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.windowui;
  
  import java.util.ArrayList;
  import java.util.List;
  
  public class NormalizationHandler {
      public static final String strNONE = "NONE";
      public static final String strVC = "VC";
      public static final String strVC_SQRT = "VC_SQRT";
      public static final String strKR = "KR";
      public static final String strGW_KR = "GW_KR";
      public static final String strINTER_KR = "INTER_KR";
      public static final String strGW_VC = "GW_VC"; // todo, should we add a GW_VC_SQRT?
      public static final String strINTER_VC = "INTER_VC";
      public static final String strSCALE = "SCALE";
      public static final String strGW_SCALE = "GW_SCALE";
      public static final String strINTER_SCALE = "INTER_SCALE";
      public static final NormalizationType NONE = new NormalizationType(strNONE, "None");
      public static final NormalizationType VC = new NormalizationType(strVC, "Coverage");
      public static final NormalizationType VC_SQRT = new NormalizationType(strVC_SQRT, "Coverage (Sqrt)");
      public static final NormalizationType KR = new NormalizationType(strKR, "Balanced");
      public static final NormalizationType GW_KR = new NormalizationType(strGW_KR, "Genome-wide balanced");
      public static final NormalizationType INTER_KR = new NormalizationType(strINTER_KR, "Inter balanced");
      public static final NormalizationType GW_VC = new NormalizationType(strGW_VC, "Genome-wide coverage");
      public static final NormalizationType INTER_VC = new NormalizationType(strINTER_VC, "Inter coverage");//,
      public static final NormalizationType SCALE = new NormalizationType(strSCALE, "Balanced++");
      public static final NormalizationType GW_SCALE = new NormalizationType(strGW_SCALE, "Genome-wide Balanced++");
      public static final NormalizationType INTER_SCALE = new NormalizationType(strINTER_SCALE, "Inter Balanced++");
  
      private final static List<NormalizationType> currentlyAvailableNorms = new ArrayList<>();
  
      public NormalizationHandler() {
          currentlyAvailableNorms.add(NONE);
          currentlyAvailableNorms.add(KR);
          currentlyAvailableNorms.add(VC);
          currentlyAvailableNorms.add(VC_SQRT);
          currentlyAvailableNorms.add(GW_KR);
          currentlyAvailableNorms.add(GW_VC);
          currentlyAvailableNorms.add(INTER_KR);
          currentlyAvailableNorms.add(INTER_VC);
          currentlyAvailableNorms.add(SCALE);
          currentlyAvailableNorms.add(GW_SCALE);
          currentlyAvailableNorms.add(INTER_SCALE);
      }
  
      public static List<NormalizationType> getAllNormTypes() {
          return currentlyAvailableNorms;
      }
  
      public static boolean isGenomeWideNorm(NormalizationType norm) {
          return isGenomeWideNormIntra(norm) || isGenomeWideNormInter(norm);
      }
  
      public static NormalizationType[] getAllGWNormTypes(boolean isUseOnlyScalingDefaults) {
          if (isUseOnlyScalingDefaults) {
              return new NormalizationType[]{GW_SCALE};
          }
          return new NormalizationType[]{GW_KR, GW_VC, GW_SCALE, INTER_KR, INTER_VC, INTER_SCALE};
      }
  
      public static boolean isGenomeWideNormIntra(NormalizationType norm) {
          return norm.equals(GW_KR) || norm.equals(GW_VC) || norm.equals(GW_SCALE);
      }
  
      public static boolean isGenomeWideNormInter(NormalizationType norm) {
          return norm.equals(INTER_KR) || norm.equals(INTER_VC) || norm.equals(INTER_SCALE);
      }
  
      public static Integer getIdealResolutionLimit(NormalizationType normalizationType) {
          if (isGenomeWideNorm(normalizationType)) {
              return 25000;
          } else {
              return 0;
          }
      }
  
      public NormalizationType getNormTypeFromString(String text) {
          if (text != null && text.length() > 0) {
              for (NormalizationType norm : currentlyAvailableNorms) {
                  if (text.equalsIgnoreCase(norm.getLabel()) || text.equalsIgnoreCase(norm.getDescription())) {
                      return norm;
                  }
              }
          }
          NormalizationType newNormType = new NormalizationType(text, text);
          currentlyAvailableNorms.add(newNormType);
          return newNormType;
      }
  
      public List<NormalizationType> getDefaultSetForHiCFileBuilding() {
          List<NormalizationType> normalizationTypes = new ArrayList<>();
          normalizationTypes.add(VC);
          normalizationTypes.add(VC_SQRT);
          //normalizationTypes.add(KR);
          normalizationTypes.add(SCALE);
          normalizationTypes.add(INTER_SCALE);
          normalizationTypes.add(GW_SCALE);
          return normalizationTypes;
      }
  }
  