* <li>SHOW_FULLSCREEN boolean</li>
* <li>FONT_NAME java font name for alignment text display</li>
* <li>FONT_SIZE size of displayed alignment text</li>
- * <li>FONT_STYLE style of font displayed (sequence labels are always italic)</li>
+ * <li>FONT_STYLE style of font displayed (sequence labels are always
+ * italic)</li>
* <li>GAP_SYMBOL character to treat as gap symbol (usually -,.,' ')</li>
* <li>LAST_DIRECTORY last directory for browsing alignment</li>
* <li>USER_DEFINED_COLOURS list of user defined colour scheme files</li>
* Sifts settings
*/
public static final String DEFAULT_SIFTS_DOWNLOAD_DIR = System
- .getProperty("user.home")
- + File.separatorChar
+ .getProperty("user.home") + File.separatorChar
+ ".sifts_downloads" + File.separatorChar;
private final static String DEFAULT_CACHE_THRESHOLD_IN_DAYS = "2";
Logger lcastor = Logger.getLogger("org.exolab.castor");
jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
- laxis.setLevel(Level.toLevel(Cache.getDefault("logs.Axis.Level",
- Level.INFO.toString())));
+ laxis.setLevel(Level.toLevel(
+ Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
Level.INFO.toString())));
lcastor = Logger.getLogger("org.exolab.castor.xml");
// lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
// lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
// Level.INFO.toString())));
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Jalview.level", Level.INFO.toString())));
+ jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
+ .getDefault("logs.Jalview.level", Level.INFO.toString())));
// laxis.addAppender(ap);
// lcastor.addAppender(ap);
// jalview.bin.Cache.log.addAppender(ap);
try
{
fis = new java.net.URL(propertiesFile).openStream();
- System.out.println("Loading jalview properties from : "
- + propertiesFile);
- System.out
- .println("Disabling Jalview writing to user's local properties file.");
+ System.out.println(
+ "Loading jalview properties from : " + propertiesFile);
+ System.out.println(
+ "Disabling Jalview writing to user's local properties file.");
propsAreReadOnly = true;
} catch (Exception ex)
if (getDefault("USE_PROXY", false))
{
- String proxyServer = getDefault("PROXY_SERVER", ""), proxyPort = getDefault(
- "PROXY_PORT", "8080");
+ String proxyServer = getDefault("PROXY_SERVER", ""),
+ proxyPort = getDefault("PROXY_PORT", "8080");
System.out.println("Using proxyServer: " + proxyServer
+ " proxyPort: " + proxyPort);
// LOAD THE AUTHORS FROM THE authors.props file
try
{
- String authorDetails = "jar:".concat(Cache.class
- .getProtectionDomain().getCodeSource().getLocation()
- .toString().concat("!/authors.props"));
+ String authorDetails = "jar:"
+ .concat(Cache.class.getProtectionDomain().getCodeSource()
+ .getLocation().toString().concat("!/authors.props"));
java.net.URL localJarFileURL = new java.net.URL(authorDetails);
SiftsSettings
.setMapWithSifts(Cache.getDefault("MAP_WITH_SIFTS", false));
- SiftsSettings.setSiftDownloadDirectory(jalview.bin.Cache.getDefault(
- "sifts_download_dir", DEFAULT_SIFTS_DOWNLOAD_DIR));
+ 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.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));
+ SiftsSettings.setCacheThresholdInDays(
+ jalview.bin.Cache.getDefault("sifts_cache_threshold_in_days",
+ DEFAULT_CACHE_THRESHOLD_IN_DAYS));
IdOrgSettings.setUrl(getDefault("ID_ORG_HOSTURL",
"http://www.jalview.org/services/identifiers"));
// "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
- && getDefault("VERSION_CHECK", true)
+ if (jnlpVersion == null && getDefault("VERSION_CHECK", true)
&& (System.getProperty("java.awt.headless") == null || System
.getProperty("java.awt.headless").equals("false")))
{
{
System.setProperty("sun.net.client.defaultConnectTimeout",
"5000");
- java.net.URL url = new java.net.URL(Cache.getDefault(
- "www.jalview.org", "http://www.jalview.org")
+ java.net.URL url = new java.net.URL(Cache
+ .getDefault("www.jalview.org", "http://www.jalview.org")
+ "/webstart/jalview.jnlp");
- BufferedReader in = new BufferedReader(new InputStreamReader(
- url.openStream()));
+ BufferedReader in = new BufferedReader(
+ new InputStreamReader(url.openStream()));
String line = null;
while ((line = in.readLine()) != null)
{
}
} catch (Exception ex)
{
- System.out
- .println("Non-fatal exception when checking version at www.jalview.org :");
+ System.out.println(
+ "Non-fatal exception when checking version at www.jalview.org :");
System.out.println(ex);
remoteVersion = getProperty("VERSION");
}
}
} catch (Exception ex)
{
- System.out.println("Error setting property: " + key + " " + obj
- + "\n" + ex);
+ System.out.println(
+ "Error setting property: " + key + " " + obj + "\n" + ex);
}
return obj;
}
{
try
{
- if (jalview.jbgui.GDesktop.class.getClassLoader().loadClass(
- "uk.ac.vamsas.client.VorbaId") != null)
+ if (jalview.jbgui.GDesktop.class.getClassLoader()
+ .loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.log
- .debug("Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
+ jalview.bin.Cache.log.debug(
+ "Found Vamsas Classes (uk.ac..vamsas.client.VorbaId can be loaded)");
vamsasJarsArePresent = 1;
Logger lvclient = Logger.getLogger("uk.ac.vamsas");
- lvclient.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Vamsas.Level", Level.INFO.toString())));
+ lvclient.setLevel(Level.toLevel(Cache
+ .getDefault("logs.Vamsas.Level", Level.INFO.toString())));
lvclient.addAppender(log.getAppender("JalviewLogger"));
// Tell the user that debug is enabled
{
try
{
- if (Cache.class.getClassLoader().loadClass(
- "groovy.lang.GroovyObject") != null)
+ if (Cache.class.getClassLoader()
+ .loadClass("groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log
- .debug("Found Groovy (groovy.lang.GroovyObject can be loaded)");
+ jalview.bin.Cache.log.debug(
+ "Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
Logger lgclient = Logger.getLogger("groovy");
- lgclient.setLevel(Level.toLevel(Cache.getDefault(
- "logs.Groovy.Level", Level.INFO.toString())));
+ lgclient.setLevel(Level.toLevel(Cache
+ .getDefault("logs.Groovy.Level", Level.INFO.toString())));
lgclient.addAppender(log.getAppender("JalviewLogger"));
// Tell the user that debug is enabled
// try to get the tracker class
try
{
- jgoogleanalyticstracker = Cache.class
- .getClassLoader()
- .loadClass(
- "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
- trackerfocus = Cache.class.getClassLoader().loadClass(
- "com.boxysystems.jgoogleanalytics.FocusPoint");
+ jgoogleanalyticstracker = Cache.class.getClassLoader().loadClass(
+ "com.boxysystems.jgoogleanalytics.JGoogleAnalyticsTracker");
+ trackerfocus = Cache.class.getClassLoader()
+ .loadClass("com.boxysystems.jgoogleanalytics.FocusPoint");
} catch (Exception e)
{
- log.debug("com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
+ log.debug(
+ "com.boxysystems.jgoogleanalytics package is not present - tracking not enabled.");
tracker = null;
jgoogleanalyticstracker = null;
trackerfocus = null;
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" });
- jgoogleanalyticstracker.getMethod("trackAsynchronously",
- new Class[] { trackerfocus }).invoke(
- tracker,
- new Object[] { trackerfocus.getConstructor(
- new Class[] { String.class }).newInstance(
- new Object[] { "Application Started." }) });
+ 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." }) });
} catch (RuntimeException e)
{
re = e;
{
if (re != null)
{
- log.debug("Caught runtime exception in googletracker init:", re);
+ log.debug("Caught runtime exception in googletracker init:",
+ re);
}
if (ex != null)
{
log.warn(
"Failed to initialise GoogleTracker for Jalview Desktop with version "
- + vrs, ex);
+ + vrs,
+ ex);
}
if (err != null)
{
log.error(
"Whilst initing GoogleTracker for Jalview Desktop version "
- + vrs, err);
+ + vrs,
+ err);
}
}
else
{
if (re != null)
{
- System.err
- .println("Debug: Caught runtime exception in googletracker init:"
+ System.err.println(
+ "Debug: Caught runtime exception in googletracker init:"
+ vrs);
re.printStackTrace();
}
if (ex != null)
{
- System.err
- .println("Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
+ System.err.println(
+ "Warning: Failed to initialise GoogleTracker for Jalview Desktop with version "
+ vrs);
ex.printStackTrace();
}
if (err != null)
{
- System.err
- .println("ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+ System.err.println(
+ "ERROR: Whilst initing GoogleTracker for Jalview Desktop version "
+ vrs);
err.printStackTrace();
}
{
return;
}
-
+
// In case colours can't be loaded, we'll remove them
// from the default list here.
StringBuffer coloursFound = new StringBuffer();
{
if (coloursFound.toString().length() > 1)
{
- setProperty(UserDefinedColours.USER_DEFINED_COLOURS, coloursFound.toString());
+ setProperty(UserDefinedColours.USER_DEFINED_COLOURS,
+ coloursFound.toString());
}
else
{
- applicationProperties.remove(UserDefinedColours.USER_DEFINED_COLOURS);
+ applicationProperties
+ .remove(UserDefinedColours.USER_DEFINED_COLOURS);
}
}
}
git://source.jalview.org / jalview.git / blobdiff