JAL-1919 set default structure file format to mmCIF, refactored some StructureImportS...

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

diff --git a/src/jalview/structure/StructureImportSettings.java b/src/jalview/structure/StructureImportSettings.java
index b23fd53..4c06e0f 100644 (file)
--- a/src/jalview/structure/StructureImportSettings.java
+++ b/src/jalview/structure/StructureImportSettings.java
@@ -26,8 +26,25 @@ public class StructureImportSettings
 
   private static boolean processHETATMs = false;
 
-  private static String currentDefaultFormat = DBRefSource.PDB;
+  public static final String JMOL_PARSER = "JMolParser";
 
+  public static final String JALVIEW_PARSER = "JalViewParser";
+
+  public static final String MMCIF = "mmCIF";
+
+  public static final String PDB = "PDB";
+
+  /**
+   * Determines the default file format for structure files to be downloaded
+   * from the PDB sequence fetcher. Possible options include: PDB|mmCIF
+   */
+  private static String defaultStructureFileFormat = DBRefSource.PDB;
+
+  /**
+   * Determines the parser used for parsing PDB format file. Possible options
+   * are : JMolParser|JalveiwParser
+   */
+  private static String defaultPDBFileParser = JMOL_PARSER;
   public static void addSettings(boolean addAlignmentAnnotations,
           boolean predictSecStr, boolean externalSecStr)
   {
@@ -80,14 +97,15 @@ public class StructureImportSettings
     StructureImportSettings.showSeqFeatures = showSeqFeatures;
   }
 
-  public static String getCurrentDefaultFormat()
+  public static String getDefaultStructureFileFormat()
   {
-    return currentDefaultFormat;
+    return defaultStructureFileFormat;
   }
 
-  public static void setCurrentDefaultFormat(String currentDefaultFormat)
+  public static void setDefaultStructureFileFormat(
+          String defaultStructureFileFormat)
   {
-    StructureImportSettings.currentDefaultFormat = currentDefaultFormat;
+    StructureImportSettings.defaultStructureFileFormat = defaultStructureFileFormat;
   }
 
   public static boolean isProcessHETATMs()
@@ -100,4 +118,14 @@ public class StructureImportSettings
     StructureImportSettings.processHETATMs = processHETATMs;
   }
 
+  public static String getDefaultPDBFileParser()
+  {
+    return defaultPDBFileParser;
+  }
+
+  public static void setDefaultPDBFileParser(String defaultPDBFileParser)
+  {
+    StructureImportSettings.defaultPDBFileParser = defaultPDBFileParser;
+  }
+
 }