package org.broadinstitute.sting.gatk.walkers;

import net.sf.samtools.SAMRecord;
import org.broadinstitute.sting.gatk.LocusContext;
import org.broadinstitute.sting.gatk.walkers.ReadWalker;

/**
 * Created by IntelliJ IDEA.
 * User: mdepristo
 * Date: Feb 22, 2009
 * Time: 2:52:28 PM
 * To change this template use File | Settings | File Templates.
 */
public abstract class BasicReadWalker<MapType, ReduceType> implements ReadWalker<MapType, ReduceType> {
    public String getName() {
        // Return name of class, trimming 'Walker' from the end if present.
        // TODO: Duplicate of BasicLociWalker.getName().  Eliminate duplication.
        String className = getClass().getSimpleName();
        if(className.endsWith(Walker.class.getSimpleName()))
            return className.substring(0,className.lastIndexOf(Walker.class.getSimpleName()));
        else
            return className;
    }

    public void initialize() { }
    public boolean requiresOrderedReads() { return false; }

    public boolean filter(LocusContext context, SAMRecord read) {
        // We are keeping all the reads
        return true;
    }

    public void onTraversalDone() {
        ;
    }

    // Three basic abstract function that *must* be overridden
    public abstract MapType map(LocusContext context, SAMRecord read);
    public abstract ReduceType reduceInit();
    public abstract ReduceType reduce(MapType value, ReduceType sum);
}