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.clt.old;
  
  import juicebox.data.ContactRecord;
  import juicebox.data.iterator.IteratorContainer;
  import juicebox.data.iterator.ListIteratorContainer;
  import juicebox.tools.clt.CommandLineParser;
  import juicebox.tools.clt.JuiceboxCLT;
  import juicebox.tools.utils.norm.NormalizationCalculations;
  import juicebox.windowui.NormalizationHandler;
  import org.broad.igv.Globals;
  
  import java.io.BufferedReader;
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.List;
  
  
  public class CalcKR extends JuiceboxCLT {
  
      private String infile = null;
  
      public CalcKR() {
          super("calcKR <input_?_file>");
      }
  
      @Override
      public void readArguments(String[] args, CommandLineParser parser) {
          //setUsage("juicebox calcKR <infile>");
          if (!(args.length == 2)) {
              printUsageAndExit();
          }
          infile = args[1];
      }
  
      public static void calcKR(String path) throws IOException {
  
          BufferedReader reader = org.broad.igv.util.ParsingUtils.openBufferedReader(path);
  
          String nextLine;
          int lineCount = 0;
          int maxBin = 0;
          List<ContactRecord> readList = new ArrayList<>();
          while ((nextLine = reader.readLine()) != null) {
              lineCount++;
              String[] tokens = Globals.singleTabMultiSpacePattern.split(nextLine);
              int nTokens = tokens.length;
              if (nTokens != 3) {
                  System.err.println("Number of columns incorrect at line" + lineCount + ": " + nextLine);
                  System.exit(62);
              }
              int binX = Integer.parseInt(tokens[0]);
              int binY = Integer.parseInt(tokens[1]);
              int count = Integer.parseInt(tokens[2]);
              ContactRecord record = new ContactRecord(binX, binY, count);
              readList.add(record);
              if (binX > maxBin) maxBin = binX;
              if (binY > maxBin) maxBin = binY;
          }
          IteratorContainer ic = new ListIteratorContainer(readList, maxBin + 1);
  
          NormalizationCalculations nc = new NormalizationCalculations(ic);
          for (float[] array : nc.getNorm(NormalizationHandler.KR).getValues()) {
              for (double d : array) {
                  System.out.println(d);
              }
          }
  
      }
  
      @Override
      public void run() {
          try {
              calcKR(infile);
          } catch (Exception e) {
              e.printStackTrace();
          }
      }
  }
  