org.ncic.bioinfo.sparkseq.algorithms.data.sam.PileupElementTracker.java Source code

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Here is the source code for org.ncic.bioinfo.sparkseq.algorithms.data.sam.PileupElementTracker.java

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/*
 * Copyright (c) 2017 NCIC, Institute of Computing Technology, Chinese Academy of Sciences
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
 */
package org.ncic.bioinfo.sparkseq.algorithms.data.sam;

import org.apache.commons.collections.iterators.IteratorChain;

import java.util.Collection;
import java.util.HashMap;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;

/**
 * Author: wbc
 */
abstract class PileupElementTracker<PE extends PileupElement> implements Iterable<PE> {
    public abstract int size();

    /**
     * Iterate through the PEs here, but in any order, which may improve performance
     * if you don't care about the underlying order the reads are coming to you in.
     * @return an iteratable over all pileup elements in this tracker
     */
    public abstract Iterable<PE> unorderedIterable();

    /**
     * Same as @see #unorderedIterable but the actual iterator itself
     * @return
     */
    public Iterator<PE> unorderedIterator() {
        return unorderedIterable().iterator();
    }

    public abstract PileupElementTracker<PE> copy();
}

class UnifiedPileupElementTracker<PE extends PileupElement> extends PileupElementTracker<PE> {
    private final List<PE> pileup;

    @Override
    public UnifiedPileupElementTracker<PE> copy() {
        UnifiedPileupElementTracker<PE> result = new UnifiedPileupElementTracker<PE>();
        for (PE element : pileup)
            result.add(element);
        return result;
    }

    public UnifiedPileupElementTracker() {
        pileup = new LinkedList<PE>();
    }

    public UnifiedPileupElementTracker(List<PE> pileup) {
        this.pileup = pileup;
    }

    public void add(PE element) {
        pileup.add(element);
    }

    public PE get(int index) {
        return pileup.get(index);
    }

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

    public Iterator<PE> iterator() {
        return pileup.iterator();
    }

    public Iterable<PE> unorderedIterable() {
        return this;
    }
}

class PerSamplePileupElementTracker<PE extends PileupElement> extends PileupElementTracker<PE> {
    private final Map<String, PileupElementTracker<PE>> pileup;
    private int size = 0;

    public PerSamplePileupElementTracker() {
        pileup = new HashMap<String, PileupElementTracker<PE>>();
    }

    public PerSamplePileupElementTracker<PE> copy() {
        PerSamplePileupElementTracker<PE> result = new PerSamplePileupElementTracker<PE>();
        for (Map.Entry<String, PileupElementTracker<PE>> entry : pileup.entrySet())
            result.addElements(entry.getKey(), entry.getValue());

        return result;
    }

    /**
     * Gets a list of all the samples stored in this pileup.
     * @return List of samples in this pileup.
     */
    public Collection<String> getSamples() {
        return pileup.keySet();
    }

    public PileupElementTracker<PE> getElements(final String sample) {
        return pileup.get(sample);
    }

    public PileupElementTracker<PE> getElements(final Collection<String> selectSampleNames) {
        PerSamplePileupElementTracker<PE> result = new PerSamplePileupElementTracker<PE>();
        for (final String sample : selectSampleNames) {
            result.addElements(sample, pileup.get(sample));
        }
        return result;
    }

    public void addElements(final String sample, PileupElementTracker<PE> elements) {
        pileup.put(sample, elements);
        size += elements.size();
    }

    public Iterator<PE> iterator() {
        return new MergingPileupElementIterator<PE>(this);
    }

    public int size() {
        return size;
    }

    public Iterable<PE> unorderedIterable() {
        return new Iterable<PE>() {
            @Override
            public Iterator<PE> iterator() {
                return new Iterator<PE>() {
                    final private IteratorChain chain = new IteratorChain();

                    { // initialize the chain with the unordered iterators of the per sample pileups
                        for (PileupElementTracker<PE> pet : pileup.values()) {
                            chain.addIterator(pet.unorderedIterator());
                        }
                    }

                    @Override
                    public boolean hasNext() {
                        return chain.hasNext();
                    }

                    @Override
                    public PE next() {
                        return (PE) chain.next();
                    }

                    @Override
                    public void remove() {
                        throw new UnsupportedOperationException("Cannot remove");
                    }
                };
            }
        };
    }
}