content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2022 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.merge.merger;
  
  import java.io.BufferedWriter;
  import java.io.FileWriter;
  import java.io.IOException;
  import java.util.Scanner;
  
  public class GraphsMerger extends Merger {
  
      private final long[] A = new long[2000];
      private final long[][] B = new long[3][200];
      private final long[][] D = new long[4][100];
      private final long[] x = new long[100];
  
      @Override
      public void parse(String s) {
  
          Scanner scanner = new Scanner(s);
          try {
              skipUntilNextArray(scanner);
              addTo1DArray(A, scanner);
  
              skipUntilNextArray(scanner);
              addTo2DArray(B, scanner);
  
              skipUntilNextArray(scanner);
              addTo2DArray(D, scanner);
  
              skipUntilNextArray(scanner);
              for (int idx = 0; idx < x.length; idx++) {
                  long newX = scanner.nextLong();
                  if (x[idx] > 0L) {
                      if (x[idx] != newX) {
                          System.err.println("X mismatch error? " + x[idx] + " - " + newX);
                      }
                  }
                  x[idx] = newX;
              }
          } catch (Exception e) {
              e.printStackTrace();
          }
      }
  
      @Override
      public void printToMergedFile(String filename) {
          try {
              BufferedWriter histWriter = new BufferedWriter(new FileWriter(filename));
              histWriter.write("A = [\n");
              write1DArray(A, histWriter);
              histWriter.write("\n];\n");
  
              histWriter.write("B = [\n");
              write2DArray(B, histWriter);
              histWriter.write("\n];\n");
  
              histWriter.write("D = [\n");
              write2DArray(D, histWriter);
              histWriter.write("\n];");
  
              histWriter.write("x = [\n");
              write1DArray(x, histWriter);
              histWriter.write("\n];\n");
              histWriter.close();
          } catch (IOException error) {
              error.printStackTrace();
          }
      }
  
      private void addTo1DArray(long[] arr, Scanner scanner) {
          for (int idx = 0; idx < arr.length; idx++) {
              arr[idx] += scanner.nextLong();
          }
      }
  
      private void write1DArray(long[] arr, BufferedWriter histWriter) throws IOException {
          for (long tmp : arr) {
              histWriter.write(tmp + " ");
          }
      }
  
      private void addTo2DArray(long[][] arr, Scanner scanner) {
          int numRows = arr.length;
          int len = arr[0].length;
          for (int idx = 0; idx < len; idx++) {
              for (int r = 0; r < numRows; r++) {
                  try {
                      arr[r][idx] += scanner.nextLong();
                  } catch (Exception e) {
                      System.err.println(scanner.next());
                      e.printStackTrace();
                  }
              }
          }
      }
  
      private void write2DArray(long[][] arr, BufferedWriter histWriter) throws IOException {
          int numRows = arr.length;
          int len = arr[0].length;
          for (int idx = 0; idx < len; idx++) {
              StringBuilder s = new StringBuilder("" + arr[0][idx]);
              for (int r = 1; r < numRows; r++) {
                  s.append(" ").append(arr[r][idx]);
              }
              histWriter.write(s + "\n");
          }
      }
  
      private void skipUntilNextArray(Scanner scanner) {
          while (!scanner.next().equals("[")) ;
      }
  }
  