*/
package jalview.bin;
-import jalview.datamodel.DBRefSource;
-import jalview.ws.dbsources.Pdb;
+import jalview.structure.StructureImportSettings;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
import jalview.ws.sifts.SiftsSettings;
private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
- private final static String DEFAULT_STRUCTURE_FORMAT = DBRefSource.MMCIF;
+ private final static String DEFAULT_STRUCTURE_FORMAT = StructureImportSettings.MMCIF;
+
+ private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.JMOL_PARSER;
/**
* Initialises the Jalview Application Log
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
- Pdb.setCurrentDefaultFomart(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