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;
  
  public class AlignmentPairLong extends AlignmentPair {
  
      private final String seq1;
      private final String seq2;
  
      public AlignmentPairLong(boolean strand1, int chr1, int pos1, int frag1, int mapq1, String seq1,
                               boolean strand2, int chr2, int pos2, int frag2, int mapq2, String seq2) {
          super(strand1, chr1, pos1, frag1, mapq1, strand2, chr2, pos2, frag2, mapq2);
          this.seq1 = seq1;
          this.seq2 = seq2;
      }
  
      public AlignmentPairLong(AlignmentPair np, String seq1, String seq2) {
          this(np.getStrand1(), np.getChr1(), np.getPos1(), np.getFrag1(), np.getMapq1(), seq1,
                  np.getStrand2(), np.getChr2(), np.getPos2(), np.getFrag2(), np.getMapq2(), seq2);
      }
  
      public String getSeq1() {
          return seq1;
      }
  
      public String getSeq2() {
          return seq2;
      }
  
  }
  
  