CompoundLocation.java

package org.gmod.schema.utils;

import java.util.ArrayList;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;


public class CompoundLocation implements StrandedLocation {

    List<SingleLocation> locs = new ArrayList<SingleLocation>();

    public CompoundLocation(org.biojava.bio.symbol.Location loc, org.biojava.bio.seq.StrandedFeature.Strand strand) {
        @SuppressWarnings("unchecked")
        Iterator<org.biojava.bio.symbol.Location> it = loc.blockIterator();
        while (it.hasNext()) {
            SingleLocation location = new SingleLocation(it.next(), strand);
            locs.add(location);
        }
    }

    private CompoundLocation(CompoundLocation other, boolean convertToInterbase) {
        for (SingleLocation loc : other.getLocations()) {
            SingleLocation convert = new SingleLocation(loc, convertToInterbase);
            this.locs.add(convert);
        }
    }

    public int getMax() {
        return locs.get(locs.size()-1).getMax();
    }

    public int getMin() {
        return locs.get(0).getMin();
    }

    public Strand getStrand() {
        return locs.get(0).getStrand();
    }

    public boolean isInterbase() {
        return locs.get(0).isInterbase();
    }

    public boolean isMaxPartial() {
        return locs.get(locs.size()-1).isMaxPartial();
    }

    public boolean isMinPartial() {
        return locs.get(0).isMinPartial();
    }

    public List<SingleLocation> getLocations() {
        return Collections.unmodifiableList(locs);
    }

    public StrandedLocation getInterbaseVersion() {
        if (this.isInterbase()) {
            return this;
        }
        return new CompoundLocation(this, true);
    }
}