94 lines
2.7 KiB
Java
94 lines
2.7 KiB
Java
/*
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* Copyright (c) 2012, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.utils;
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import java.util.*;
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/**
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* Utility class for calculating median from a data set, potentially limiting the size of data to a
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* fixed amount
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*
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* @author Your Name
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* @since Date created
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*/
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public class Median<T extends Comparable> {
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final List<T> values;
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final int maxValuesToKeep;
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boolean sorted = false;
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public Median() {
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this(Integer.MAX_VALUE);
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}
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public Median(final int maxValuesToKeep) {
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this.maxValuesToKeep = maxValuesToKeep;
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this.values = new ArrayList<T>();
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}
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public boolean isFull() {
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return values.size() >= maxValuesToKeep;
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}
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public int size() {
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return values.size();
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}
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public boolean isEmpty() {
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return values.isEmpty();
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}
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public T getMedian() {
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if ( isEmpty() )
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throw new IllegalStateException("Cannot get median value from empty array");
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return getMedian(null); // note that value null will never be used
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}
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/**
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* Returns the floor(n + 1 / 2) item from the list of values if the list
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* has values, or defaultValue is the list is empty.
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*/
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public T getMedian(final T defaultValue) {
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if ( isEmpty() )
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return defaultValue;
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if ( ! sorted ) {
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sorted = true;
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Collections.sort(values);
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}
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final int offset = (int)Math.floor((values.size() + 1) * 0.5) - 1;
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return values.get(offset);
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}
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public boolean add(final T value) {
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if ( ! isFull() ) {
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sorted = false;
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return values.add(value);
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}
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else
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return false;
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}
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}
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