Merge branch 'releases/Release_2_11_3_Branch'

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

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index f5963de..22ecdc7 100644 (file)
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -1,7 +1,30 @@
+/*
+ * 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.datamodel.PDBEntry;
 import jalview.datamodel.PDBEntry.Type;
+import jalview.util.MessageManager;
 
 /**
  * bean holding settings for structure IO. TODO: tests for validation of values
@@ -37,6 +60,17 @@ public class StructureImportSettings
     JMOL_PARSER, JALVIEW_PARSER
   }
 
+  public static enum TFType
+  {
+    DEFAULT, PLDDT;
+
+    @Override
+    public String toString()
+    {
+      return MessageManager.getString(
+              "label.tftype_" + this.name().toLowerCase(Locale.ROOT));
+    }
+  }
 
   /**
    * Determines the default file format for structure files to be downloaded
@@ -49,6 +83,9 @@ public class StructureImportSettings
    * are : JMolParser|JalveiwParser
    */
   private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
+
+  private static TFType temperatureFactorType;
+
   public static void addSettings(boolean addAlignmentAnnotations,
           boolean processSecStr, boolean externalSecStr)
   {
@@ -63,6 +100,11 @@ public class StructureImportSettings
     return visibleChainAnnotation;
   }
 
+  public static void setTemperatureFactorType(TFType t)
+  {
+    StructureImportSettings.temperatureFactorType = t;
+  }
+
   public static void setVisibleChainAnnotation(
           boolean visibleChainAnnotation)
   {
@@ -110,7 +152,7 @@ public class StructureImportSettings
           String defaultStructureFileFormat)
   {
     StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
-            .valueOf(defaultStructureFileFormat.toUpperCase());
+            .valueOf(defaultStructureFileFormat.toUpperCase(Locale.ROOT));
   }
 
   public static String getDefaultPDBFileParser()
@@ -127,7 +169,12 @@ public class StructureImportSettings
   public static void setDefaultPDBFileParser(String defaultPDBFileParser)
   {
     StructureImportSettings.defaultPDBFileParser = StructureParser
-            .valueOf(defaultPDBFileParser.toUpperCase());
+            .valueOf(defaultPDBFileParser.toUpperCase(Locale.ROOT));
+  }
+
+  public static TFType getTemperatureFactorType()
+  {
+    return temperatureFactorType;
   }
 
 }