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.track;
  
  /**
   * @author jrobinso
   *         Date: 9/14/12
   *         Time: 8:54 AM
   */
  public class HiCFixedGridAxis implements HiCGridAxis {
  
      private final long binCount;
      private final int binSize;
      private final int igvZoom;
      private final int[] sites;
      private final double log2 = Math.log(2.0D);
      
      public HiCFixedGridAxis(long binCount, int binSize, int[] sites) {
          
          this.binCount = binCount;
          this.binSize = binSize;
          this.sites = sites;
          
          // Compute an approximate igv zoom level
          igvZoom = Math.max(0, (int) (Math.log(binCount / 700) / log2));
          
      }
  
      @Override
      public int getBinSize() {
          return binSize;
      }
      
      @Override
      public long getGenomicStart(double binNumber) {
          return (long) (binNumber * binSize);
      }
      
      @Override
      public long getGenomicEnd(double binNumber) {
          return (long) ((binNumber + 1) * binSize);
      }
      
      @Override
      public long getGenomicMid(double binNumber) {
          return (long) ((binNumber + 0.5) * binSize);
      }
  
      @Override
      public int getIGVZoom() {
          return igvZoom;
      }
      
      @Override
      public int getBinNumberForGenomicPosition(long genomicPosition) {
          return (int) (genomicPosition / ((double) binSize));
      }
  
      @Override
      public int getBinNumberForFragment(int fragment) {
  
          if (fragment < sites.length && fragment >= 0) {
              int genomicPosition = sites[fragment];
              return getBinNumberForGenomicPosition(genomicPosition);
          }
          throw new RuntimeException("Fragment: " + fragment + " is out of range");
      }
      
      @Override
      public long getBinCount() {
          return binCount;
      }
  
  }
  