X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fstructure%2FStructureImportSettings.java;h=9662fee4f916e994f01921f423d6aa500f2acf40;hb=9c16178c0601ea3169d7a5d5d623dafa45c54f85;hp=ed5342541f698237c46cdd617bc8836e7b060b51;hpb=08c202dd3ef0f34bde305c11da9eec03520174dc;p=jalview.git

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index ed53425..9662fee 100644
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -1,6 +1,35 @@
+/*
+ * 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;
+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
+ *
+ */
 public class StructureImportSettings
 {
   /**
@@ -23,14 +52,22 @@ public class StructureImportSettings
 
   private static boolean showSeqFeatures = true;
 
-  private static boolean processHETATMs = false;
-
-  public enum StructureFormat
+  public enum StructureParser
   {
-    PDB, MMCIF
-  };
+    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 static StructureFormat currentDefaultFormat = StructureFormat.PDB;
+  /**
+   * 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)
@@ -84,25 +121,33 @@ public class StructureImportSettings
     StructureImportSettings.showSeqFeatures = showSeqFeatures;
   }
 
-  public static String getCurrentDefaultFormat()
+  public static PDBEntry.Type getDefaultStructureFileFormat()
+  {
+    return defaultStructureFileFormat;
+  }
+
+  public static void setDefaultStructureFileFormat(
+          String defaultStructureFileFormat)
   {
-    return currentDefaultFormat.toString();
+    StructureImportSettings.defaultStructureFileFormat = PDBEntry.Type
+            .valueOf(defaultStructureFileFormat.toUpperCase());
   }
 
-  public static void setCurrentDefaultFormat(String currentDefaultFormat)
+  public static String getDefaultPDBFileParser()
   {
-    StructureImportSettings.currentDefaultFormat = StructureFormat
-            .valueOf(currentDefaultFormat);
+    return defaultPDBFileParser.toString();
   }
 
-  public static boolean isProcessHETATMs()
+  public static void setDefaultPDBFileParser(
+          StructureParser defaultPDBFileParser)
   {
-    return processHETATMs;
+    StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
   }
 
-  public static void setProcessHETATMs(boolean processHETATMs)
+  public static void setDefaultPDBFileParser(String defaultPDBFileParser)
   {
-    StructureImportSettings.processHETATMs = processHETATMs;
+    StructureImportSettings.defaultPDBFileParser = StructureParser
+            .valueOf(defaultPDBFileParser.toUpperCase());
   }
 
 }