X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fstructure%2FStructureImportSettings.java;h=9edcda02e0a6e54d487cbf9819ce5a0e1b8af06b;hb=6c03a34084889aebdb94a8653a9955f8efd0da88;hp=82b5f693c47005220be281ce1cf6810a8d04a229;hpb=dde2abe99b75477853a09b4668a6b46cc14bc3ef;p=jalview.git

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index 82b5f69..9edcda0 100644
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -1,5 +1,32 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ * 
+ * This file is part of Jalview.
+ * 
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License 
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *  
+ * Jalview is distributed in the hope that it will be useful, but 
+ * WITHOUT ANY WARRANTY; without even the implied warranty 
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR 
+ * PURPOSE.  See the GNU General Public License for more details.
+ * 
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
 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;
 
@@ -10,13 +37,23 @@ import jalview.datamodel.PDBEntry.Type;
  * @author tcofoegbu
  *
  */
-public class StructureImportSettings
+public class StructureImportSettings implements ApplicationSingletonI
 {
+  private StructureImportSettings()
+  {
+    // private singleton
+  }
+
+  private static StructureImportSettings getInstance()
+  {
+    return 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
@@ -28,7 +65,7 @@ public class StructureImportSettings
    * 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;
 
@@ -37,97 +74,98 @@ public class StructureImportSettings
     JMOL_PARSER, JALVIEW_PARSER
   }
 
-
   /**
    * 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; // TODO 2.12 should be mmCIF now ?
 
   /**
    * 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 String getDefaultStructureFileFormat()
+  public static PDBEntry.Type getDefaultStructureFileFormat()
   {
-    return defaultStructureFileFormat.toString();
+    return getInstance().defaultStructureFileFormat;
   }
 
   public static void setDefaultStructureFileFormat(
           String defaultStructureFileFormat)
   {
-    StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
-            .valueOf(defaultStructureFileFormat.toUpperCase());
+    getInstance().defaultStructureFileFormat = PDBEntry.Type
+            .valueOf(defaultStructureFileFormat.toUpperCase(Locale.ROOT));
   }
 
   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
-            .valueOf(defaultPDBFileParser.toUpperCase());
+    getInstance().defaultPDBFileParser = StructureParser
+            .valueOf(defaultPDBFileParser.toUpperCase(Locale.ROOT));
   }
 
 }