gatk-3.8/java/src/org/broadinstitute/sting/gatk/walkers/Walker.java

package org.broadinstitute.sting.gatk.walkers;

import java.io.PrintStream;
import java.util.HashMap;
import java.util.Map;
import java.util.List;

import org.broadinstitute.sting.gatk.GenomeAnalysisTK;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.Pair;

/**
 * Created by IntelliJ IDEA.
 * User: hanna
 * Date: Mar 17, 2009
 * Time: 1:53:31 PM
 * To change this template use File | Settings | File Templates.
 */
public abstract class Walker<MapType, ReduceType> {
    // TODO: Can a walker be templatized so that map and reduce live here?

    /**
     * A stream for writing normal (non-error) output.  System.out by default.
     */
    protected PrintStream out = null;

    /**
     * A stream for writing error output.  System.err by default.
     */
    protected PrintStream err = null;

    protected Walker() {
	if( GenomeAnalysisTK.Instance != null ) {
	    GenomeAnalysisTK.Instance.loadArgumentsIntoObject(this);
	    out = GenomeAnalysisTK.Instance.out;
	    err = GenomeAnalysisTK.Instance.err;
	}
	else {
	    out = System.out;
	    err = System.err;
	}
    }

    /**
     * Retrieve the toolkit, for peering into internal structures that can't
     * otherwise be read.  Use sparingly, and discuss uses with software engineering
     * team.
     * @return The genome analysis toolkit.
     */
    protected GenomeAnalysisTK getToolkit() {
        return GenomeAnalysisTK.Instance;
    }

    public void initialize() { }

    public void onTraversalDone(ReduceType result) {
        out.println("[REDUCE RESULT] Traversal result is: " + result);
    }

    /**
     * General interval reduce routine called after all of the traversals are done
     * @param results
     */
    public void onTraversalDone(List<Pair<GenomeLoc, ReduceType>> results) {
        for ( Pair<GenomeLoc, ReduceType> result : results ) {
            out.printf("[INTERVAL REDUCE RESULT] at %s ", result.getFirst());
            this.onTraversalDone(result.getSecond());
        }
    }

    /**
     * Return true if your walker wants to reduce each interval separately.  Default is false.
     *
     * If you set this flag, several things will happen.
     *
     * The system will invoke reduceInit() once for each interval being processed, starting a fresh reduce
     * Reduce will accumulate normally at each map unit in the interval
     * However, onTraversalDone(reduce) will be called after each interval is processed.
     * The system will call onTraversalDone( GenomeLoc -> reduce ), after all reductions are done,
     *   which is overloaded here to call onTraversalDone(reduce) for each location
     */
    public boolean isReduceByInterval() {
        return false;
    }
}