JAL-3746 JAL-3841 new README and finalising 2.11.2.0 release notes

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

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index f168413..cbd59b1 100644 (file)
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -1,5 +1,27 @@
+/*
+ * 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;
 
@@ -37,7 +59,6 @@ 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
@@ -48,6 +69,8 @@ public class StructureImportSettings
    * Determines the parser used for parsing PDB format file. Possible options
    * are : JMolParser|JalveiwParser
    */
+  private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
+
   public static void addSettings(boolean addAlignmentAnnotations,
           boolean processSecStr, boolean externalSecStr)
   {
@@ -100,17 +123,33 @@ public class StructureImportSettings
     StructureImportSettings.showSeqFeatures = showSeqFeatures;
   }
 
-  public static String getDefaultStructureFileFormat()
+  public static PDBEntry.Type getDefaultStructureFileFormat()
   {
-    return defaultStructureFileFormat.toString();
+    return defaultStructureFileFormat;
   }
 
   public static void setDefaultStructureFileFormat(
           String defaultStructureFileFormat)
   {
     StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
-            .valueOf(defaultStructureFileFormat.toUpperCase());
+            .valueOf(defaultStructureFileFormat.toUpperCase(Locale.ROOT));
   }
 
+  public static String getDefaultPDBFileParser()
+  {
+    return defaultPDBFileParser.toString();
+  }
+
+  public static void setDefaultPDBFileParser(
+          StructureParser defaultPDBFileParser)
+  {
+    StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
+  }
+
+  public static void setDefaultPDBFileParser(String defaultPDBFileParser)
+  {
+    StructureImportSettings.defaultPDBFileParser = StructureParser
+            .valueOf(defaultPDBFileParser.toUpperCase(Locale.ROOT));
+  }
 
 }