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;
  
  import juicebox.data.ChromosomeHandler;
  import juicebox.data.Dataset;
  import juicebox.data.Matrix;
  import juicebox.data.basics.Chromosome;
  import juicebox.windowui.HiCZoom;
  import juicebox.windowui.NormalizationHandler;
  import juicebox.windowui.NormalizationType;
  
  import java.util.ArrayList;
  import java.util.List;
  
  /**
   * Created by muhammadsaadshamim on 9/21/15.
   */
  public abstract class JuicerCLT extends JuiceboxCLT {
  
      protected NormalizationType norm = NormalizationHandler.SCALE;
      protected List<String> givenChromosomes = null; //TODO set to protected
  
      protected JuicerCLT(String usage) {
          super(usage);
      }
  
      protected int determineHowManyChromosomesWillActuallyRun(Dataset ds, ChromosomeHandler chromosomeHandler, HiCZoom zoom) {
          int maxProgressStatus = 0;
          for (Chromosome chr : chromosomeHandler.getChromosomeArrayWithoutAllByAll()) {
              Matrix matrix = ds.getMatrix(chr, chr);
              if (matrix == null) continue;
              if (matrix.getZoomData(zoom) == null) continue;
              maxProgressStatus++;
          }
          return maxProgressStatus;
      }
  
      @Override
      public void readArguments(String[] args, CommandLineParser parser) {
          CommandLineParserForJuicer juicerParser = (CommandLineParserForJuicer)parser;
          assessIfChromosomesHaveBeenSpecified(juicerParser);
          readJuicerArguments(args, juicerParser);
      }
  
      protected abstract void readJuicerArguments(String[] args, CommandLineParserForJuicer juicerParser);
  
      private void assessIfChromosomesHaveBeenSpecified(CommandLineParserForJuicer juicerParser) {
          List<String> possibleChromosomes = juicerParser.getChromosomeListOption();
          if (possibleChromosomes != null && possibleChromosomes.size() > 0) {
              givenChromosomes = new ArrayList<>(possibleChromosomes);
          }
      }
  }
  