* </li><li>SHOW_QUALITY show alignment quality annotation
* </li><li>SHOW_ANNOTATIONS show alignment annotation rows
* </li><li>SHOW_CONSERVATION show alignment conservation annotation
+ * </li><li>CENTRE_COLUMN_LABELS centre the labels at each column in a displayed annotation row
* </li><li>DEFAULT_COLOUR default colour scheme to apply for a new alignment
* </li><li>DEFAULT_FILE_FORMAT file format used to save
* </li><li>STARTUP_FILE file loaded on startup (may be a fully qualified url)
/**
* property giving log4j level for AXIS loggers
*/
- public static final String AXISLOGLEVEL = "logs.Castor.level";
+ public static final String AXISLOGLEVEL = "logs.Axis.level";
/**
* property giving log4j level for Jalview Log
*/
lcastor = Logger.getLogger("org.exolab.castor.xml");
lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
Level.INFO.toString())));
+ //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())));
{
public void run()
{
+ String orgtimeout = System.getProperty("sun.net.client.defaultConnectTimeout");
+ if (orgtimeout==null)
+ {
+ orgtimeout="30";
+ System.out.println("# INFO: Setting default net timeout to "+orgtimeout+" seconds.");
+ }
String jnlpVersion = null;
try
{
+ System.setProperty("sun.net.client.defaultConnectTimeout", "5000");
java.net.URL url = new java.net.URL(
"http://www.jalview.org/webstart/jalview.jnlp");
BufferedReader in = new BufferedReader(new InputStreamReader(url.
}
catch (Exception ex)
{
+ System.out.println("Non-fatal exceptions when checking version at www.jalview.org :");
System.out.println(ex);
jnlpVersion = getProperty("VERSION");
}
+ System.setProperty("sun.net.client.defaultConnectTimeout", orgtimeout);
setProperty("LATEST_VERSION", jnlpVersion);
}