*/
package jalview.bin;
+import jalview.datamodel.DBRefSource;
+import jalview.ws.dbsources.Pdb;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
import jalview.ws.sifts.SiftsSettings;
public static final String DAS_ACTIVE_SOURCE = "DAS_ACTIVE_SOURCE";
+ public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
+ .getProperty("user.home")
+ + File.separatorChar
+ + ".sifts_downloads" + File.separatorChar;
+
+ private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
+
+ private final static String DEFAULT_FAIL_SAFE_PID_THRESHOLD = "30";
+
+ private final static String DEFAULT_STRUCTURE_FORMAT = DBRefSource.PDB;
+
/**
* Initialises the Jalview Application Log
*/
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
+ SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
+ "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+
+ SiftsSettings.setFailSafePIDThreshold(jalview.bin.Cache.getDefault(
+ "sifts_fail_safe_pid_threshold",
+ DEFAULT_FAIL_SAFE_PID_THRESHOLD));
+
+ SiftsSettings.setCacheThresholdInDays(jalview.bin.Cache.getDefault(
+ "sifts_cache_threshold_in_days",
+ DEFAULT_CACHE_THRESHOLD_IN_DAYS));
+
System.out
.println("Jalview Version: " + codeVersion + codeInstallation);
+ Pdb.setCurrentDefaultFormat(jalview.bin.Cache.getDefault(
+ "DEFAULT_STRUCTURE_FORMAT", DEFAULT_STRUCTURE_FORMAT));
// jnlpVersion will be null if we're using InstallAnywhere
// Dont do this check if running in headless mode
if (jnlpVersion == null