JAL-3829 TDBeacons fetcher needs a sequence with at least one canonical uniprot accession

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

diff --git a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
index 733e6fc..45c58cf 100644 (file)
--- a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
@@ -28,9 +28,6 @@ import jalview.jbgui.FilterOption;
  */
 public abstract class StructureChooserQuerySource
 {
-  protected FTSRestRequest lastPdbRequest;
-
-  protected FTSRestClientI pdbRestClient;
 
   protected FTSDataColumnPreferences docFieldPrefs;
 
@@ -170,6 +167,7 @@ public abstract class StructureChooserQuerySource
    * 
    * @param seq
    *          - seq to generate a query for
+   * @param discoveredStructuresSet - existing set of entries - allows client side selection
    * @param wantedFields
    *          - fields to retrieve
    * @param selectedFilterOpt
@@ -180,7 +178,7 @@ public abstract class StructureChooserQuerySource
    * @throws Exception
    */
   public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
-          Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+          Collection<FTSData> discoveredStructuresSet, Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
           boolean b) throws Exception;
 
   /**
@@ -191,10 +189,12 @@ public abstract class StructureChooserQuerySource
   public TableModel getTableModel(
           Collection<FTSData> discoveredStructuresSet)
   {
-    return FTSRestResponse.getTableModel(lastPdbRequest,
+    return FTSRestResponse.getTableModel(getLastFTSRequest(),
             discoveredStructuresSet);
   }
 
+  protected abstract FTSRestRequest getLastFTSRequest();
+
   public abstract PDBEntry[] collectSelectedRows(JTable restable,
           int[] selectedRows, List<SequenceI> selectedSeqsToView);
 
@@ -206,4 +206,62 @@ public abstract class StructureChooserQuerySource
    *         will be constructed with 'addSeparator==true'
    */
   public abstract List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER);
-}
\ No newline at end of file
+
+  /**
+   * construct a structure chooser query source for the given set of sequences
+   * @param selectedSeqs
+   * @return PDBe or 3DB query source
+   */
+  public static StructureChooserQuerySource getQuerySourceFor(
+          SequenceI[] selectedSeqs)
+  {
+    ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
+    boolean hasUniprot=false,hasCanonical=false;
+    boolean hasNA=false,hasProtein=false;
+    int protWithoutUni=0;
+    for (SequenceI seq : selectedSeqs)
+    {
+      hasNA |= !seq.isProtein();
+      hasProtein |= seq.isProtein();
+      if (seq.isProtein())
+      {
+        int refsAvailable = ThreeDBStructureChooserQuerySource.checkUniprotRefs(seq.getDBRefs());
+        if (refsAvailable > -2)
+        {
+          if (refsAvailable > -1)
+            hasCanonical = true;
+        }
+        hasUniprot = true;
+      }
+      else
+      {
+        protWithoutUni++;
+      }
+    }
+    //
+    // logic: all canonicals - no fetchdb
+    // some uniprot no canonicals: prompt do fetchDb for remaining
+    // no uniprot but protein: offer 3d-beacons search
+    //
+    if (hasProtein && hasCanonical && !hasNA)
+    {
+      return tdbSource;
+    }
+    return new PDBStructureChooserQuerySource();
+  }
+
+  /**
+   * some filter options may mean the original query needs to be executed again. 
+   * @param selectedFilterOpt
+   * @return true if the fetchStructuresMetadata method needs to be called again
+   */
+  public abstract boolean needsRefetch(FilterOption selectedFilterOpt);
+
+  
+  
+  public void updateAvailableFilterOptions(String VIEWS_FILTER,
+          List<FilterOption> xtantOptions, Collection<FTSData> lastFTSData)
+  {
+    // TODO Auto-generated method stub
+    
+  }}
\ No newline at end of file