JAL-3829 insert title for structures from PDBe

[jalview.git] / src / jalview / gui / structurechooser / ThreeDBStructureChooserQuerySource.java

diff --git a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
index e5f96be..2c6afe8 100644 (file)
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -157,9 +157,24 @@ public class ThreeDBStructureChooserQuerySource
     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;
   }
 
+  PDBStructureChooserQuerySource pdbQuerySource=null;
+  private PDBStructureChooserQuerySource getPDBQuerySource()
+  {
+    if (pdbQuerySource==null)
+    {
+      pdbQuerySource = new PDBStructureChooserQuerySource();
+    }
+    return pdbQuerySource;
+  }
+
   private FTSRestRequest getTDBeaconsRequest(SequenceI seq,
           Collection<FTSDataColumnI> wantedFields)
   {
@@ -369,27 +384,31 @@ 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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