content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2020 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
   *
   * 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 juicebox.tools.utils.common;
  
  import java.util.Arrays;
  
  public class StatPercentile {
  
      private final double[] statsData;
  
      public StatPercentile(double[] data) {
          statsData = new double[data.length];
          System.arraycopy(data, 0, statsData, 0, data.length);
          Arrays.sort(statsData);
      }
  
      // TODO actually could be much more optimized since same vals are queried
      // some binary search like technique etc
      public double evaluate(double val) {
          return internalEvaluate(val) * 100;
      }
  
      /**
       * @param val
       * @return percentile of given value as ranked relative to values in internal array
       */
      private double internalEvaluate(double val) {
          for (int i = 0; i < statsData.length; i++) {
              if (statsData[i] >= val) {
                  if (statsData[i] > val) {
                      return Math.max(0.0, i / statsData.length);
                  } else {
                      double percentile = 0;
                      int num = 0;
                      for (int j = i; j < statsData.length; j++) {
                          if (statsData[j] > val) {
                              break;
                          }
                          percentile += ((double) i) / statsData.length;
                          num++;
                      }
                      return percentile / num;
                  }
              }
          }
          return 1.0;
      }
  }
  