JAL-3933 remove obsolete Castor logging configuration

[jalview.git] / src / jalview / bin / Cache.java

diff --git a/src/jalview/bin/Cache.java b/src/jalview/bin/Cache.java
index 600d19c..d2c234d 100755 (executable)
--- a/src/jalview/bin/Cache.java
+++ b/src/jalview/bin/Cache.java
@@ -47,6 +47,12 @@ 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.core.config.Configurator;
+import org.apache.logging.log4j.core.config.builder.api.AppenderComponentBuilder;
+import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilder;
+import org.apache.logging.log4j.core.config.builder.api.ConfigurationBuilderFactory;
+import org.apache.logging.log4j.core.config.builder.impl.BuiltConfiguration;
 
 import jalview.datamodel.PDBEntry;
 import jalview.gui.UserDefinedColours;
@@ -167,6 +173,8 @@ import jalview.ws.sifts.SiftsSettings;
  * <li>FOLLOW_SELECTIONS (true) Controls whether a new alignment view should
  * respond to selections made in other alignments containing the same sequences.
  * </li>
+ * <li>SHOW_JWS2_SERVICES (true) when set to false, jalview will not
+ * auto-discover JABAWS services</li>
  * <li>JWS2HOSTURLS comma-separated list of URLs to try for JABAWS services</li>
  * <li>SHOW_WSDISCOVERY_ERRORS (true) Controls if the web service URL discovery
  * warning dialog box is displayed.</li>
@@ -194,7 +202,13 @@ import jalview.ws.sifts.SiftsSettings;
  * <li>CHIMERA_PATH specify full path to Chimera program (if non-standard)</li>
  * <li>ID_ORG_HOSTURL location of jalview service providing identifiers.org urls
  * </li>
- * 
+ * <li>NONEWS - when set disables Jalview News from automatically appearing</li>
+ * <li>NOHTMLTEMPLATES - when set, the
+ * https://github.com/jalview/exporter-templates/tree/master/biojs repository is
+ * not downloaded automatically</li>
+ * <li>NOIDENTIFIERSSERVICE - when set, jalview won't automatically download
+ * available URL linkouts via www.jalview.org/services/identifiers</li>
+ * <li>
  * </ul>
  * Deprecated settings:
  * <ul>
@@ -295,23 +309,16 @@ public class Cache
     {
       // TODO: redirect stdout and stderr here in order to grab the output of
       // the log
-
-      ConsoleAppender ap = new ConsoleAppender(new SimpleLayout(),
-              "System.err");
-      ap.setName("JalviewLogger");
-      org.apache.log4j.Logger.getRootLogger().addAppender(ap); // catch all for
+      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");
-      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())));
-      lcastor.setLevel(Level.toLevel(Cache.getDefault("logs.Castor.Level",
-              Level.INFO.toString())));
-      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())));