JAL-629 Change all stdout and stderr output to use Console.outPrintln and Console...

[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 175ad77..e32ba50 100644 (file)
--- a/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/ThreeDBStructureChooserQuerySource.java
@@ -92,6 +92,7 @@ public class ThreeDBStructureChooserQuerySource
    * @return the built query string
    */
 
+  @Override
   public String buildQuery(SequenceI seq)
   {
     List<DBRefEntry> refs = seq.getDBRefs();
@@ -181,6 +182,7 @@ public class ThreeDBStructureChooserQuerySource
    * @return
    * @throws Exception
    */
+  @Override
   public FTSRestResponse fetchStructuresMetaData(SequenceI seq,
           Collection<FTSDataColumnI> wantedFields,
           FilterOption selectedFilterOpt, boolean b) throws Exception
@@ -345,6 +347,7 @@ public class ThreeDBStructureChooserQuerySource
    * @return
    * @throws Exception
    */
+  @Override
   public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
           Collection<FTSData> collectedResults,
           Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
@@ -450,7 +453,10 @@ public class ThreeDBStructureChooserQuerySource
           pdbEntry.setRetrievalUrl(urlStr);
         }
         pdbEntry.setProvider(typeColumn);
-        pdbEntry.setProviderPage(modelPage);
+        if (modelPage != null)
+        {
+          pdbEntry.setProviderPage(modelPage);
+        }
         selectedSeq.getDatasetSequence().addPDBId(pdbEntry);
       }
       pdbEntriesToView[count++] = pdbEntry;
@@ -543,6 +549,11 @@ public class ThreeDBStructureChooserQuerySource
       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)
@@ -576,7 +587,7 @@ 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