Merge branch 'apifix/JAL-1926_JAL-2106' into develop

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

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 38aa55f..6f16a6e 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -20,8 +20,8 @@
  */
 package jalview.bin;
 
-import jalview.datamodel.DBRefSource;
-import jalview.ws.dbsources.Pdb;
+import jalview.datamodel.PDBEntry;
+import jalview.structure.StructureImportSettings;
 import jalview.ws.dbsources.das.api.DasSourceRegistryI;
 import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
 import jalview.ws.sifts.SiftsSettings;
@@ -227,8 +227,15 @@ 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
+   */
+  private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
+          .toString();
 
-  private final static String DEFAULT_STRUCTURE_FORMAT = DBRefSource.PDB;
+  private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+          .toString();
 
   /**
    * Initialises the Jalview Application Log
@@ -426,8 +433,14 @@ public class Cache
     System.out
             .println("Jalview Version: " + codeVersion + codeInstallation);
 
-    Pdb.setCurrentDefaultFormat(jalview.bin.Cache.getDefault(
+    StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
+            .getDefault(
             "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
+    StructureImportSettings
+            .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+                    "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
+    StructureImportSettings.setProcessHETATMs(jalview.bin.Cache.getDefault(
+            "PROCESS_HETATM", false));
     // jnlpVersion will be null if we're using InstallAnywhere
     // Dont do this check if running in headless mode
     if (jnlpVersion == null