import javax.swing.LookAndFeel;
import javax.swing.UIManager;
-import org.apache.log4j.ConsoleAppender;
-import org.apache.log4j.Level;
-import org.apache.log4j.Logger;
-import org.apache.log4j.SimpleLayout;
-import org.apache.log4j.builders.appender.ConsoleAppenderBuilder;
+import org.apache.logging.log4j.Level;
+import org.apache.logging.log4j.LogManager;
+import org.apache.logging.log4j.Logger;
import org.apache.logging.log4j.core.config.Configurator;
import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
import jalview.urls.IdOrgSettings;
import jalview.util.ChannelProperties;
import jalview.util.ColorUtils;
+import jalview.util.Log4j;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.sifts.SiftsSettings;
try
{
// configure the root logger to stderr
- ConfigurationBuilder<BuiltConfiguration> builder = ConfigurationBuilderFactory.newConfigurationBuilder();
- AppenderComponentBuilder consoleApp = builder.newAppender("stderr", "Console");
+ ConfigurationBuilder<BuiltConfiguration> builder = ConfigurationBuilderFactory
+ .newConfigurationBuilder();
+ AppenderComponentBuilder consoleApp = builder.newAppender("stderr",
+ "Console");
builder.add(consoleApp);
Configurator.initialize(builder.build());
// log output
- Logger laxis = Logger.getLogger("org.apache.axis");
- jalview.bin.Cache.log = Logger.getLogger("jalview.bin.Jalview");
+ Logger laxis = LogManager.getLogger("org.apache.axis");
+ log = LogManager.getLogger("jalview.bin.Jalview");
- laxis.setLevel(Level.toLevel(
+ Log4j.setLevel(laxis, Level.toLevel(
Cache.getDefault("logs.Axis.Level", Level.INFO.toString())));
// lcastor = Logger.getLogger("org.exolab.castor.xml.Marshaller");
// lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
// Level.INFO.toString())));
// we shouldn't need to do this
- org.apache.log4j.Logger.getRootLogger()
- .setLevel(org.apache.log4j.Level.INFO);
+ Log4j.setRootLevel(Level.INFO);
- jalview.bin.Cache.log.setLevel(Level.toLevel(Cache
+ Log4j.setLevel(log, Level.toLevel(Cache
.getDefault("logs.Jalview.level", Level.INFO.toString())));
// laxis.addAppender(ap);
// lcastor.addAppender(ap);
// jalview.bin.Cache.log.addAppender(ap);
// Tell the user that debug is enabled
- jalview.bin.Cache.log.debug(ChannelProperties.getProperty("app_name")
+ log.debug(ChannelProperties.getProperty("app_name")
+ " Debugging Output Follows.");
} catch (Exception ex)
{
}
/**
- * Loads properties from the given properties file. Any existing properties are
- * first cleared.
+ * Loads properties from the given properties file. Any existing properties
+ * are first cleared.
*/
public static void loadProperties(String propsFile)
{
}
/**
- * Gets Jalview application property of given key. Returns null if key not found
+ * Gets Jalview application property of given key. Returns null if key not
+ * found
*
* @param key
- * Name of property
+ * Name of property
*
* @return Property value
*/
}
/**
- * These methods are used when checking if the saved preference is different to
- * the default setting
+ * These methods are used when checking if the saved preference is different
+ * to the default setting
*/
public static boolean getDefault(String property, boolean def)
}
/**
- * Answers the value of the given property, or the supplied default value if the
- * property is not set
+ * Answers the value of the given property, or the supplied default value if
+ * the property is not set
*/
public static String getDefault(String property, String def)
{
* Stores property in the file "HOME_DIR/.jalview_properties"
*
* @param key
- * Name of object
+ * Name of object
* @param obj
- * String value of property
+ * String value of property
*
* @return previous value of property (or null)
*/
if (jalview.jbgui.GDesktop.class.getClassLoader()
.loadClass("uk.ac.vamsas.client.VorbaId") != null)
{
- jalview.bin.Cache.log.debug(
+ 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
+ Logger lvclient = LogManager.getLogger("uk.ac.vamsas");
+ Log4j.setLevel(lvclient, Level.toLevel(Cache
.getDefault("logs.Vamsas.Level", Level.INFO.toString())));
- lvclient.addAppender(log.getAppender("JalviewLogger"));
+ Log4j.addAppender(lvclient, log, "JalviewLogger");
// Tell the user that debug is enabled
lvclient.debug(ChannelProperties.getProperty("app_name")
+ " Vamsas Client Debugging Output Follows.");
} catch (Exception e)
{
vamsasJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Vamsas Classes are not present");
+ log.debug("Vamsas Classes are not present");
}
}
return (vamsasJarsArePresent > 0);
if (Cache.class.getClassLoader()
.loadClass("groovy.lang.GroovyObject") != null)
{
- jalview.bin.Cache.log.debug(
+ log.debug(
"Found Groovy (groovy.lang.GroovyObject can be loaded)");
groovyJarsArePresent = 1;
- Logger lgclient = Logger.getLogger("groovy");
- lgclient.setLevel(Level.toLevel(Cache
+ Logger lgclient = LogManager.getLogger("groovy");
+ Log4j.setLevel(lgclient, Level.toLevel(Cache
.getDefault("logs.Groovy.Level", Level.INFO.toString())));
- lgclient.addAppender(log.getAppender("JalviewLogger"));
+ Log4j.addAppender(lgclient, log, "JalviewLogger");
// Tell the user that debug is enabled
lgclient.debug(ChannelProperties.getProperty("app_name")
+ " Groovy Client Debugging Output Follows.");
} catch (Error e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present", e);
+ log.debug("Groovy Classes are not present", e);
} catch (Exception e)
{
groovyJarsArePresent = 0;
- jalview.bin.Cache.log.debug("Groovy Classes are not present");
+ log.debug("Groovy Classes are not present");
}
}
return (groovyJarsArePresent > 0);
* Loads in user colour schemes from files.
*
* @param files
- * a '|'-delimited list of file paths
+ * a '|'-delimited list of file paths
*/
public static void initUserColourSchemes(String files)
{
git://source.jalview.org / jalview.git / blobdiff