X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureImportSettings.java;h=9662fee4f916e994f01921f423d6aa500f2acf40;hb=8193add590cf13e5bdb422347473f1d96755c4f3;hp=388ccbdfc3e865cfa475e70617d54ed6eb57468f;hpb=82a6c8e2e25b7534168b68b2c89b9cf195f815a5;p=jalview.git

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index 388ccbd..9662fee 100644
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -1,3 +1,23 @@
+/*
+ * 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 jalview.datamodel.PDBEntry;
@@ -5,6 +25,7 @@ import jalview.datamodel.PDBEntry.Type;
 
 /**
  * bean holding settings for structure IO. TODO: tests for validation of values
+ * TODO: tests for race conditions (all fields are static, is that correct ?)
  * 
  * @author tcofoegbu
  *
@@ -31,14 +52,11 @@ public class StructureImportSettings
 
   private static boolean showSeqFeatures = true;
 
-  private static boolean processHETATMs = false;
-
   public enum StructureParser
   {
     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
@@ -50,6 +68,7 @@ public class StructureImportSettings
    * are : JMolParser|JalveiwParser
    */
   private static StructureParser defaultPDBFileParser = StructureParser.JMOL_PARSER;
+
   public static void addSettings(boolean addAlignmentAnnotations,
           boolean processSecStr, boolean externalSecStr)
   {
@@ -102,26 +121,16 @@ 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);
-  }
-
-  public static boolean isProcessHETATMs()
-  {
-    return processHETATMs;
-  }
-
-  public static void setProcessHETATMs(boolean processHETATMs)
-  {
-    StructureImportSettings.processHETATMs = processHETATMs;
+            .valueOf(defaultStructureFileFormat.toUpperCase());
   }
 
   public static String getDefaultPDBFileParser()
@@ -138,7 +147,7 @@ public class StructureImportSettings
   public static void setDefaultPDBFileParser(String defaultPDBFileParser)
   {
     StructureImportSettings.defaultPDBFileParser = StructureParser
-            .valueOf(defaultPDBFileParser);
+            .valueOf(defaultPDBFileParser.toUpperCase());
   }
 
 }