JAL-2383 restore PID colour threshold from project; enable/disable

[jalview.git] / src / jalview / bin / Cache.java

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 31dbeac..8412dab 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -228,7 +228,7 @@ public class Cache
   private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
 
   private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
-  
+
   /**
    * Allowed values are PDB or mmCIF
    */
@@ -444,8 +444,9 @@ public class Cache
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
     StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
-            .getDefault(
-"PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+            .getDefault("PDB_DOWNLOAD_FORMAT", PDB_DOWNLOAD_FORMAT));
+    StructureImportSettings
+            .setDefaultPDBFileParser(DEFAULT_PDB_FILE_PARSER);
     // StructureImportSettings
     // .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
     // "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
@@ -894,7 +895,7 @@ public class Cache
   {
     setProperty(property, jalview.util.Format.getHexString(colour));
   }
-  
+
   /**
    * Stores a formatted date in a jalview property, using a fixed locale.
    *