de.charite.compbio.jannovar.cmd.JannovarCommand Maven / Gradle / Ivy
package de.charite.compbio.jannovar.cmd;
import de.charite.compbio.jannovar.JannovarException;
import org.apache.logging.log4j.Level;
import org.apache.logging.log4j.LogManager;
import org.apache.logging.log4j.core.LoggerContext;
import org.apache.logging.log4j.core.config.Configuration;
/**
* Super class for all commands, i.e. the classes implementing one Jannovar execution step.
*
* @author Manuel Holtgrewe
*/
public abstract class JannovarCommand {
/**
* Set log level, depending on this.verbosity.
*/
protected void setLogLevel(int verbosity) {
LoggerContext ctx = (LoggerContext) LogManager.getContext(false);
Configuration conf = ctx.getConfiguration();
if (verbosity <= 1)
conf.getLoggerConfig(LogManager.ROOT_LOGGER_NAME).setLevel(Level.INFO);
else if (verbosity <= 2)
conf.getLoggerConfig(LogManager.ROOT_LOGGER_NAME).setLevel(Level.DEBUG);
else
conf.getLoggerConfig(LogManager.ROOT_LOGGER_NAME).setLevel(Level.TRACE);
ctx.updateLoggers(conf);
}
/**
* Function for the execution of the command.
*
* @throws JannovarException on problems executing the command.
*/
public abstract void run() throws JannovarException;
}