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

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package de.charite.compbio.jannovar.cmd;

import com.google.common.collect.ImmutableMap;
import de.charite.compbio.jannovar.JannovarException;
import de.charite.compbio.jannovar.data.Chromosome;
import de.charite.compbio.jannovar.data.JannovarData;
import de.charite.compbio.jannovar.data.JannovarDataSerializer;
import de.charite.compbio.jannovar.data.ReferenceDictionary;

/**
 * Base class for commands needing annotation data.
 *
 * @author Manuel Holtgrewe
 */
public abstract class JannovarAnnotationCommand extends JannovarCommand {

	/**
	 * {@link JannovarData} with the information
	 */
	protected JannovarData jannovarData = null;

	/**
	 * {@link ReferenceDictionary} with genome information.
	 */
	protected ReferenceDictionary refDict = null;

	/**
	 * Map of Chromosomes, used in the annotation.
	 */
	protected ImmutableMap chromosomeMap = null;

	/**
	 * Deserialize the transcript definition file from {@link pathToDataFile}.
	 *
	 * @param pathToDataFile String with the path to the data file to deserialize
	 * @throws JannovarException      when there is a problem with the deserialization
	 * @throws HelpRequestedException when the user requested the help page
	 */
	protected void deserializeTranscriptDefinitionFile(String pathToDataFile)
		throws JannovarException, HelpRequestedException {
		this.jannovarData = new JannovarDataSerializer(pathToDataFile).load();
		this.refDict = this.jannovarData.getRefDict();
		this.chromosomeMap = this.jannovarData.getChromosomes();
	}

}