Merge commit 'alpha/update_2_12_for_2_11_2_series_merge^2' into HEAD

[jalview.git] / src / jalview / structure / StructureImportSettings.java

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index b5672ab..0489e1f 100644 (file)
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -20,8 +20,13 @@
  */
 package jalview.structure;
 
+
+import java.util.Locale;
+
 import jalview.bin.ApplicationSingletonProvider;
 import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
+
+
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 
@@ -34,7 +39,6 @@ import jalview.datamodel.PDBEntry.Type;
  */
 public class StructureImportSettings implements ApplicationSingletonI
 {
-
   private StructureImportSettings()
   {
     // private singleton
@@ -45,7 +49,6 @@ public class StructureImportSettings implements ApplicationSingletonI
     return (StructureImportSettings) ApplicationSingletonProvider
             .getInstance(StructureImportSettings.class);
   }
-
   /**
    * set to true to add derived sequence annotations (temp factor read from
    * file, or computed secondary structure) to the alignment
@@ -56,7 +59,7 @@ public class StructureImportSettings implements ApplicationSingletonI
    * Set true to predict secondary structure (using JMol for protein, Annotate3D
    * for RNA)
    */
-  private boolean processSecStr = false;
+  private static boolean processSecStr = false;
 
   /**
    * Set true (with predictSecondaryStructure=true) to predict secondary
@@ -64,7 +67,7 @@ public class StructureImportSettings implements ApplicationSingletonI
    */
   private boolean externalSecondaryStructure = false;
 
-  private boolean showSeqFeatures = true;
+  private static boolean showSeqFeatures = true;
 
   public enum StructureParser
   {
@@ -75,7 +78,7 @@ public class StructureImportSettings implements ApplicationSingletonI
    * Determines the default file format for structure files to be downloaded
    * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
    */
-  private PDBEntry.Type defaultStructureFileFormat = Type.PDB;
+  private PDBEntry.Type defaultStructureFileFormat = Type.PDB; // TODO 2.12 should be mmCIF now ?
 
   /**
    * Determines the parser used for parsing PDB format file. Possible options
@@ -145,7 +148,7 @@ public class StructureImportSettings implements ApplicationSingletonI
           String defaultStructureFileFormat)
   {
     getInstance().defaultStructureFileFormat = PDBEntry.Type
-            .valueOf(defaultStructureFileFormat.toUpperCase());
+            .valueOf(defaultStructureFileFormat.toUpperCase(Locale.ROOT));
   }
 
   public static String getDefaultPDBFileParser()
@@ -162,7 +165,7 @@ public class StructureImportSettings implements ApplicationSingletonI
   public static void setDefaultPDBFileParser(String defaultPDBFileParser)
   {
     getInstance().defaultPDBFileParser = StructureParser
-            .valueOf(defaultPDBFileParser.toUpperCase());
+            .valueOf(defaultPDBFileParser.toUpperCase(Locale.ROOT));
   }
 
 }