JAL-3438 spotless for 2.11.2.0

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

diff --git a/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java b/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
index 0f38e9f..da2c02b 100644 (file)
--- a/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
+++ b/src/jalview/gui/structurechooser/PDBStructureChooserQuerySource.java
@@ -1,5 +1,7 @@
 package jalview.gui.structurechooser;
 
+import java.util.Locale;
+
 import java.util.ArrayList;
 import java.util.Collection;
 import java.util.HashSet;
@@ -50,7 +52,6 @@ public class PDBStructureChooserQuerySource
 
   }
 
-
   /**
    * Builds a query string for a given sequences using its DBRef entries
    * 
@@ -78,7 +79,7 @@ public class PDBStructureChooserQuerySource
       {
         if (isValidSeqName(entry.getId()))
         {
-          String id = entry.getId().toLowerCase();
+          String id = entry.getId().toLowerCase(Locale.ROOT);
           queryBuilder.append("pdb_id:").append(id).append(" OR ");
           isPDBRefsFound = true;
           pdbids.add(id);
@@ -106,7 +107,7 @@ public class PDBStructureChooserQuerySource
           else if (dbRef.getSource().equalsIgnoreCase(DBRefSource.PDB))
           {
 
-            String id = getDBRefId(dbRef).toLowerCase();
+            String id = getDBRefId(dbRef).toLowerCase(Locale.ROOT);
             if (!pdbids.contains(id))
             {
               queryBuilder.append("pdb_id:").append(id).append(" OR ");
@@ -126,7 +127,7 @@ public class PDBStructureChooserQuerySource
     {
       String seqName = seq.getName();
       seqName = sanitizeSeqName(seqName);
-      String[] names = seqName.toLowerCase().split("\\|");
+      String[] names = seqName.toLowerCase(Locale.ROOT).split("\\|");
       for (String name : names)
       {
         // System.out.println("Found name : " + name);
@@ -185,7 +186,7 @@ public class PDBStructureChooserQuerySource
     {
       return false;
     }
-    seqName = seqName.toLowerCase();
+    seqName = seqName.toLowerCase(Locale.ROOT);
     for (String ignoredEntry : ignoreList.split(","))
     {
       if (seqName.contains(ignoredEntry))
@@ -235,25 +236,28 @@ public class PDBStructureChooserQuerySource
     lastPdbRequest = pdbRequest;
     return resultList;
   }
+
   public List<FilterOption> getAvailableFilterOptions(String VIEWS_FILTER)
   {
     List<FilterOption> filters = new ArrayList<FilterOption>();
     filters.add(new FilterOption(
-            MessageManager.getString("label.best_quality"),
-            "overall_quality", VIEWS_FILTER, false,this));
+            "PDBe " + MessageManager.getString("label.best_quality"),
+            "overall_quality", VIEWS_FILTER, false, this));
     filters.add(new FilterOption(
-            MessageManager.getString("label.best_resolution"),
-            "resolution", VIEWS_FILTER, false,this));
+            "PDBe " + MessageManager.getString("label.best_resolution"),
+            "resolution", VIEWS_FILTER, false, this));
     filters.add(new FilterOption(
-            MessageManager.getString("label.most_protein_chain"),
-            "number_of_protein_chains", VIEWS_FILTER, false,this));
+            "PDBe " + MessageManager.getString("label.most_protein_chain"),
+            "number_of_protein_chains", VIEWS_FILTER, false, this));
     filters.add(new FilterOption(
-            MessageManager.getString("label.most_bound_molecules"),
-            "number_of_bound_molecules", VIEWS_FILTER, false,this));
+            "PDBe " + MessageManager
+                    .getString("label.most_bound_molecules"),
+            "number_of_bound_molecules", VIEWS_FILTER, false, this));
     filters.add(new FilterOption(
-            MessageManager.getString("label.most_polymer_residues"),
-            "number_of_polymer_residues", VIEWS_FILTER, true,this));
-  
+            "PDBe " + MessageManager
+                    .getString("label.most_polymer_residues"),
+            "number_of_polymer_residues", VIEWS_FILTER, true, this));
+
     return filters;
   }
 
@@ -279,7 +283,8 @@ public class PDBStructureChooserQuerySource
    * @return
    * @throws Exception
    */
-  public FTSRestResponse selectFirstRankedQuery(SequenceI seq, Collection<FTSData> collectedResults,
+  public FTSRestResponse selectFirstRankedQuery(SequenceI seq,
+          Collection<FTSData> collectedResults,
           Collection<FTSDataColumnI> wantedFields, String fieldToFilterBy,
           boolean b) throws Exception
   {
@@ -314,33 +319,29 @@ public class PDBStructureChooserQuerySource
     return resultList;
   }
 
-
   @Override
   public PDBEntry[] collectSelectedRows(JTable restable, int[] selectedRows,
           List<SequenceI> selectedSeqsToView)
   {
-    int refSeqColIndex = restable.getColumn("Ref Sequence")
-            .getModelIndex();
+    int refSeqColIndex = restable.getColumn("Ref Sequence").getModelIndex();
 
-    PDBEntry[] pdbEntriesToView=new PDBEntry[selectedRows.length];
+    PDBEntry[] pdbEntriesToView = new PDBEntry[selectedRows.length];
     int count = 0;
-    int idColumnIndex=-1;
-    boolean fromTDB=true;
+    int idColumnIndex = -1;
+    boolean fromTDB = true;
     idColumnIndex = restable.getColumn("PDB Id").getModelIndex();
-    
+
     for (int row : selectedRows)
     {
-      
-      String pdbIdStr = restable.getValueAt(row,idColumnIndex)
-              .toString();
+
+      String pdbIdStr = restable.getValueAt(row, idColumnIndex).toString();
       SequenceI selectedSeq = (SequenceI) restable.getValueAt(row,
               refSeqColIndex);
       selectedSeqsToView.add(selectedSeq);
       PDBEntry pdbEntry = selectedSeq.getPDBEntry(pdbIdStr);
       if (pdbEntry == null)
       {
-        pdbEntry = getFindEntry(pdbIdStr,
-                selectedSeq.getAllPDBEntries());
+        pdbEntry = getFindEntry(pdbIdStr, selectedSeq.getAllPDBEntries());
       }
 
       if (pdbEntry == null)
@@ -355,15 +356,14 @@ public class PDBStructureChooserQuerySource
     return pdbEntriesToView;
   }
 
-
   @Override
   protected FTSRestRequest getLastFTSRequest()
   {
     return lastPdbRequest;
   }
 
-
-  public FTSRestResponse executePDBFTSRestRequest(FTSRestRequest pdbRequest) throws Exception
+  public FTSRestResponse executePDBFTSRestRequest(FTSRestRequest pdbRequest)
+          throws Exception
   {
     return pdbRestClient.executeRequest(pdbRequest);
   }