JAL-3829 provide both PDBe queries and 3D-Beacons queries in the filter combo box
[jalview.git] / src / jalview / gui / structurechooser / ThreeDBStructureChooserQuerySource.java
index b3242de..d64d643 100644 (file)
@@ -1,7 +1,10 @@
 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;
@@ -33,6 +36,8 @@ public class ThreeDBStructureChooserQuerySource
         extends StructureChooserQuerySource
 {
 
+  private static final String FILTER_TDBEACONS_COVERAGE = "3d_beacons_coverage";
+
   private static int MAX_QLENGTH = 7820;
 
   protected FTSRestRequest lastTdbRequest;
@@ -48,7 +53,7 @@ public class ThreeDBStructureChooserQuerySource
             PreferenceSource.STRUCTURE_CHOOSER,
             TDBeaconsFTSRestClient.getInstance());
 
-  }
+  }  
 
   /**
    * Builds a query string for a given sequences using its DBRef entries 3d
@@ -150,11 +155,34 @@ 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;
+    } 
+    // 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,
@@ -177,26 +205,23 @@ public class ThreeDBStructureChooserQuerySource
   @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);
+  }
 
+  @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
@@ -213,25 +238,30 @@ public class ThreeDBStructureChooserQuerySource
    * @throws Exception
    */
   public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+          Collection<FTSData> collectedResults,
           Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
           boolean b) throws Exception
   {
-
-    FTSRestResponse resultList;
-    FTSRestRequest pdbRequest = getTDBeaconsRequest(seq, wantedFields);
-    if (pdbRequest == null)
+    if (tdBeaconsFilter(fieldToFilterBy))
     {
-      return null;
-    }
-    pdbRequest.setResponseSize(1);
-    resultList = tdbRestClient.executeRequest(pdbRequest);
+      TDBResultAnalyser analyser = new TDBResultAnalyser(seq,
+              collectedResults, lastTdbRequest);
 
-    // TODO: client side filtering - sort results and pick top one (or N)
+      FTSRestResponse resultList = new FTSRestResponse();
 
-    lastTdbRequest = pdbRequest;
-    return resultList;
+      List<FTSData> filteredResponse = analyser.getFilteredResponse();
+
+      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)
@@ -245,8 +275,30 @@ 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;
+    
+    // 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
 
@@ -345,27 +397,31 @@ public class ThreeDBStructureChooserQuerySource
     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;
   }
 
 }
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