Merge branch 'develop' into releases/Release_2_11_2_Branch

[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 9861b1a..1aad2e0 100644 (file)
--- a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
@@ -1,29 +1,25 @@
 package jalview.gui.structurechooser;
 
+import java.util.Locale;
+
 import java.util.Collection;
-import java.util.HashSet;
-import java.util.LinkedHashSet;
 import java.util.List;
 import java.util.Objects;
-import java.util.Set;
 import java.util.Vector;
 
 import javax.swing.JTable;
 import javax.swing.table.TableModel;
 
 import jalview.datamodel.DBRefEntry;
-import jalview.datamodel.DBRefSource;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.SequenceI;
 import jalview.fts.api.FTSData;
 import jalview.fts.api.FTSDataColumnI;
 import jalview.fts.api.FTSRestClientI;
 import jalview.fts.core.FTSDataColumnPreferences;
-import jalview.fts.core.FTSDataColumnPreferences.PreferenceSource;
 import jalview.fts.core.FTSRestRequest;
 import jalview.fts.core.FTSRestResponse;
-import jalview.fts.service.pdb.PDBFTSRestClient;
-import jalview.jbgui.GStructureChooser.FilterOption;
+import jalview.jbgui.FilterOption;
 
 /**
  * logic for querying sources of structural data for structures of sequences
@@ -34,9 +30,6 @@ import jalview.jbgui.GStructureChooser.FilterOption;
  */
 public abstract class StructureChooserQuerySource
 {
-  protected FTSRestRequest lastPdbRequest;
-
-  protected FTSRestClientI pdbRestClient;
 
   protected FTSDataColumnPreferences docFieldPrefs;
 
@@ -51,7 +44,7 @@ public abstract class StructureChooserQuerySource
 
   public static StructureChooserQuerySource getPDBfts()
   {
-          return new PDBStructureChooserQuerySource();
+    return new PDBStructureChooserQuerySource();
   }
 
   public static StructureChooserQuerySource getTDBfts()
@@ -74,7 +67,6 @@ public abstract class StructureChooserQuerySource
     return docFieldPrefs;
   }
 
-
   /**
    * Builds a query string for a given sequences using its DBRef entries
    * 
@@ -84,7 +76,6 @@ public abstract class StructureChooserQuerySource
    */
 
   public abstract String buildQuery(SequenceI seq);
-  
 
   /**
    * Remove the following special characters from input string +, -, &, !, (, ),
@@ -119,7 +110,7 @@ public abstract class StructureChooserQuerySource
     {
       return false;
     }
-    seqName = seqName.toLowerCase();
+    seqName = seqName.toLowerCase(Locale.ROOT);
     for (String ignoredEntry : ignoreList.split(","))
     {
       if (seqName.contains(ignoredEntry))
@@ -176,6 +167,8 @@ 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
@@ -186,6 +179,7 @@ public abstract class StructureChooserQuerySource
    * @throws Exception
    */
   public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+          Collection<FTSData> discoveredStructuresSet,
           Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
           boolean b) throws Exception;
 
@@ -197,11 +191,86 @@ 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);
 
+  /**
+   * @param VIEWS_FILTER
+   *          - a String key that can be used by the caller to tag the returned
+   *          filter options to distinguish them in a collection
+   * @return list of FilterOption - convention is that the last one in the list
+   *         will be constructed with 'addSeparator==true'
+   */
+  public abstract List<FilterOption> getAvailableFilterOptions(
+          String VIEWS_FILTER);
+
+  /**
+   * 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;
+    int protWithoutCanon = 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;
+          } else {
+            protWithoutCanon++;
+          }
+          hasUniprot = true;
+        } else {
+          protWithoutUni++;
+          
+        }
+      }
+    }
+    //
+    // logic: all canonicals - no fetchdb
+    // some uniprot no canonicals: defer to PDB, user can optionally fetch
+    //
+    if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0 && protWithoutUni == 0)
+
+    {
+      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