*/
package jalview.bin;
+import jalview.datamodel.PDBEntry;
import jalview.structure.StructureImportSettings;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
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 = "PDB";
+ private final static String DEFAULT_STRUCTURE_FORMAT = PDBEntry.Type.MMCIF
+ .toString();
+
+ private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.StructureParser.JMOL_PARSER
+ .toString();
/**
* Initialises the Jalview Application Log
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
- StructureImportSettings.setCurrentDefaultFormat(jalview.bin.Cache
+ StructureImportSettings.setDefaultStructureFileFormat(jalview.bin.Cache
.getDefault(
"DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
-
- StructureImportSettings.setProcessHETATMs(jalview.bin.Cache.getDefault(
- "PROCESS_HETATM", false));
+ StructureImportSettings
+ .setDefaultPDBFileParser(jalview.bin.Cache.getDefault(
+ "DEFAULT_PDB_FILE_PARSER", DEFAULT_PDB_FILE_PARSER));
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
if (jnlpVersion == null