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 NON-INFRINGEMENT. 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.original.mnditerator;
  
  import java.util.HashMap;
  import java.util.Map;
  
  public class SimpleLineParser extends MNDLineParser {
  
      private final Map<String, Integer> chrNameToIndex = new HashMap<>();
      private final Map<Integer, String> chrIndexToName = new HashMap<>();
      private int nextChromIndex = 1;
  
      @Override
      protected int getChromosomeOrdinal(String chrom) {
          if (!chrNameToIndex.containsKey(chrom)) {
              chrNameToIndex.put(chrom, nextChromIndex);
              chrNameToIndex.put(chrom.toLowerCase(), nextChromIndex);
              chrNameToIndex.put(chrom.toUpperCase(), nextChromIndex);
              chrIndexToName.put(nextChromIndex, chrom);
              nextChromIndex++;
          }
  
          return chrNameToIndex.get(chrom);
      }
  
      @Override
      public AlignmentPair generateBasicPair(String[] tokens, int chrom1Index, int chrom2Index, int pos1Index, int pos2Index) {
          String chrom1 = getInternedString(tokens[chrom1Index]);
          String chrom2 = getInternedString(tokens[chrom2Index]);
          return createPair(tokens, chrom1, chrom2, pos1Index, pos2Index);
      }
  
      @Override
      public String getChromosomeNameFromIndex(int chrIndex) {
          return chrIndexToName.get(chrIndex);
      }
  }
  