org.broadinstitute.hellbender.utils.CompressedDataList Maven / Gradle / Ivy

Show more of this group Show more artifacts with this name
Show all versions of gatk Show documentation
Development on GATK 4
There is a newer version: 4.6.0.0
package org.broadinstitute.hellbender.utils;

import java.util.Arrays;
import java.util.HashMap;
import java.util.Iterator;
import java.util.Map;

/**
 * A class to represent data as a list of  pairs.  For example, the list 2,2,2,2,2,2,3,4,4,4,5,5
 * would be compressed as 2,6,3,1,4,3,5,2. The compressed list should be sorted in ascending order by value.
 *
 * Created by gauthier on 9/25/15.
 */
public final class CompressedDataList  implements Iterable {
    protected Map valueCounts = new HashMap<>();

    public Map getValueCounts(){
        return valueCounts;
    }

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

    @Override
    public Iterator iterator(){
        Iterator it = new Iterator() {
            private Iterator keySetIterator = valueCounts.keySet().iterator();
            private T currentKey = valueCounts.isEmpty() ? null : keySetIterator.next();
            private int currentValueIndex = 0;
            private int currentValueSize = valueCounts.isEmpty() ? 0 : valueCounts.get(currentKey);

            @Override
            public boolean hasNext() {
                return !valueCounts.isEmpty() && (keySetIterator.hasNext() || currentValueIndex < currentValueSize);
            }

            @Override
            public T next() {
                final T retKey = currentKey;
                currentValueIndex++;
                if(currentValueIndex==currentValueSize){
                    if(keySetIterator.hasNext()) {
                        currentKey = keySetIterator.next();
                        currentValueIndex = 0;
                        currentValueSize = valueCounts.get(currentKey);
                    }
                }
                return retKey;
            }

            @Override
            public void remove() {
                throw new UnsupportedOperationException();
            }
        };
        return it;
    }

    @Override
    public String toString(){
        String str = "";
        Object[] keys = valueCounts.keySet().toArray();
        Arrays.sort(keys);
        for (Object i: keys){
            if(!str.isEmpty()) {
                str += ",";
            }
            str+=(i+","+valueCounts.get(i));
        }
        return str;
    }

    public void add(final T val){
        add(val, 1);
    }

    public void add(final T val, final int count){
        if(valueCounts.containsKey(val)){
            valueCounts.put(val, valueCounts.get(val)+count);
        } else {
            valueCounts.put(val, count);
        }

    }

    public void add(final CompressedDataList obj){
        for(final Map.Entry pair : obj.valueCounts.entrySet()){
            this.add(pair.getKey(), pair.getValue());
        }
    }

}