Merge branch 'Jalview-JS/develop' into merge_js_develop

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

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index 9662fee..b5672ab 100644 (file)
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -20,6 +20,8 @@
  */
 package jalview.structure;
 
+import jalview.bin.ApplicationSingletonProvider;
+import jalview.bin.ApplicationSingletonProvider.ApplicationSingletonI;
 import jalview.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
 
@@ -30,27 +32,39 @@ import jalview.datamodel.PDBEntry.Type;
  * @author tcofoegbu
  *
  */
-public class StructureImportSettings
+public class StructureImportSettings implements ApplicationSingletonI
 {
+
+  private StructureImportSettings()
+  {
+    // private singleton
+  }
+
+  private static StructureImportSettings getInstance()
+  {
+    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
    */
-  private static boolean visibleChainAnnotation = false;
+  private boolean visibleChainAnnotation = false;
 
   /**
    * Set true to predict secondary structure (using JMol for protein, Annotate3D
    * for RNA)
    */
-  private static boolean processSecStr = false;
+  private boolean processSecStr = false;
 
   /**
    * Set true (with predictSecondaryStructure=true) to predict secondary
    * structure using an external service (currently Annotate3D for RNA only)
    */
-  private static boolean externalSecondaryStructure = false;
+  private boolean externalSecondaryStructure = false;
 
-  private static boolean showSeqFeatures = true;
+  private boolean showSeqFeatures = true;
 
   public enum StructureParser
   {
@@ -61,92 +75,93 @@ public class StructureImportSettings
    * Determines the default file format for structure files to be downloaded
    * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
    */
-  private static PDBEntry.Type defaultStructureFileFormat = Type.PDB;
+  private PDBEntry.Type defaultStructureFileFormat = Type.PDB;
 
   /**
    * Determines the parser used for parsing PDB format file. Possible options
    * are : JMolParser|JalveiwParser
    */
-  private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
+  private StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
 
   public static void addSettings(boolean addAlignmentAnnotations,
           boolean processSecStr, boolean externalSecStr)
   {
-    StructureImportSettings.visibleChainAnnotation = addAlignmentAnnotations;
-    StructureImportSettings.processSecStr = processSecStr;
-    StructureImportSettings.externalSecondaryStructure = externalSecStr;
-    StructureImportSettings.showSeqFeatures = true;
+    StructureImportSettings s = getInstance();
+    s.visibleChainAnnotation = addAlignmentAnnotations;
+    s.processSecStr = processSecStr;
+    s.externalSecondaryStructure = externalSecStr;
+    s.showSeqFeatures = true;
   }
 
   public static boolean isVisibleChainAnnotation()
   {
-    return visibleChainAnnotation;
+    return getInstance().visibleChainAnnotation;
   }
 
   public static void setVisibleChainAnnotation(
           boolean visibleChainAnnotation)
   {
-    StructureImportSettings.visibleChainAnnotation = visibleChainAnnotation;
+    getInstance().visibleChainAnnotation = visibleChainAnnotation;
   }
 
   public static boolean isProcessSecondaryStructure()
   {
-    return processSecStr;
+    return getInstance().processSecStr;
   }
 
   public static void setProcessSecondaryStructure(
           boolean processSecondaryStructure)
   {
-    StructureImportSettings.processSecStr = processSecondaryStructure;
+    getInstance().processSecStr = processSecondaryStructure;
   }
 
   public static boolean isExternalSecondaryStructure()
   {
-    return externalSecondaryStructure;
+    return getInstance().externalSecondaryStructure;
   }
 
   public static void setExternalSecondaryStructure(
           boolean externalSecondaryStructure)
   {
-    StructureImportSettings.externalSecondaryStructure = externalSecondaryStructure;
+    getInstance().externalSecondaryStructure = externalSecondaryStructure;
   }
 
   public static boolean isShowSeqFeatures()
   {
-    return showSeqFeatures;
+    return getInstance().showSeqFeatures;
   }
 
   public static void setShowSeqFeatures(boolean showSeqFeatures)
   {
-    StructureImportSettings.showSeqFeatures = showSeqFeatures;
+    getInstance().showSeqFeatures = showSeqFeatures;
   }
 
   public static PDBEntry.Type getDefaultStructureFileFormat()
   {
-    return defaultStructureFileFormat;
+    return getInstance().defaultStructureFileFormat;
   }
 
   public static void setDefaultStructureFileFormat(
           String defaultStructureFileFormat)
   {
-    StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
+    getInstance().defaultStructureFileFormat = PDBEntry.Type
             .valueOf(defaultStructureFileFormat.toUpperCase());
   }
 
   public static String getDefaultPDBFileParser()
   {
-    return defaultPDBFileParser.toString();
+    return getInstance().defaultPDBFileParser.toString();
   }
 
   public static void setDefaultPDBFileParser(
           StructureParser defaultPDBFileParser)
   {
-    StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
+    getInstance().defaultPDBFileParser = defaultPDBFileParser;
   }
 
   public static void setDefaultPDBFileParser(String defaultPDBFileParser)
   {
-    StructureImportSettings.defaultPDBFileParser = StructureParser
+    getInstance().defaultPDBFileParser = StructureParser
             .valueOf(defaultPDBFileParser.toUpperCase());
   }