X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2Fstructurechooser%2FThreeDBStructureChooserQuerySource.java;h=f5a1065f8f35b6728ca6bab2cb56590b8c908b12;hb=e7e3ef45b167b7b823fdc76a7d05e78ae91a7fd3;hp=b1ad65fc432e30d532df17f4b0119cb207bdf3e7;hpb=a1984b1c8c273ed33c7ce9283039f4027dcae2de;p=jalview.git

diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index b1ad65f..f5a1065 100644
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -1,3 +1,23 @@
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 package jalview.gui.structurechooser;
 
 import java.util.ArrayList;
@@ -12,7 +32,7 @@ import java.util.Set;
 
 import javax.swing.JTable;
 
-import jalview.bin.Cache;
+import jalview.bin.Console;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
@@ -72,6 +92,7 @@ public class ThreeDBStructureChooserQuerySource
    * @return the built query string
    */
 
+  @Override
   public String buildQuery(SequenceI seq)
   {
     List<DBRefEntry> refs = seq.getDBRefs();
@@ -161,6 +182,7 @@ public class ThreeDBStructureChooserQuerySource
    * @return
    * @throws Exception
    */
+  @Override
   public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
           Collection<FTSDataColumnI> wantedFields,
           FilterOption selectedFilterOpt, boolean b) throws Exception
@@ -175,7 +197,7 @@ public class ThreeDBStructureChooserQuerySource
       lastTdbRequest = tdbRequest;
       if (resultList != null)
       { // Query the PDB and add additional metadata
-        FTSRestResponse pdbResponse = fetchStructuresMetaDataFor(
+        List<FTSRestResponse> pdbResponse = fetchStructuresMetaDataFor(
                 getPDBQuerySource(), resultList);
 
         resultList = joinResponses(resultList, pdbResponse);
@@ -246,7 +268,7 @@ public class ThreeDBStructureChooserQuerySource
       {
         // tdb returns custom object
         TDB_FTSData row = (TDB_FTSData) _row;
-        String provider = (String) row.getProvider();
+        String provider = row.getProvider();
         FilterOption providerOpt = new FilterOption(
                 "3DB Provider - " + provider,
                 FILTER_SOURCE_PREFIX + provider, VIEWS_FILTER, false, this);
@@ -288,7 +310,7 @@ public class ThreeDBStructureChooserQuerySource
             && tdBeaconsFilters.contains(fieldToFilterBy);
   }
 
-  private String remove_prefix(String fieldToFilterBy)
+  protected String remove_prefix(String fieldToFilterBy)
   {
     if (tdBeaconsFilters != null
             && tdBeaconsFilters.contains(fieldToFilterBy)
@@ -325,6 +347,7 @@ public class ThreeDBStructureChooserQuerySource
    * @return
    * @throws Exception
    */
+  @Override
   public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
           Collection<FTSData> collectedResults,
           Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
@@ -364,6 +387,9 @@ public class ThreeDBStructureChooserQuerySource
     int typeColumnIndex = restable.getColumn("Provider").getModelIndex();
     int humanUrl = restable.getColumn("Page URL").getModelIndex();
     int modelformat = restable.getColumn("Model Format").getModelIndex();
+    int tftype = restable.getColumn("Confidence Score Type").getModelIndex();
+    int tftypev = restable.getColumn("Confidence Score Version").getModelIndex();
+    
     final int up_start_idx = restable.getColumn("Uniprot Start")
             .getModelIndex();
     final int up_end_idx = restable.getColumn("Uniprot End")
@@ -401,7 +427,8 @@ public class ThreeDBStructureChooserQuerySource
       String modelPage = humanUrl < 1 ? null
               : (String) restable.getValueAt(row, humanUrl);
       String strucFormat = restable.getValueAt(row, modelformat).toString();
-
+      String strucTfType = tftype<1 ? null : restable.getValueAt(row, tftype)==null ? null : restable.getValueAt(row, tftype).toString();
+      String strucTfType_v = tftypev<1 ? null : restable.getValueAt(row, tftypev)==null ? null : restable.getValueAt(row, tftypev).toString();
       SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
               refSeqColIndex);
       selectedSeqsToView.add(selectedSeq);
@@ -415,12 +442,13 @@ public class ThreeDBStructureChooserQuerySource
       {
         pdbEntry = new PDBEntry();
         pdbEntry.setId(pdbIdStr);
+        pdbEntry.setAuthoritative(true);
         try
         {
           pdbEntry.setType(PDBEntry.Type.valueOf(strucFormat));
         } catch (Exception q)
         {
-          Cache.warn("Unknown filetype for 3D Beacons Model from: "
+          Console.warn("Unknown filetype for 3D Beacons Model from: "
                   + strucFormat + " - " + pdbIdStr + " - " + modelPage);
         }
 
@@ -429,7 +457,24 @@ public class ThreeDBStructureChooserQuerySource
           pdbEntry.setRetrievalUrl(urlStr);
         }
         pdbEntry.setProvider(typeColumn);
-        pdbEntry.setProviderPage(modelPage);
+        if (modelPage != null)
+        {
+          pdbEntry.setProviderPage(modelPage);
+        }
+        try
+        {
+          if (strucTfType!=null && !"".equals(strucTfType)) {
+            pdbEntry.setTempFacType(strucTfType);
+          }
+          if (strucTfType_v!=null && !"".equals(strucTfType_v)) {
+            pdbEntry.setTempFacTypeVersion(strucTfType_v);
+          }
+        } catch (Exception q)
+        {
+          Console.warn("Unknown filetype for 3D Beacons Model from: "
+                  + strucFormat + " - " + pdbIdStr + " - " + modelPage);
+        }
+
         selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
       }
       pdbEntriesToView[count++] = pdbEntry;
@@ -451,8 +496,9 @@ public class ThreeDBStructureChooserQuerySource
    * @return
    */
 
-  public String buildPDBFTSQueryFor(FTSRestResponse upResponse)
+  public List<String> buildPDBFTSQueryFor(FTSRestResponse upResponse)
   {
+    List<String> ftsQueries = new ArrayList<String>();
     Set<String> pdbIds = new HashSet<String>();
     int idx_modelId = getLastFTSRequest().getFieldIndex("Model id");
     int idx_provider = getLastFTSRequest().getFieldIndex("Provider");
@@ -465,7 +511,25 @@ 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;
   }
 
   /**
@@ -475,34 +539,53 @@ public class ThreeDBStructureChooserQuerySource
    * @param upResponse
    * @return FTSRestResponse via PDBStructureChooserQuerySource
    */
-  public FTSRestResponse fetchStructuresMetaDataFor(
+  public List<FTSRestResponse> fetchStructuresMetaDataFor(
           PDBStructureChooserQuerySource pdbquery,
           FTSRestResponse upResponse) throws Exception
   {
-
-    String pdb_Query = buildPDBFTSQueryFor(upResponse);
-    if (pdb_Query.length() == 0)
+    List<String> pdb_Queries = buildPDBFTSQueryFor(upResponse);
+    if (pdb_Queries.size() == 0)
     {
       return null;
     }
-    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 + ")");
+    List<FTSRestResponse> results = new ArrayList<FTSRestResponse>();
+
+    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);
+      }
 
-    resultList = pdbquery.executePDBFTSRestRequest(pdbRequest);
+    }
 
-    lastPdbRequest = pdbRequest;
-    return resultList;
+    return results;
   }
 
   public FTSRestResponse joinResponses(FTSRestResponse upResponse,
-          FTSRestResponse pdbResponse)
+          List<FTSRestResponse> pdbResponses)
   {
     boolean hasPdbResp = lastPdbRequest != null;
 
@@ -522,18 +605,21 @@ public class ThreeDBStructureChooserQuerySource
       {
         if (!hasPdbResp)
         {
-          System.out.println(
+          jalview.bin.Console.outPrintln(
                   "Warning: seems like we couldn't get to the PDBe search interface.");
         }
         else
         {
-          for (final FTSData pdbrow : pdbResponse.getSearchSummary())
+          for (final FTSRestResponse pdbResponse : pdbResponses)
           {
-            String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
-            if (id.equalsIgnoreCase(pdbid))
+            for (final FTSData pdbrow : pdbResponse.getSearchSummary())
             {
-              row.getSummaryData()[tdbTitle_idx] = pdbrow
-                      .getSummaryData()[pdbTitle_idx];
+              String pdbid = (String) pdbrow.getSummaryData()[pdbIdx];
+              if (id.equalsIgnoreCase(pdbid))
+              {
+                row.getSummaryData()[tdbTitle_idx] = pdbrow
+                        .getSummaryData()[pdbTitle_idx];
+              }
             }
           }
         }