Changed logging to more general

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/Logging.scala

@@ -7,9 +7,13 @@ import org.apache.log4j.WriterAppender
 import org.apache.log4j.helpers.DateLayout
 
 trait Logging {
-  protected val logger = Logger.getLogger(getClass.getSimpleName.split("\\$").last)
+  def logger = Logging.logger
+}
+
+object Logging {
+  val logger = Logger.getLogger("Logging")
 
-  private[core] val logLayout = new DateLayout() {
+  val logLayout = new DateLayout() {
     val ignoresThrowable = false
     def format(event: org.apache.log4j.spi.LoggingEvent): String = {
       val calendar: Calendar = Calendar.getInstance
@@ -18,10 +22,13 @@ trait Logging {
       val formattedDate: String = formatter.format(calendar.getTime)
       var logLevel = event.getLevel.toString
       while (logLevel.size < 6) logLevel += " "
-      logLevel + " [" + formattedDate + "] [" + event.getLoggerName + "] " + event.getMessage + "\n"
+      val className = event.getLocationInformation.getClassName.split("\\.").last.split("\\$").head
+      logLevel + " [" + formattedDate + "] [" + className + "] " + event.getMessage + "\n"
     }
   }
-  private[core] val stderrAppender = new WriterAppender(logLayout, sys.process.stderr)
+
+  val stderrAppender = new WriterAppender(logLayout, sys.process.stderr)
+
   logger.setLevel(org.apache.log4j.Level.INFO)
-  logger.addAppender(stderrAppender)
-}
+  logger.addAppender(Logging.stderrAppender)
+}
\ No newline at end of file

biopet-framework/src/main/scala/nl/lumc/sasc/biopet/core/ToolCommand.scala

@@ -9,10 +9,10 @@ trait ToolCommand extends MainCommand with Logging {
 
   abstract class AbstractOptParser extends scopt.OptionParser[Args](commandName) {
     opt[Unit]("log_nostderr") foreach { _ =>
-      logger.removeAppender(stderrAppender)
+      logger.removeAppender(Logging.stderrAppender)
     } text ("No output to stderr")
     opt[File]("log_file") foreach { x =>
-      logger.addAppender(new WriterAppender(logLayout, new java.io.PrintStream(x)))
+      logger.addAppender(new WriterAppender(Logging.logLayout, new java.io.PrintStream(x)))
     } text ("Log file") valueName ("<file>")
     opt[String]('l', "log_level") foreach { x =>
       x.toLowerCase match {