content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2021 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.data.v9depth;
  
  public abstract class V9Depth {
      protected final int blockBinCount;
      protected double BASE;
  
      V9Depth(int blockBinCount) {
          this.blockBinCount = blockBinCount;
      }
  
      public static V9Depth setDepthMethod(int depthBase, int blockBinCount) {
          if (depthBase > 1) {
              return new LogDepth(depthBase, blockBinCount);
          } else if (depthBase < 0) {
              return new ConstantDepth(-depthBase, blockBinCount);
          }
  
          // Default
          return new LogDepth(2, blockBinCount);
      }
  
      public int getDepth(int val1, int val2) {
          return logBase(Math.abs(val1 - val2) / Math.sqrt(2) / blockBinCount);
      }
  
      protected abstract int logBase(double value);
  }
  