de.charite.compbio.jannovar.cmd.JannovarDBOptions Maven / Gradle / Ivy

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package de.charite.compbio.jannovar.cmd;

import net.sourceforge.argparse4j.inf.Namespace;

import java.util.ArrayList;
import java.util.List;

/**
 * Configuration for database-related commands in Jannovar
 *
 * @author Manuel Holtgrewe
 */
public class JannovarDBOptions extends JannovarBaseOptions {

	/**
	 * paths to INI files ot use for parsing
	 */
	public List dataSourceFiles = new ArrayList<>();

	public List getDataSourceFiles() {
		return dataSourceFiles;
	}

	public void setDataSourceFiles(List dataSourceFiles) {
		this.dataSourceFiles = dataSourceFiles;
	}

	@Override
	public void setFromArgs(Namespace args) throws CommandLineParsingException {
		super.setFromArgs(args);

		dataSourceFiles = args.getList("data_source_list");
	}

	@Override
	public String toString() {
		return "JannovarDBOptions [dataSourceFiles=" + dataSourceFiles + ", isReportProgress()=" + isReportProgress()
			+ ", getHttpProxy()=" + getHttpProxy() + ", getHttpsProxy()=" + getHttpsProxy() + ", getFtpProxy()="
			+ getFtpProxy() + "]";
	}

}