/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.bin;
+import jalview.structure.StructureImportSettings;
import jalview.ws.dbsources.das.api.DasSourceRegistryI;
import jalview.ws.dbsources.das.datamodel.DasSourceRegistry;
+import jalview.ws.sifts.SiftsSettings;
import java.awt.Color;
import java.io.BufferedReader;
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 = StructureImportSettings.MMCIF;
+
+ private final static String DEFAULT_PDB_FILE_PARSER = StructureImportSettings.JMOL_PARSER;
+
/**
* Initialises the Jalview Application Log
*/
public static Logger log;
/** Jalview Properties */
- public static Properties applicationProperties = new Properties() {
+ public static Properties applicationProperties = new Properties()
+ {
// override results in properties output in alphabetical order
@Override
- public synchronized Enumeration<Object> keys() {
- return Collections.enumeration(new TreeSet<Object>(super.keySet()));
+ public synchronized Enumeration<Object> keys()
+ {
+ return Collections.enumeration(new TreeSet<Object>(super.keySet()));
}
};
fis = new FileInputStream(propertiesFile);
}
applicationProperties.load(fis);
-
+
// remove any old build properties
-
+
deleteBuildProperties();
fis.close();
} catch (Exception ex)
{
codeInstallation = " (" + codeInstallation + ")";
}
+ new BuildDetails(codeVersion, null, codeInstallation);
+
+ 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);
+ 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
class VersionChecker extends Thread
{
+ @Override
public void run()
{
String orgtimeout = System
System.out.println("# INFO: Setting default net timeout to "
+ orgtimeout + " seconds.");
}
- String jnlpVersion = null;
+ String remoteVersion = null;
try
{
System.setProperty("sun.net.client.defaultConnectTimeout",
line = line.substring(line.indexOf("value=") + 7);
line = line.substring(0, line.lastIndexOf("\""));
- jnlpVersion = line;
+ remoteVersion = line;
break;
}
} catch (Exception ex)
{
System.out
- .println("Non-fatal exceptions when checking version at www.jalview.org :");
+ .println("Non-fatal exception when checking version at www.jalview.org :");
System.out.println(ex);
- jnlpVersion = getProperty("VERSION");
+ remoteVersion = getProperty("VERSION");
}
System.setProperty("sun.net.client.defaultConnectTimeout",
orgtimeout);
- setProperty("LATEST_VERSION", jnlpVersion);
+ setProperty("LATEST_VERSION", remoteVersion);
}
}
try
{
// Google analytics tracking code for Library Finder
- tracker = jgoogleanalyticstracker.getConstructor(new Class[]
- { String.class, String.class, String.class }).newInstance(
- new Object[]
- {
- "Jalview Desktop",
- (vrs = jalview.bin.Cache.getProperty("VERSION")
- + "_"
- + jalview.bin.Cache.getDefault("BUILD_DATE",
- "unknown")), "UA-9060947-1" });
+ tracker = jgoogleanalyticstracker.getConstructor(
+ new Class[] { String.class, String.class, String.class })
+ .newInstance(
+ new Object[] {
+ "Jalview Desktop",
+ (vrs = jalview.bin.Cache.getProperty("VERSION")
+ + "_"
+ + jalview.bin.Cache.getDefault(
+ "BUILD_DATE", "unknown")),
+ "UA-9060947-1" });
jgoogleanalyticstracker.getMethod("trackAsynchronously",
- new Class[]
- { trackerfocus }).invoke(tracker, new Object[]
- { trackerfocus.getConstructor(new Class[]
- { String.class }).newInstance(new Object[]
- { "Application Started." }) });
+ new Class[] { trackerfocus }).invoke(
+ tracker,
+ new Object[] { trackerfocus.getConstructor(
+ new Class[] { String.class }).newInstance(
+ new Object[] { "Application Started." }) });
} catch (RuntimeException e)
{
re = e;