JAL-3691 automatic insertion of Locale.ROOT to toUpperCase() and toLowerCase() and...

[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 45c58cf..1aad2e0 100644 (file)
--- a/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/StructureChooserQuerySource.java
@@ -1,5 +1,7 @@
 package jalview.gui.structurechooser;
 
+import java.util.Locale;
+
 import java.util.Collection;
 import java.util.List;
 import java.util.Objects;
@@ -42,7 +44,7 @@ public abstract class StructureChooserQuerySource
 
   public static StructureChooserQuerySource getPDBfts()
   {
-          return new PDBStructureChooserQuerySource();
+    return new PDBStructureChooserQuerySource();
   }
 
   public static StructureChooserQuerySource getTDBfts()
@@ -65,7 +67,6 @@ public abstract class StructureChooserQuerySource
     return docFieldPrefs;
   }
 
-
   /**
    * Builds a query string for a given sequences using its DBRef entries
    * 
@@ -75,7 +76,6 @@ public abstract class StructureChooserQuerySource
    */
 
   public abstract String buildQuery(SequenceI seq);
-  
 
   /**
    * Remove the following special characters from input string +, -, &, !, (, ),
@@ -110,7 +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))
@@ -167,7 +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 discoveredStructuresSet
+   *          - existing set of entries - allows client side selection
    * @param wantedFields
    *          - fields to retrieve
    * @param selectedFilterOpt
@@ -178,7 +179,8 @@ public abstract class StructureChooserQuerySource
    * @throws Exception
    */
   public abstract FTSRestResponse selectFirstRankedQuery(SequenceI seq,
-          Collection<FTSData> discoveredStructuresSet, Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
+          Collection<FTSData> discoveredStructuresSet,
+          Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
           boolean b) throws Exception;
 
   /**
@@ -200,15 +202,17 @@ public abstract class StructureChooserQuerySource
 
   /**
    * @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
+   *          - 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);
+  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
    */
@@ -216,34 +220,39 @@ public abstract class StructureChooserQuerySource
           SequenceI[] selectedSeqs)
   {
     ThreeDBStructureChooserQuerySource tdbSource = new ThreeDBStructureChooserQuerySource();
-    boolean hasUniprot=false,hasCanonical=false;
-    boolean hasNA=false,hasProtein=false;
-    int protWithoutUni=0;
+    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());
+        int refsAvailable = ThreeDBStructureChooserQuerySource
+                .checkUniprotRefs(seq.getDBRefs());
         if (refsAvailable > -2)
         {
           if (refsAvailable > -1)
+          {
             hasCanonical = true;
+          } else {
+            protWithoutCanon++;
+          }
+          hasUniprot = true;
+        } else {
+          protWithoutUni++;
+          
         }
-        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
+    // some uniprot no canonicals: defer to PDB, user can optionally fetch
     //
-    if (hasProtein && hasCanonical && !hasNA)
+    if (hasProtein && hasCanonical && !hasNA && protWithoutCanon == 0 && protWithoutUni == 0)
+
     {
       return tdbSource;
     }
@@ -251,17 +260,17 @@ public abstract class StructureChooserQuerySource
   }
 
   /**
-   * some filter options may mean the original query needs to be executed again. 
+   * 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
+
+  }
+}
\ No newline at end of file