JAL-3210 Barebones gradle/buildship/eclipse. See README

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

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