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.io.BufferedReader;
  import java.io.IOException;
  
  public abstract class GenericPairIterator implements PairIterator {
  
      protected final MNDFileParser mndFileParser;
      protected AlignmentPair nextPair = null;
      protected BufferedReader reader;
  
      public GenericPairIterator(MNDFileParser mndFileParser) {
          this.mndFileParser = mndFileParser;
      }
  
      public boolean hasNext() {
          return nextPair != null;
      }
  
      public AlignmentPair next() {
          AlignmentPair p = nextPair;
          advance();
          return p;
      }
  
      protected void advance() {
  
          try {
              String nextLine = reader.readLine();
              nextLine = validateLine(nextLine);
              if (nextLine != null) {
                  nextPair = mndFileParser.parse(nextLine);
                  return;
              }
          } catch (IOException e) {
              e.printStackTrace();
          }
          nextPair = null;
      }
  
      protected String validateLine(String nextLine) {
          return nextLine;
      }
  
      public void remove() {
          // Not implemented
      }
  
      public void close() {
          try {
              reader.close();
          } catch (IOException e) {
              e.printStackTrace();  //To change body of catch statement use File | Settings | File Templates.
          }
      }
  }
  