X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2Fstructurechooser%2FThreeDBStructureChooserQuerySource.java;h=d465e230f1da0e43a72b932a7694ae025c0a877d;hb=896b63f7908297dfe7a48e198d7bce847e2804b8;hp=d64d643d436f2c85be3d89db6068622026344906;hpb=fbd878d0ad686c65f9c9e42db37494535e63aa29;p=jalview.git diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java index d64d643..d465e23 100644 --- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java +++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java @@ -36,7 +36,13 @@ public class ThreeDBStructureChooserQuerySource extends StructureChooserQuerySource { - private static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage"; + private Set tdBeaconsFilters = null, defaultFilters = null; + + 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_"; private static int MAX_QLENGTH = 7820; @@ -48,12 +54,15 @@ 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 @@ -155,30 +164,34 @@ public class ThreeDBStructureChooserQuerySource 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; + + // 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); + 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 +218,71 @@ 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) + { + int prov_idx = lastTdbRequest.getFieldIndex("Provider"); + + for (FTSData row : tdbEntries) + { + String provider = (String) row.getSummaryData()[prov_idx]; + 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); + + } + } + } + + } + 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 @@ -242,10 +303,11 @@ public class ThreeDBStructureChooserQuerySource 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 +320,10 @@ 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) @@ -275,29 +337,32 @@ public class ThreeDBStructureChooserQuerySource 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; - + 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) + 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 @@ -400,7 +465,7 @@ public class ThreeDBStructureChooserQuerySource int pdbIdx = lastPdbRequest.getFieldIndex("PDB Id"); int pdbTitle_idx = lastPdbRequest.getFieldIndex("Title"); int tdbTitle_idx = getLastFTSRequest().getFieldIndex("Title"); - + List joinedRows = new ArrayList(); for (final FTSData row : upResponse.getSearchSummary()) { @@ -417,7 +482,9 @@ public class ThreeDBStructureChooserQuerySource .getSummaryData()[pdbTitle_idx]; } } - } else { + } + else + { row.getSummaryData()[tdbTitle_idx] = "Model from TDB"; } }