X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2Fstructurechooser%2FThreeDBStructureChooserQuerySource.java;h=cbc6addea6a872ff6636f0edf003b4404c781297;hb=456e7b01bf201167e0063d0e8b56d4717322d6c0;hp=d64d643d436f2c85be3d89db6068622026344906;hpb=a35bdf653fe2f56b6600c57f53991a0191cb0032;p=jalview.git diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java index d64d643..cbc6add 100644 --- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java +++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java @@ -1,17 +1,38 @@ +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ package jalview.gui.structurechooser; import java.util.ArrayList; import java.util.Arrays; import java.util.Collection; -import java.util.Collections; import java.util.Comparator; import java.util.HashSet; import java.util.LinkedHashSet; import java.util.List; +import java.util.Locale; import java.util.Set; import javax.swing.JTable; +import jalview.bin.Console; import jalview.datamodel.DBRefEntry; import jalview.datamodel.DBRefSource; import jalview.datamodel.PDBEntry; @@ -23,9 +44,9 @@ 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.threedbeacons.TDB_FTSData; import jalview.fts.service.threedbeacons.TDBeaconsFTSRestClient; import jalview.jbgui.FilterOption; -import jalview.util.MessageManager; /** * logic for querying the 3DBeacons API for structures of sequences @@ -36,9 +57,13 @@ public class ThreeDBStructureChooserQuerySource extends StructureChooserQuerySource { - private static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage"; + private Set tdBeaconsFilters = null, defaultFilters = null; - private static int MAX_QLENGTH = 7820; + public static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage"; + + public static final String FILTER_FIRST_BEST_COVERAGE = "3d_beacons_first_best_coverage"; + + private static final String FILTER_SOURCE_PREFIX = "only_"; protected FTSRestRequest lastTdbRequest; @@ -48,12 +73,15 @@ public class ThreeDBStructureChooserQuerySource public ThreeDBStructureChooserQuerySource() { + defaultFilters = new LinkedHashSet(); + defaultFilters.add(FILTER_TDBEACONS_COVERAGE); + defaultFilters.add(FILTER_FIRST_BEST_COVERAGE); + tdbRestClient = TDBeaconsFTSRestClient.getInstance(); docFieldPrefs = new FTSDataColumnPreferences( PreferenceSource.STRUCTURE_CHOOSER, TDBeaconsFTSRestClient.getInstance()); - - } + } /** * Builds a query string for a given sequences using its DBRef entries 3d @@ -64,39 +92,44 @@ public class ThreeDBStructureChooserQuerySource * @return the built query string */ + @Override public String buildQuery(SequenceI seq) { - boolean isPDBRefsFound = false; - boolean isUniProtRefsFound = false; - StringBuilder queryBuilder = new StringBuilder(); - Set seqRefs = new LinkedHashSet<>(); - - /* - * note PDBs as DBRefEntry so they are not duplicated in query - */ - Set pdbids = new HashSet<>(); - List refs = seq.getDBRefs(); + int ib = checkUniprotRefs(refs); + if (ib > -1) + { + return getDBRefId(refs.get(ib)); + } + return null; + } + + /** + * Searches DBRefEntry for uniprot refs + * + * @param seq + * @return -2 if no uniprot refs, -1 if no canonical ref., otherwise index of + * Uniprot canonical DBRefEntry + */ + public static int checkUniprotRefs(List refs) + { + boolean hasUniprot = false; 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)) { - if (dbRef.getSource().equalsIgnoreCase(DBRefSource.UNIPROT) - && dbRef.isCanonical()) + hasUniprot = true; + if (dbRef.isCanonical()) { - // TODO: pick best Uniprot accession - isUniProtRefsFound = true; - return getDBRefId(dbRef); - + return ib; } } } } - return null; + return hasUniprot ? -1 : -2; } /** @@ -108,7 +141,6 @@ public class ThreeDBStructureChooserQuerySource */ static boolean isValidSeqName(String seqName) { - // System.out.println("seqName : " + seqName); String ignoreList = "pdb,uniprot,swiss-prot"; if (seqName.length() < 3) { @@ -118,7 +150,7 @@ public class ThreeDBStructureChooserQuerySource { return false; } - seqName = seqName.toLowerCase(); + seqName = seqName.toLowerCase(Locale.ROOT); for (String ignoredEntry : ignoreList.split(",")) { if (seqName.contains(ignoredEntry)) @@ -150,35 +182,43 @@ public class ThreeDBStructureChooserQuerySource * @return * @throws Exception */ + @Override public FTSRestResponse fetchStructuresMetaData(SequenceI seq, Collection wantedFields, 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; - } + if (selectedFilterOpt != null + && tdBeaconsFilter(selectedFilterOpt.getValue())) + { + FTSRestRequest tdbRequest = getTDBeaconsRequest(seq, wantedFields); + resultList = tdbRestClient.executeRequest(tdbRequest); + + lastTdbRequest = tdbRequest; + if (resultList != null) + { // Query the PDB and add additional metadata + List pdbResponse = fetchStructuresMetaDataFor( + getPDBQuerySource(), resultList); + + resultList = joinResponses(resultList, pdbResponse); + } + return resultList; + } // use the PDBFTS directly - resultList = getPDBQuerySource().fetchStructuresMetaData(seq, wantedFields, selectedFilterOpt, b); + resultList = getPDBQuerySource().fetchStructuresMetaData(seq, + wantedFields, selectedFilterOpt, b); lastTdbRequest = getPDBQuerySource().lastPdbRequest; - lastPdbRequest = lastTdbRequest; // both queries the same - indicates we rank using PDBe + lastPdbRequest = lastTdbRequest; // both queries the same - indicates we + // rank using PDBe return resultList; - + } - PDBStructureChooserQuerySource pdbQuerySource=null; + PDBStructureChooserQuerySource pdbQuerySource = null; + private PDBStructureChooserQuerySource getPDBQuerySource() { - if (pdbQuerySource==null) + if (pdbQuerySource == null) { pdbQuerySource = new PDBStructureChooserQuerySource(); } @@ -205,23 +245,93 @@ public class ThreeDBStructureChooserQuerySource @Override public List getAvailableFilterOptions(String VIEWS_FILTER) { - List filters = getPDBQuerySource().getAvailableFilterOptions(VIEWS_FILTER); - - filters.add(0, - new FilterOption("3D-Beacons Coverage", - FILTER_TDBEACONS_COVERAGE, VIEWS_FILTER, true, this)); + List filters = getPDBQuerySource() + .getAvailableFilterOptions(VIEWS_FILTER); + tdBeaconsFilters = new LinkedHashSet(); + tdBeaconsFilters.addAll(defaultFilters); + filters.add(0, new FilterOption("Best 3D-Beacons Coverage", + FILTER_FIRST_BEST_COVERAGE, VIEWS_FILTER, false, this)); + filters.add(1, new FilterOption("Multiple 3D-Beacons Coverage", + FILTER_TDBEACONS_COVERAGE, VIEWS_FILTER, true, this)); + return filters; } + + @Override + public void updateAvailableFilterOptions(String VIEWS_FILTER, + List xtantOptions, Collection tdbEntries) + { + if (tdbEntries != null && lastTdbRequest != null) + { + boolean hasPDBe = false; + for (FTSData _row : tdbEntries) + { + // tdb returns custom object + TDB_FTSData row = (TDB_FTSData) _row; + String provider = row.getProvider(); + FilterOption providerOpt = new FilterOption( + "3DB Provider - " + provider, + FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER, false, this); + if (!xtantOptions.contains(providerOpt)) + { + xtantOptions.add(1, providerOpt); + tdBeaconsFilters.add(FILTER_SOURCE_PREFIX + provider); + if ("PDBe".equalsIgnoreCase(provider)) + { + hasPDBe = true; + } + } + } + if (!hasPDBe) + { + // remove the PDBe options from the available filters + int op = 0; + while (op < xtantOptions.size()) + { + FilterOption filter = xtantOptions.get(op); + if (filter + .getQuerySource() instanceof PDBStructureChooserQuerySource) + { + xtantOptions.remove(op); + } + else + { + op++; + } + } + } + } + + } + private boolean tdBeaconsFilter(String fieldToFilterBy) { - return FILTER_TDBEACONS_COVERAGE.equals(fieldToFilterBy); + return tdBeaconsFilters != null + && tdBeaconsFilters.contains(fieldToFilterBy); + } + + private String remove_prefix(String fieldToFilterBy) + { + if (tdBeaconsFilters != null + && tdBeaconsFilters.contains(fieldToFilterBy) + && !defaultFilters.contains(fieldToFilterBy)) + { + return fieldToFilterBy.substring(FILTER_SOURCE_PREFIX.length()); + } + else + { + return null; + } } @Override public boolean needsRefetch(FilterOption selectedFilterOpt) { - return tdBeaconsFilter(selectedFilterOpt.getValue()) && lastPdbRequest!=lastTdbRequest; + return selectedFilterOpt == null + || !tdBeaconsFilter(selectedFilterOpt.getValue()) + && lastPdbRequest != lastTdbRequest; } + /** * FTSRestClient specific query builder to pick top ranked entry from a * fetchStructuresMetaData query @@ -237,15 +347,17 @@ public class ThreeDBStructureChooserQuerySource * @return * @throws Exception */ + @Override public FTSRestResponse selectFirstRankedQuery(SequenceI seq, Collection collectedResults, Collection wantedFields, String fieldToFilterBy, boolean b) throws Exception { - if (tdBeaconsFilter(fieldToFilterBy)) + if (fieldToFilterBy != null && tdBeaconsFilter(fieldToFilterBy)) { TDBResultAnalyser analyser = new TDBResultAnalyser(seq, - collectedResults, lastTdbRequest); + collectedResults, lastTdbRequest, fieldToFilterBy, + remove_prefix(fieldToFilterBy)); FTSRestResponse resultList = new FTSRestResponse(); @@ -258,10 +370,10 @@ public class ThreeDBStructureChooserQuerySource return resultList; } // Fall back to PDBe rankings - return getPDBQuerySource().selectFirstRankedQuery(seq, collectedResults, wantedFields, fieldToFilterBy, b); + return getPDBQuerySource().selectFirstRankedQuery(seq, collectedResults, + wantedFields, fieldToFilterBy, b); } - @Override public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows, List selectedSeqsToView) @@ -273,31 +385,34 @@ public class ThreeDBStructureChooserQuerySource int idColumnIndex = restable.getColumn("Model id").getModelIndex(); int urlColumnIndex = restable.getColumn("Url").getModelIndex(); int typeColumnIndex = restable.getColumn("Provider").getModelIndex(); - int categoryColumnIndex = restable.getColumn("Model Category") + int humanUrl = restable.getColumn("Page URL").getModelIndex(); + int modelformat = restable.getColumn("Model Format").getModelIndex(); + final int up_start_idx = restable.getColumn("Uniprot Start") + .getModelIndex(); + final int up_end_idx = restable.getColumn("Uniprot End") .getModelIndex(); - final int up_start_idx = restable.getColumn("Uniprot Start").getModelIndex(); - final int up_end_idx = restable.getColumn("Uniprot End").getModelIndex(); - int i=0; - + int i = 0; + // bleugh! Integer[] sellist = new Integer[selectedRows.length]; - for (Integer row: selectedRows) + for (Integer row : selectedRows) { sellist[i++] = row; } // Sort rows by coverage - Arrays.sort(sellist,new Comparator() + Arrays.sort(sellist, new Comparator() { @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; + 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 : sellist) { // unique id - could be a horrible hash @@ -306,6 +421,10 @@ public class ThreeDBStructureChooserQuerySource String urlStr = restable.getValueAt(row, urlColumnIndex).toString(); String typeColumn = restable.getValueAt(row, typeColumnIndex) .toString(); + String modelPage = humanUrl < 1 ? null + : (String) restable.getValueAt(row, humanUrl); + String strucFormat = restable.getValueAt(row, modelformat).toString(); + SequenceI selectedSeq = (SequenceI) restable.getValueAt(row, refSeqColIndex); selectedSeqsToView.add(selectedSeq); @@ -319,11 +438,25 @@ public class ThreeDBStructureChooserQuerySource { pdbEntry = new PDBEntry(); pdbEntry.setId(pdbIdStr); - pdbEntry.setType(PDBEntry.Type.MMCIF); + pdbEntry.setAuthoritative(true); + try + { + pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat)); + } catch (Exception q) + { + Console.warn("Unknown filetype for 3D Beacons Model from: " + + strucFormat + " - " + pdbIdStr + " - " + modelPage); + } + if (!"PDBe".equalsIgnoreCase(typeColumn)) { pdbEntry.setRetrievalUrl(urlStr); } + pdbEntry.setProvider(typeColumn); + if (modelPage != null) + { + pdbEntry.setProviderPage(modelPage); + } selectedSeq.getDatasetSequence().addPDBId(pdbEntry); } pdbEntriesToView[count++] = pdbEntry; @@ -345,9 +478,10 @@ public class ThreeDBStructureChooserQuerySource * @return */ - public String buildPDBFTSQueryFor(FTSRestResponse upResponse) + public List buildPDBFTSQueryFor(FTSRestResponse upResponse) { - List pdbIds = new ArrayList(); + List ftsQueries = new ArrayList(); + Set pdbIds = new HashSet(); int idx_modelId = getLastFTSRequest().getFieldIndex("Model id"); int idx_provider = getLastFTSRequest().getFieldIndex("Provider"); for (FTSData row : upResponse.getSearchSummary()) @@ -359,7 +493,25 @@ public class ThreeDBStructureChooserQuerySource pdbIds.add(id); } } - return String.join(" OR ", pdbIds).toString(); + StringBuilder sb = new StringBuilder(); + for (String pdbId : pdbIds) + { + if (sb.length() > 2500) + { + ftsQueries.add(sb.toString()); + sb.setLength(0); + } + if (sb.length() > 0) + { + sb.append(" OR "); + } + sb.append(pdbId); + } + if (sb.length() > 0) + { + ftsQueries.add(sb.toString()); + } + return ftsQueries; } /** @@ -369,59 +521,116 @@ public class ThreeDBStructureChooserQuerySource * @param upResponse * @return FTSRestResponse via PDBStructureChooserQuerySource */ - public FTSRestResponse fetchStructuresMetaDataFor( + public List fetchStructuresMetaDataFor( PDBStructureChooserQuerySource pdbquery, FTSRestResponse upResponse) throws Exception { + List pdb_Queries = buildPDBFTSQueryFor(upResponse); + if (pdb_Queries.size() == 0) + { + return null; + } + List results = new ArrayList(); - String pdb_Query = buildPDBFTSQueryFor(upResponse); + for (String pdb_Query : pdb_Queries) + { + FTSRestResponse resultList; + FTSRestRequest pdbRequest = new FTSRestRequest(); + pdbRequest.setAllowEmptySeq(false); + pdbRequest.setResponseSize(500); + pdbRequest.setFieldToSearchBy("("); + // pdbRequest.setFieldToSortBy("pdb_id"); + pdbRequest.setWantedFields( + pdbquery.getDocFieldPrefs().getStructureSummaryFields()); + pdbRequest.setSearchTerm(pdb_Query + ")"); + + // handle exceptions like server errors here - means the threedbeacons + // discovery isn't broken by issues to do with the PDBe SOLR api + try + { + resultList = pdbquery.executePDBFTSRestRequest(pdbRequest); + if (resultList.getNumberOfItemsFound() == 0) + { + Console.info("Unexpectedly returned no results for pdbe query: " + + pdb_Query); + } + results.add(resultList); + lastPdbRequest = pdbRequest; + } catch (Exception ex) + { + Console.error("PDBFTSQuery failed", ex); + } - FTSRestResponse resultList; - FTSRestRequest pdbRequest = new FTSRestRequest(); - pdbRequest.setAllowEmptySeq(false); - pdbRequest.setResponseSize(500); - pdbRequest.setFieldToSearchBy("("); - // pdbRequest.setFieldToSortBy("pdb_id"); - pdbRequest.setWantedFields( - pdbquery.getDocFieldPrefs().getStructureSummaryFields()); - pdbRequest.setSearchTerm(pdb_Query + ")"); - resultList = pdbquery.executePDBFTSRestRequest(pdbRequest); - - lastPdbRequest = pdbRequest; - return resultList; + } + + return results; } public FTSRestResponse joinResponses(FTSRestResponse upResponse, - FTSRestResponse pdbResponse) + List pdbResponses) { + boolean hasPdbResp = lastPdbRequest != null; + int idx_provider = getLastFTSRequest().getFieldIndex("Provider"); // join on int idx_modelId = getLastFTSRequest().getFieldIndex("Model id"); - int pdbIdx = lastPdbRequest.getFieldIndex("PDB Id"); - int pdbTitle_idx = lastPdbRequest.getFieldIndex("Title"); + int pdbIdx = hasPdbResp ? lastPdbRequest.getFieldIndex("PDB Id") : -1; + int pdbTitle_idx = hasPdbResp ? lastPdbRequest.getFieldIndex("Title") + : -1; int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title"); - - List joinedRows = new ArrayList(); + 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 (final FTSData pdbrow : pdbResponse.getSearchSummary()) + if (!hasPdbResp) { - String pdbid = (String) pdbrow.getSummaryData()[pdbIdx]; - if (id.equalsIgnoreCase(pdbid)) + System.out.println( + "Warning: seems like we couldn't get to the PDBe search interface."); + } + else + { + for (final FTSRestResponse pdbResponse : pdbResponses) { - row.getSummaryData()[tdbTitle_idx] = pdbrow - .getSummaryData()[pdbTitle_idx]; + for (final FTSData pdbrow : pdbResponse.getSearchSummary()) + { + String pdbid = (String) pdbrow.getSummaryData()[pdbIdx]; + if (id.equalsIgnoreCase(pdbid)) + { + row.getSummaryData()[tdbTitle_idx] = pdbrow + .getSummaryData()[pdbTitle_idx]; + } + } } } - } else { + + } + else + { row.getSummaryData()[tdbTitle_idx] = "Model from TDB"; } } return upResponse; } + public TDB_FTSData getFTSDataFor(JTable restable, int selectedRow, + Collection discoveredStructuresSet) + { + int idColumnIndex = restable.getColumn("Model id").getModelIndex(); + + String modelId = (String) restable.getValueAt(selectedRow, + idColumnIndex); + for (FTSData row : discoveredStructuresSet) + { + if (row instanceof TDB_FTSData + && ((TDB_FTSData) row).getModelId().equals(modelId)) + { + return ((TDB_FTSData) row); + } + } + return null; + } + } \ No newline at end of file