
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSDataColumnI.FTSDataColumnGroupI;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.api.FTSRestClientI;
/**
return defaultResponsePageSize;
}
+ @Override
+ public String[] getPreferencesColumnsFor(PreferenceSource source)
+ {
+ String[] columnNames = null;
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ default:
+ // non structure sources don't return any other kind of preferences columns
+ break;
+ }
+ return columnNames;
+ }
}
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.api.StructureFTSRestClientI;
+import jalview.fts.core.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
*
* @author tcnofoegbu
*/
-public class PDBFTSRestClient extends FTSRestClient
+public class PDBFTSRestClient extends FTSRestClient implements StructureFTSRestClientI
{
private static FTSRestClientI instance = null;
}
private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
-
+ @Override
public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
{
if (allDefaultDisplayedStructureDataColumns == null
}
return allDefaultDisplayedStructureDataColumns;
}
-
-
+ @Override
+ public String[] getPreferencesColumnsFor(PreferenceSource source) {
+ String[] columnNames = null;
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case STRUCTURE_CHOOSER:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case PREFERENCES:
+ columnNames = new String[] { "PDB Field", "Show in search summary",
+ "Show in structure summary" };
+ break;
+ default:
+ break;
+ }
+ return columnNames;
+ }
}
import jalview.fts.api.FTSData;
import jalview.fts.api.FTSDataColumnI;
import jalview.fts.api.FTSRestClientI;
+import jalview.fts.api.StructureFTSRestClientI;
import jalview.fts.core.FTSRestClient;
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
import jalview.fts.service.pdb.PDBFTSRestClient;
import jalview.util.JSONUtils;
import jalview.util.MessageManager;
import jalview.util.Platform;
public class TDBeaconsFTSRestClient extends FTSRestClient
+ implements StructureFTSRestClientI
{
- private static final String DEFAULT_THREEDBEACONS_DOMAIN =
- "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
-
+ private static final String DEFAULT_THREEDBEACONS_DOMAIN = "https://wwwdev.ebi.ac.uk/pdbe/pdbe-kb/3dbeacons/api/uniprot/summary/";
+
private static FTSRestClientI instance = null;
-
+
protected TDBeaconsFTSRestClient()
- {
+ {
}
-
+
@SuppressWarnings("unchecked")
@Override
public FTSRestResponse executeRequest(FTSRestRequest tdbRestRequest)
else
/**
* Java only
+ *
* @j2sIgnore
*/
{
.path(query);
URI uri = webResource.getURI();
System.out.println(uri.toString());
-
+
// Execute the REST request
ClientResponse clientResponse = webResource
.accept(MediaType.APPLICATION_JSON).get(clientResponseClass);
-
+
// Get the JSON string from the response object or directly from the
// client (JavaScript)
Map<String, Object> jsonObj = null;
String responseString = null;
-
+
// Check the response status and report exception if one occurs
int responseStatus = clientResponse.getStatus();
switch (responseStatus)
getMessageByHTTPStatusCode(responseStatus, "3DBeacons"));
}
// Process the response and return the result to the caller.
- return parseTDBeaconsJsonResponse(responseString, jsonObj, tdbRestRequest);
+ return parseTDBeaconsJsonResponse(responseString, jsonObj,
+ tdbRestRequest);
} catch (Exception e)
{
String exceptionMsg = e.getMessage();
throw e;
}
}
-
+
}
-
- public String setSearchTerm(String term) {
+
+ public String setSearchTerm(String term)
+ {
return term;
}
-
+
public static FTSRestResponse parseTDBeaconsJsonResponse(
String tdbJsonResponseString, FTSRestRequest tdbRestRequest)
{
return parseTDBeaconsJsonResponse(tdbJsonResponseString,
(Map<String, Object>) null, tdbRestRequest);
}
-
+
@SuppressWarnings("unchecked")
- public static FTSRestResponse parseTDBeaconsJsonResponse(String tdbJsonResponseString,
- Map<String, Object> jsonObj, FTSRestRequest tdbRestRequest)
+ public static FTSRestResponse parseTDBeaconsJsonResponse(
+ String tdbJsonResponseString, Map<String, Object> jsonObj,
+ FTSRestRequest tdbRestRequest)
{
FTSRestResponse searchResult = new FTSRestResponse();
List<FTSData> result = null;
-
+
try
{
if (jsonObj == null)
{
- jsonObj = (Map<String, Object>) JSONUtils.parse(tdbJsonResponseString);
+ jsonObj = (Map<String, Object>) JSONUtils
+ .parse(tdbJsonResponseString);
}
-
- Object uniprot_entry = jsonObj.get("uniprot_entry");
- // TODO: decide if anything from uniprot_entry needs to be reported via the FTSRestResponse object
- // Arnaud added seqLength = (Long) ((Map<String, Object>) jsonObj.get("uniprot_entry")).get("sequence_length");
+
+ Object uniprot_entry = jsonObj.get("uniprot_entry");
+ // TODO: decide if anything from uniprot_entry needs to be reported via
+ // the FTSRestResponse object
+ // Arnaud added seqLength = (Long) ((Map<String, Object>)
+ // jsonObj.get("uniprot_entry")).get("sequence_length");
List<Object> structures = (List<Object>) jsonObj.get("structures");
result = new ArrayList<>();
-
+
int numFound = 0;
- for (Iterator<Object> strucIter = structures.iterator(); strucIter.hasNext();)
+ for (Iterator<Object> strucIter = structures.iterator(); strucIter
+ .hasNext();)
{
- Map<String, Object> structure = (Map<String, Object>) strucIter.next();
+ Map<String, Object> structure = (Map<String, Object>) strucIter
+ .next();
result.add(getFTSData(structure, tdbRestRequest));
numFound++;
}
-
- searchResult.setNumberOfItemsFound(numFound);
+
+ searchResult.setNumberOfItemsFound(numFound);
searchResult.setSearchSummary(result);
-
+
} catch (ParseException e)
{
e.printStackTrace();
return searchResult;
}
-private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
+ private static FTSData getFTSData(Map<String, Object> tdbJsonStructure,
FTSRestRequest tdbRequest)
{
- // TODO Auto-generated method stub
+ // TODO: consider reusing PDBFTSRestClient.getFTSData ?
+
String primaryKey = null;
Object[] summaryRowData;
+
+ SequenceI associatedSequence;
+
Collection<FTSDataColumnI> displayFields = tdbRequest.getWantedFields();
+ SequenceI associatedSeq = tdbRequest.getAssociatedSequence();
int colCounter = 0;
- summaryRowData = new Object[displayFields.size()];
-
- for (FTSDataColumnI field : displayFields) {
- String fieldData = (tdbJsonStructure.get(field.getCode()) == null) ? " "
+ summaryRowData = new Object[(associatedSeq != null)
+ ? displayFields.size() + 1
+ : displayFields.size()];
+ if (associatedSeq != null)
+ {
+ associatedSequence = associatedSeq;
+ summaryRowData[0] = associatedSequence;
+ colCounter = 1;
+ }
+
+ for (FTSDataColumnI field : displayFields)
+ {
+ String fieldData = (tdbJsonStructure.get(field.getCode()) == null)
+ ? " "
: tdbJsonStructure.get(field.getCode()).toString();
- // System.out.println("Field : " + field + " Data : " + fieldData);
+ // System.out.println("Field : " + field + " Data : " + fieldData);
if (field.isPrimaryKeyColumn())
{
primaryKey = fieldData;
{
summaryRowData[colCounter++] = null;
}
- else
+ else
{
try
{
: fieldData;
} catch (Exception e)
{
- //e.printStackTrace();
+ // e.printStackTrace();
System.out.println("offending value:" + fieldData + fieldData);
}
}
}
final String primaryKey1 = primaryKey;
final Object[] summaryRowData1 = summaryRowData;
-
+
return new FTSData()
{
{
return primaryKey1;
}
-
+
/**
* Returns a string representation of this object;
*/
}
return summaryFieldValues.toString();
}
-
+
/**
* Returns hash code value for this object
*/
};
}
-// private static FTSData getFTSData(Map<String, Object> doc,
-// FTSRestRequest tdbRestRequest)
-// {
-// String primaryKey = null;
-//
-// Object[] summaryRowData;
-//
-// Collection<FTSDataColumnI> displayFields = tdbRestRequest.getWantedFields();
-// int colCounter = 0;
-// summaryRowData = new Object[displayFields.size() + 1];
-//
-// return null;
-// }
+ // private static FTSData getFTSData(Map<String, Object> doc,
+ // FTSRestRequest tdbRestRequest)
+ // {
+ // String primaryKey = null;
+ //
+ // Object[] summaryRowData;
+ //
+ // Collection<FTSDataColumnI> displayFields =
+ // tdbRestRequest.getWantedFields();
+ // int colCounter = 0;
+ // summaryRowData = new Object[displayFields.size() + 1];
+ //
+ // return null;
+ // }
private String parseJsonExceptionString(String jsonErrorString)
{
{
return "/fts/tdbeacons_data_columns.txt";
}
-
+
public static FTSRestClientI getInstance()
{
if (instance == null)
}
return instance;
}
-
+
private Collection<FTSDataColumnI> allDefaultDisplayedStructureDataColumns;
public Collection<FTSDataColumnI> getAllDefaultDisplayedStructureDataColumns()
}
return allDefaultDisplayedStructureDataColumns;
}
-
+
+ @Override
+ public String[] getPreferencesColumnsFor(PreferenceSource source)
+ {
+ String[] columnNames = null;
+ switch (source)
+ {
+ case SEARCH_SUMMARY:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case STRUCTURE_CHOOSER:
+ columnNames = new String[] { "", "Display", "Group" };
+ break;
+ case PREFERENCES:
+ columnNames = new String[] { "3DB Beacons Field", "Show in search summary",
+ "Show in structure summary" };
+ break;
+ default:
+ break;
+ }
+ return columnNames;
+ }
}
import jalview.fts.core.FTSRestRequest;
import jalview.fts.core.FTSRestResponse;
import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.StructureChooserQuerySource;
import jalview.io.DataSourceType;
import jalview.jbgui.GStructureChooser;
import jalview.jbgui.GStructureChooser.FilterOption;
{
// which FTS engine to use
data = StructureChooserQuerySource
- .getPDBfts();
+ .getTDBfts();
initDialog();
this.ap = ap;
{
resultList = data.fetchStructuresMetaData(seq, wantedFields,
selectedFilterOpt, !chk_invertFilter.isSelected());
+ // null response means the FTSengine didn't yield a query for this
+ // consider designing a special exception if we really wanted to be OOCrazy
+ if (resultList==null)
+ {
+ continue;
+ }
} catch (Exception e)
{
e.printStackTrace();
if (currentView == VIEWS_FILTER)
{
- int pdbIdColIndex = restable.getColumn("PDB Id").getModelIndex();
- int refSeqColIndex = restable.getColumn("Ref Sequence")
- .getModelIndex();
int[] selectedRows = restable.getSelectedRows();
PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
- int count = 0;
List<SequenceI> selectedSeqsToView = new ArrayList<>();
- for (int row : selectedRows)
- {
- String pdbIdStr = restable.getValueAt(row, pdbIdColIndex)
- .toString();
- SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
- refSeqColIndex);
- selectedSeqsToView.add(selectedSeq);
- PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
- if (pdbEntry == null)
- {
- pdbEntry = getFindEntry(pdbIdStr,
- selectedSeq.getAllPDBEntries());
- }
+ pdbEntriesToView = data.collectSelectedRows(restable,selectedRows,selectedSeqsToView);
- 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()]);
sViewer = launchStructureViewer(ssm, pdbEntriesToView, ap,
}
}
- 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;
- }
-
/**
* Answers a structure viewer (new or existing) configured to superimpose
* added structures or not according to the user's choice
+++ /dev/null
-package jalview.gui;
-
-import java.util.Collection;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
-import java.util.List;
-import java.util.Objects;
-import java.util.Set;
-
-import javax.swing.table.TableModel;
-
-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.FTSDataColumnPreferences;
-import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
-import jalview.fts.core.FTSRestRequest;
-import jalview.fts.core.FTSRestResponse;
-import jalview.fts.service.pdb.PDBFTSRestClient;
-import jalview.jbgui.GStructureChooser.FilterOption;
-
-/**
- * logic for querying sources of structural data for structures of sequences
- *
- * @author jprocter
- *
- * @param <T>
- */
-public class StructureChooserQuerySource
-{
- private FTSRestRequest lastPdbRequest;
-
- private FTSRestClientI pdbRestClient;
-
- private FTSDataColumnPreferences docFieldPrefs;
-
- private static int MAX_QLENGTH = 7820;
-
- public StructureChooserQuerySource()
- {
- }
-
- public static StructureChooserQuerySource getPDBfts()
- {
- StructureChooserQuerySource pdbfts = new StructureChooserQuerySource();
- pdbfts.pdbRestClient = PDBFTSRestClient.getInstance();
- pdbfts.docFieldPrefs = new FTSDataColumnPreferences(
- PreferenceSource.STRUCTURE_CHOOSER,
- PDBFTSRestClient.getInstance());
- return pdbfts;
- }
-
- public FTSDataColumnPreferences getDocFieldPrefs()
- {
- return docFieldPrefs;
- }
-
- public void setDocFieldPrefs(FTSDataColumnPreferences docFieldPrefs)
- {
- this.docFieldPrefs = docFieldPrefs;
- }
-
- /**
- * Builds a query string for a given sequences using its DBRef entries
- *
- * @param seq
- * the sequences to build a query for
- * @return the built query string
- */
-
- String buildQuery(SequenceI seq)
- {
- boolean isPDBRefsFound = false;
- boolean isUniProtRefsFound = false;
- StringBuilder queryBuilder = new StringBuilder();
- Set<String> seqRefs = new LinkedHashSet<>();
-
- /*
- * note PDBs as DBRefEntry so they are not duplicated in query
- */
- Set<String> pdbids = new HashSet<>();
-
- if (seq.getAllPDBEntries() != null
- && queryBuilder.length() < MAX_QLENGTH)
- {
- for (PDBEntry entry : seq.getAllPDBEntries())
- {
- if (isValidSeqName(entry.getId()))
- {
- String id = entry.getId().toLowerCase();
- queryBuilder.append("pdb_id:").append(id).append(" OR ");
- isPDBRefsFound = true;
- pdbids.add(id);
- }
- }
- }
-
- List<DBRefEntry> refs = seq.getDBRefs();
- if (refs != null && refs.size() != 0)
- {
- for (int ib = 0, nb = refs.size(); ib < nb; ib++)
- {
- DBRefEntry dbRef = refs.get(ib);
- if (isValidSeqName(getDBRefId(dbRef))
- && queryBuilder.length() < MAX_QLENGTH)
- {
- if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT))
- {
- queryBuilder.append("uniprot_accession:")
- .append(getDBRefId(dbRef)).append(" OR ");
- queryBuilder.append("uniprot_id:").append(getDBRefId(dbRef))
- .append(" OR ");
- isUniProtRefsFound = true;
- }
- else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
- {
-
- String id = getDBRefId(dbRef).toLowerCase();
- if (!pdbids.contains(id))
- {
- queryBuilder.append("pdb_id:").append(id).append(" OR ");
- isPDBRefsFound = true;
- pdbids.add(id);
- }
- }
- else
- {
- seqRefs.add(getDBRefId(dbRef));
- }
- }
- }
- }
-
- if (!isPDBRefsFound && !isUniProtRefsFound)
- {
- String seqName = seq.getName();
- seqName = sanitizeSeqName(seqName);
- String[] names = seqName.toLowerCase().split("\\|");
- for (String name : names)
- {
- // System.out.println("Found name : " + name);
- name.trim();
- if (isValidSeqName(name))
- {
- seqRefs.add(name);
- }
- }
-
- for (String seqRef : seqRefs)
- {
- queryBuilder.append("text:").append(seqRef).append(" OR ");
- }
- }
-
- int endIndex = queryBuilder.lastIndexOf(" OR ");
- if (queryBuilder.toString().length() < 6)
- {
- return null;
- }
- String query = queryBuilder.toString().substring(0, endIndex);
- return query;
- }
-
- /**
- * Remove the following special characters from input string +, -, &, !, (, ),
- * {, }, [, ], ^, ", ~, *, ?, :, \
- *
- * @param seqName
- * @return
- */
- 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
- *
- * @param seqName
- * @return
- */
- static boolean isValidSeqName(String seqName)
- {
- // 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.contains(ignoredEntry))
- {
- return false;
- }
- }
- return true;
- }
-
- static String getDBRefId(DBRefEntry dbRef)
- {
- String ref = dbRef.getAccessionId().replaceAll("GO:", "");
- return ref;
- }
-
- /**
- * FTSRestClient specific query builder to recover associated structure data
- * records for a sequence
- *
- * @param seq
- * - seq to generate a query for
- * @param wantedFields
- * - fields to retrieve
- * @param selectedFilterOpt
- * - criterion for ranking results (e.g. resolution)
- * @param b
- * - sort ascending or descending
- * @return
- * @throws Exception
- */
- public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
- Collection<FTSDataColumnI> wantedFields,
- FilterOption selectedFilterOpt, boolean b) throws Exception
- {
- FTSRestResponse resultList;
- FTSRestRequest pdbRequest = new FTSRestRequest();
- pdbRequest.setAllowEmptySeq(false);
- pdbRequest.setResponseSize(500);
- pdbRequest.setFieldToSearchBy("(");
- pdbRequest.setFieldToSortBy(selectedFilterOpt.getValue(), b);
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setAssociatedSequence(seq);
- resultList = pdbRestClient.executeRequest(pdbRequest);
-
- lastPdbRequest = pdbRequest;
- return resultList;
- }
-
- /**
- * FTSRestClient specific query builder to pick top ranked entry from a
- * fetchStructuresMetaData query
- *
- * @param seq
- * - seq to generate a query for
- * @param wantedFields
- * - fields to retrieve
- * @param selectedFilterOpt
- * - criterion for ranking results (e.g. resolution)
- * @param b
- * - sort ascending or descending
- * @return
- * @throws Exception
- */
- public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
- Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
- boolean b) throws Exception
- {
-
- FTSRestResponse resultList;
- FTSRestRequest pdbRequest = new FTSRestRequest();
- if (fieldToFilterBy.equalsIgnoreCase("uniprot_coverage"))
- {
- 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, b);
- pdbRequest.setSearchTerm(buildQuery(seq) + ")");
- pdbRequest.setWantedFields(wantedFields);
- pdbRequest.setAssociatedSequence(seq);
- }
- resultList = pdbRestClient.executeRequest(pdbRequest);
-
- lastPdbRequest = pdbRequest;
- return resultList;
- }
-
- public TableModel getTableModel(
- Collection<FTSData> discoveredStructuresSet)
- {
- return FTSRestResponse.getTableModel(lastPdbRequest,
- discoveredStructuresSet);
- }
-
- public FTSDataColumnPreferences getInitialFieldPreferences()
- {
- // TODO Auto-generated method stub
- return null;
- }
-
-}
\ No newline at end of file
--- /dev/null
+package jalview.gui.structurechooser;
+
+import java.util.Collection;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Objects;
+import java.util.Set;
+import java.util.Vector;
+
+import javax.swing.JTable;
+import javax.swing.table.TableModel;
+
+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.FTSDataColumnPreferences;
+import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
+import jalview.fts.core.FTSRestRequest;
+import jalview.fts.core.FTSRestResponse;
+import jalview.fts.service.pdb.PDBFTSRestClient;
+import jalview.jbgui.GStructureChooser.FilterOption;
+
+/**
+ * logic for querying sources of structural data for structures of sequences
+ *
+ * @author jprocter
+ *
+ * @param <T>
+ */
+public abstract class StructureChooserQuerySource
+{
+ protected FTSRestRequest lastPdbRequest;
+
+ protected FTSRestClientI pdbRestClient;
+
+ protected FTSDataColumnPreferences docFieldPrefs;
+
+ /**
+ * max length of a GET URL (probably :( )
+ */
+ protected static int MAX_QLENGTH = 7820;
+
+ public StructureChooserQuerySource()
+ {
+ }
+
+ public static StructureChooserQuerySource getPDBfts()
+ {
+ return new PDBStructureChooserQuerySource();
+ }
+
+ public static StructureChooserQuerySource getTDBfts()
+ {
+ return new ThreeDBStructureChooserQuerySource();
+ }
+
+ public FTSDataColumnPreferences getDocFieldPrefs()
+ {
+ return docFieldPrefs;
+ }
+
+ public void setDocFieldPrefs(FTSDataColumnPreferences docFieldPrefs)
+ {
+ this.docFieldPrefs = docFieldPrefs;
+ }
+
+ public FTSDataColumnPreferences getInitialFieldPreferences()
+ {
+ return docFieldPrefs;
+ }
+
+
+ /**
+ * Builds a query string for a given sequences using its DBRef entries
+ *
+ * @param seq
+ * the sequences to build a query for
+ * @return the built query string
+ */
+
+ public abstract String buildQuery(SequenceI seq);
+
+
+ /**
+ * Remove the following special characters from input string +, -, &, !, (, ),
+ * {, }, [, ], ^, ", ~, *, ?, :, \
+ *
+ * @param seqName
+ * @return
+ */
+ public 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
+ *
+ * @param seqName
+ * @return
+ */
+ static boolean isValidSeqName(String seqName)
+ {
+ // 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.contains(ignoredEntry))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ static String getDBRefId(DBRefEntry dbRef)
+ {
+ String ref = dbRef.getAccessionId().replaceAll("GO:", "");
+ return ref;
+ }
+
+ static 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;
+ }
+
+ /**
+ * FTSRestClient specific query builder to recover associated structure data
+ * records for a sequence
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public abstract FTSRestResponse fetchStructuresMetaData(SequenceI seq,
+ Collection<FTSDataColumnI> wantedFields,
+ FilterOption selectedFilterOpt, boolean b) throws Exception;
+
+ /**
+ * FTSRestClient specific query builder to pick top ranked entry from a
+ * fetchStructuresMetaData query
+ *
+ * @param seq
+ * - seq to generate a query for
+ * @param wantedFields
+ * - fields to retrieve
+ * @param selectedFilterOpt
+ * - criterion for ranking results (e.g. resolution)
+ * @param b
+ * - sort ascending or descending
+ * @return
+ * @throws Exception
+ */
+ public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+ Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+ boolean b) throws Exception;
+
+ /**
+ *
+ * @param discoveredStructuresSet
+ * @return the table model for the given result set for this engine
+ */
+ public TableModel getTableModel(
+ Collection<FTSData> discoveredStructuresSet)
+ {
+ return FTSRestResponse.getTableModel(lastPdbRequest,
+ discoveredStructuresSet);
+ }
+
+ public abstract PDBEntry[] collectSelectedRows(JTable restable,
+ int[] selectedRows, List<SequenceI> selectedSeqsToView);
+
+}
\ No newline at end of file
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.fts.api.FTSData;
+import jalview.gui.structurechooser.PDBStructureChooserQuerySource;
+import jalview.gui.structurechooser.StructureChooserQuerySource;
import jalview.jbgui.GStructureChooser.FilterOption;
import jalview.ws.params.InvalidArgumentException;
public void sanitizeSeqNameTest()
{
String name = "ab_cdEF|fwxyz012349";
- assertEquals(name, StructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals(name, PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove a [nn] substring
name = "abcde12[345]fg";
- assertEquals("abcde12fg", StructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde12fg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
// remove characters other than a-zA-Z0-9 | or _
name = "ab[cd],.\t£$*!- \\\"@:e";
- assertEquals("abcde", StructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde", PDBStructureChooserQuerySource.sanitizeSeqName(name));
name = "abcde12[345a]fg";
- assertEquals("abcde12345afg", StructureChooserQuerySource.sanitizeSeqName(name));
+ assertEquals("abcde12345afg", PDBStructureChooserQuerySource.sanitizeSeqName(name));
}
}
git://source.jalview.org / jalview.git / commitdiff