extends StructureChooserQuerySource
{
+ private static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage";
+
private static int MAX_QLENGTH = 7820;
protected FTSRestRequest lastTdbRequest;
PreferenceSource.STRUCTURE_CHOOSER,
TDBeaconsFTSRestClient.getInstance());
- }
+ }
/**
* Builds a query string for a given sequences using its DBRef entries 3d
FilterOption selectedFilterOpt, boolean b) throws Exception
{
FTSRestResponse resultList;
+ if (tdBeaconsFilter(selectedFilterOpt.getValue())) {
FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields);
resultList = tdbRestClient.executeRequest(tdbRequest);
lastTdbRequest = tdbRequest;
+
+ // Query the PDB and add additional metadata
+ FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(getPDBQuerySource(), resultList);
+ FTSRestResponse joinedResp = joinResponses(resultList,
+ pdbResponse);
return resultList;
+ }
+ // use the PDBFTS directly
+ resultList = getPDBQuerySource().fetchStructuresMetaData(seq, wantedFields, selectedFilterOpt, b);
+ lastTdbRequest = getPDBQuerySource().lastPdbRequest;
+ lastPdbRequest = lastTdbRequest; // both queries the same - indicates we rank using PDBe
+ return resultList;
+
+ }
+
+ PDBStructureChooserQuerySource pdbQuerySource=null;
+ private PDBStructureChooserQuerySource getPDBQuerySource()
+ {
+ if (pdbQuerySource==null)
+ {
+ pdbQuerySource = new PDBStructureChooserQuerySource();
+ }
+ return pdbQuerySource;
}
private FTSRestRequest getTDBeaconsRequest(SequenceI seq,
@Override
public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
{
- List<FilterOption> filters = new ArrayList<FilterOption>();
- filters.add(
- new FilterOption(MessageManager.getString("label.best_quality"),
- "overall_quality", VIEWS_FILTER, false));
- filters.add(new FilterOption(
- MessageManager.getString("label.best_resolution"), "resolution",
- VIEWS_FILTER, false));
- filters.add(new FilterOption(
- MessageManager.getString("label.most_protein_chain"),
- "number_of_protein_chains", VIEWS_FILTER, false));
- filters.add(new FilterOption(
- MessageManager.getString("label.most_bound_molecules"),
- "number_of_bound_molecules", VIEWS_FILTER, false));
- filters.add(new FilterOption(
- MessageManager.getString("label.most_polymer_residues"),
- "number_of_polymer_residues", VIEWS_FILTER, true));
-
+ List<FilterOption> filters = getPDBQuerySource().getAvailableFilterOptions(VIEWS_FILTER);
+
+ filters.add(0,
+ new FilterOption("3D-Beacons Coverage",
+ FILTER_TDBEACONS_COVERAGE, VIEWS_FILTER, true, this));
return filters;
}
+ private boolean tdBeaconsFilter(String fieldToFilterBy)
+ {
+ return FILTER_TDBEACONS_COVERAGE.equals(fieldToFilterBy);
+ }
- /**
- * model categories - update as needed. warnings output if unknown types
- * encountered.
- *
- * Order denotes 'trust'
- */
- private static List<String> EXP_CATEGORIES = Arrays
- .asList(new String[]
- { "EXPERIMENTALLY DETERMINED", "DEEP LEARNING", "TEMPLATE-BASED" });
-
+ @Override
+ public boolean needsRefetch(FilterOption selectedFilterOpt)
+ {
+ return tdBeaconsFilter(selectedFilterOpt.getValue()) && lastPdbRequest!=lastTdbRequest;
+ }
/**
* FTSRestClient specific query builder to pick top ranked entry from a
* fetchStructuresMetaData query
Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
boolean b) throws Exception
{
-
- List<FTSData> filteredResponse = new ArrayList<FTSData>();
- final int idx_ups = lastTdbRequest.getFieldIndex("Uniprot Start");
- final int idx_upe = lastTdbRequest.getFieldIndex("Uniprot End");
- final int idx_mcat = lastTdbRequest.getFieldIndex("Model Category");
- final int idx_mqual = lastTdbRequest.getFieldIndex("Qmean");
- final int idx_resol = lastTdbRequest.getFieldIndex("Resolution");
-
- // ignore anything outside the sequence region
- for (FTSData row : collectedResults)
- {
- int up_s = (Integer) row.getSummaryData()[idx_ups];
- int up_e = (Integer) row.getSummaryData()[idx_upe];
-
- if (seq == row.getSummaryData()[0] && up_e > seq.getStart()
- && up_s < seq.getEnd())
- {
- filteredResponse.add(row);
- }
- }
- // sort according to decreasing length,
- // increasing start
- Collections.sort(filteredResponse, new Comparator<FTSData>()
+ if (tdBeaconsFilter(fieldToFilterBy))
{
+ TDBResultAnalyser analyser = new TDBResultAnalyser(seq,
+ collectedResults, lastTdbRequest);
- private final int scoreCategory(String cat)
- {
- // TODO: make quicker
- int idx = EXP_CATEGORIES.indexOf(cat.toUpperCase());
- if (idx == -1)
- {
- System.out.println("Unknown category: '" + cat + "'");
- }
- return -EXP_CATEGORIES.size() - idx;
- }
+ FTSRestResponse resultList = new FTSRestResponse();
- @Override
- public int compare(FTSData o1, FTSData o2)
- {
- int o1_s = (Integer) o1.getSummaryData()[idx_ups];
- int o1_e = (Integer) o1.getSummaryData()[idx_upe];
- int o1_cat = scoreCategory((String) o1.getSummaryData()[idx_mcat]);
- int o2_s = (Integer) o2.getSummaryData()[idx_ups];
- int o2_e = (Integer) o2.getSummaryData()[idx_upe];
- int o2_cat = scoreCategory((String) o2.getSummaryData()[idx_mcat]);
-
- if (o1_cat == o2_cat)
- {
- if (o1_s == o2_s)
- {
- int o1_xtent = o1_e - o1_s;
- int o2_xtent = o2_e - o2_s;
- if (o1_xtent == o2_xtent)
- {
- if (o1_cat == scoreCategory(EXP_CATEGORIES.get(0)))
- {
- // experimental structures, so rank on quality
- double o1_res = (Double) o1.getSummaryData()[idx_resol];
- double o2_res = (Double) o2.getSummaryData()[idx_resol];
- return (o2_res < o1_res) ? 1 : (o2_res == o1_res) ? 0 : -1;
- }
- else
- {
- // models, so rank on qmean
- float o1_mq = (Float) o1.getSummaryData()[idx_mqual];
- float o2_mq = (Float) o2.getSummaryData()[idx_mqual];
- return (o2_mq < o1_mq) ? 1 : (o2_mq == o1_mq) ? 0 : -1;
- }
- }
- else
- {
- return o1_xtent - o2_xtent;
- }
- }
- else
- {
- return o1_s - o2_s;
- }
- }
- else
- {
- return o2_cat - o1_cat;
- }
- }
+ List<FTSData> filteredResponse = analyser.getFilteredResponse();
- @Override
- public boolean equals(Object obj)
- {
- return super.equals(obj);
- }
- });
- FTSRestResponse resultList = new FTSRestResponse();
- resultList.setNumberOfItemsFound(filteredResponse.size());
- resultList.setSearchSummary(filteredResponse);
- return resultList;
+ List<FTSData> selectedStructures = analyser
+ .selectStructures(filteredResponse);
+ resultList.setNumberOfItemsFound(selectedStructures.size());
+ resultList.setSearchSummary(selectedStructures);
+ return resultList;
+ }
+ // Fall back to PDBe rankings
+ return getPDBQuerySource().selectFirstRankedQuery(seq, collectedResults, wantedFields, fieldToFilterBy, b);
}
+
@Override
public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
List<SequenceI> selectedSeqsToView)
int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
int categoryColumnIndex = restable.getColumn("Model Category")
.getModelIndex();
+ final int up_start_idx = restable.getColumn("Uniprot Start").getModelIndex();
+ final int up_end_idx = restable.getColumn("Uniprot End").getModelIndex();
+ int i=0;
+
+ // bleugh!
+ Integer[] sellist = new Integer[selectedRows.length];
+ for (Integer row: selectedRows)
+ {
+ sellist[i++] = row;
+ }
+ // Sort rows by coverage
+ Arrays.sort(sellist,new Comparator<Integer>()
+ {
+ @Override
+ public int compare(Integer o1, Integer o2)
+ {
+ int o1_xt = ((Integer)restable.getValueAt(o1, up_end_idx)) - (Integer)restable.getValueAt(o1, up_start_idx);
+ int o2_xt = ((Integer)restable.getValueAt(o2, up_end_idx)) - (Integer)restable.getValueAt(o2, up_start_idx);
+ return o2_xt-o1_xt;
+ }
+ });
- for (int row : selectedRows)
+
+ for (int row : sellist)
{
// unique id - could be a horrible hash
int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
// join on
int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
- int pdbIdx = lastPdbRequest.getFieldIndex("pdb_id");
- for (FTSData row : upResponse.getSearchSummary())
+ int pdbIdx = lastPdbRequest.getFieldIndex("PDB Id");
+ int pdbTitle_idx = lastPdbRequest.getFieldIndex("Title");
+ int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title");
+
+ List<FTSData> joinedRows = new ArrayList<FTSData>();
+ for (final FTSData row : upResponse.getSearchSummary())
{
String id = (String) row.getSummaryData()[idx_modelId];
String provider = (String) row.getSummaryData()[idx_provider];
if ("PDBe".equalsIgnoreCase(provider))
{
- for (FTSData pdbrow : pdbResponse.getSearchSummary())
+ for (final FTSData pdbrow : pdbResponse.getSearchSummary())
{
String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
if (id.equalsIgnoreCase(pdbid))
{
- // often multiple entries per PDB ID so we bail after first
- // get wanted fields
- // append to FTSRestResponse array
+ row.getSummaryData()[tdbTitle_idx] = pdbrow
+ .getSummaryData()[pdbTitle_idx];
}
}
+ } else {
+ row.getSummaryData()[tdbTitle_idx] = "Model from TDB";
}
}
- // TODO Auto-generated method stub
- return null;
+ return upResponse;
}
}
\ No newline at end of file
git://source.jalview.org / jalview.git / blobdiff