gatk-3.8/java/src/org/broadinstitute/sting/utils/RefHanger.java

package org.broadinstitute.sting.utils;

import org.broadinstitute.sting.utils.GenomeLoc;
import org.apache.log4j.Logger;

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

/**
 * Hanging data off the reference sequence
 * <p/>
 * Supports in effect the following data structure
 * <p/>
 * <-- reference bases: A T G C -->
 * d d d d
 * d d d d
 * d d d d
 * d d   d
 * d   d
 * d
 * <p/>
 * Where the little d's are data associated with each position in the reference.
 * Supports adding and removing data to either side of the data structure, as well as
 * randomly accessing data anywhere within window.
 */
public class RefHanger<T> {

    // -----------------------------------------------------------------------------------------------------------------
    //
    // member fields
    //
    // -----------------------------------------------------------------------------------------------------------------
    ArrayList<Hanger> hangers;

    /**
     * our log, which we want to capture anything from this class
     */
    private static Logger logger = Logger.getLogger(RefHanger.class);

    // -----------------------------------------------------------------------------------------------------------------
    //
    // Info structure
    //
    // -----------------------------------------------------------------------------------------------------------------
    public class Hanger {
        public GenomeLoc loc = null;
        public ArrayList<T> data = null;

        public Hanger(GenomeLoc loc, ArrayList<T> data) {
            this.loc = loc;
            this.data = data;
        }

        public final ArrayList<T> getData() {
            return data;
        }

        public final int size() {
            return this.data.size();
        }

        public final T get(int i) {
            return this.data.get(i);
        }
    }


    // -----------------------------------------------------------------------------------------------------------------
    //
    // constructors and other basic operations
    //
    // -----------------------------------------------------------------------------------------------------------------
    public RefHanger() {
        hangers = new ArrayList<Hanger>();
    }

    public void clear() {
        hangers.clear();
        //System.out.printf("leftLoc is %s%n", getLeftLoc());
    }

    protected int getLeftOffset() {
        return 0;
    }

    protected int getRightOffset() {
        //return hangers.size() - 1;
        return isEmpty() ? 0 : hangers.size() - 1;
    }

    protected int getOffset(GenomeLoc loc) {
        //System.out.printf("Loc: %s vs %s%n", loc, getLeftLoc());
        return loc.minus(getLeftLoc());
    }

    public GenomeLoc getLeftLoc() {
        return hangers.get(getLeftOffset()).loc;
    }

    public GenomeLoc getRightLoc() {
        return hangers.get(getRightOffset()).loc;
    }

    public GenomeLoc getLoc(int i) {
        return hangers.get(i).loc;
    }

    public boolean hasLocation(GenomeLoc loc) {
        return !isEmpty() && loc.isBetween(getLeftLoc(), getRightLoc());
    }

    public boolean isEmpty() {
        return hangers.isEmpty();
    }

    public boolean hasHangers() {
        return !isEmpty();
    }

    /**
     * Pops off the left most data from the structure
     *
     * @return
     */
    public Hanger popLeft() {
        assert hasHangers();
        return hangers.remove(0);
    }

    public void dropLeft() {
        popLeft();
    }

    /**
     * Looks at the left most data from the structure
     *
     * @return
     */
    public Hanger getLeft() {
        assert hasHangers();
        return getHanger(0);
    }

    /**
     * Returns data at offset relativePos
     *
     * @return
     */
    public Hanger getHanger(int relativePos) {
        //assert hangers.contains(relativePos) : hangers + " " + relativePos;
        return hangers.get(relativePos);
    }

    /**
     * Returns data at GenomeLoc
     *
     * @return
     */
    public Hanger getHanger(GenomeLoc pos) {
        return getHanger(getOffset(pos));
    }

    public int size() {
        return hangers.size();
    }

    public String toString() {
        StringBuilder s = new StringBuilder();
        for ( int i = 0; i < size(); i++) {
            s.append(String.format("%s => %s%n", getLoc(i), Utils.join(",", getHanger(i).data)));
        }
        return s.toString();
    }

    // -----------------------------------------------------------------------------------------------------------------
    //
    // Adding data to the left and right
    //
    // -----------------------------------------------------------------------------------------------------------------

    public void pushLeft(GenomeLoc pos) {
        pushLeft(pos, new ArrayList<T>());
    }

    public void pushLeft(GenomeLoc pos, T datum) {
        pushLeft(pos, new ArrayList<T>(Arrays.asList(datum)));
    }

    public void pushLeft(GenomeLoc pos, ArrayList<T> data) {
        hangers.add(0, new Hanger(pos, data));
    }

    public void pushLeft(GenomeLoc pos, List<T> data) {
        hangers.add(0, new Hanger(pos, new ArrayList<T>(data)));
    }

    public void pushRight(GenomeLoc pos) {
        pushRight(pos, new ArrayList<T>());
    }

    public void pushRight(GenomeLoc pos, T datum) {
        pushRight(pos, new ArrayList<T>(Arrays.asList(datum)));
    }

    public void pushRight(GenomeLoc pos, ArrayList<T> data) {
        hangers.add(new Hanger(pos, data));
    }

    public boolean ensurePos(GenomeLoc pos) {
        if (hasLocation(pos))
            return true;
        else {
            pushRight(pos);
            return false;
        }
    }

    public void extendData(GenomeLoc pos, T datum) {
        getHanger(pos).data.add(datum);
    }

    public void addData(List<GenomeLoc> positions, List<T> dataByPos) {
        assert (positions.size() == dataByPos.size());

        for (int i = 0; i < positions.size(); i++) {
            GenomeLoc pos = positions.get(i);
            T datum = dataByPos.get(i);
            expandingPut1(pos, datum);
        }
    }

    public void addDataList(List<GenomeLoc> positions, List<List<T>> dataByPos) {
        assert (positions.size() == dataByPos.size());

        for (int i = 0; i < positions.size(); i++) {
            GenomeLoc pos = positions.get(i);
            for ( T datum : dataByPos.get(i) ) {
                expandingPut1(pos, datum);
            }
        }
    }

    public void expandingPut1(final GenomeLoc loc, T datum) {
        ensurePos(loc);
        extendData(loc, datum);
    }

    public void printState() {
        logger.info("Hanger: ");
        for (Hanger hanger : hangers) {
            logger.info(String.format("  -> %s => %s:%n", hanger.loc, Utils.join("/", hanger.data)));
        }
    }

    /**
     * Pushes locations on the right until we reach the expected position for pos.
     * <p/>
     * For example, if we have chr1:1 and 2 in the hanger, and we push 4 into the hangers
     * this function will add 3 -> {} to the hanger too
     *
     * @param pos
     * @param datum
     */
    public void expandingPut(GenomeLoc pos, T datum) {
        //System.out.printf("expandingPut(%s, %s)%n", pos, datum);
        //printState();
        if (isEmpty())
            // we have nothing, just push right
            pushRight(pos, datum);
        else {
            //assert pos.compareTo(getRightLoc()) == 1 : pos + " " + getRightLoc() + " => " + pos.compareTo(getRightLoc());

            GenomeLoc nextRight = getRightLoc().nextLoc();
            while (pos.compareTo(nextRight) == 1) {
                //printState();
                //System.out.printf("    *** Extending %s, heading for %s%n", nextRight, pos);
                ensurePos(nextRight);
                nextRight = nextRight.nextLoc();
            }

            ensurePos(pos);
            extendData(pos, datum);
        }
        //printState();
    }
}