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.data;
  
  import juicebox.HiC;
  import juicebox.data.basics.Chromosome;
  import juicebox.data.basics.ListOfDoubleArrays;
  import juicebox.data.basics.ListOfFloatArrays;
  import juicebox.data.iterator.IteratorContainer;
  import juicebox.tools.utils.norm.ZeroScale;
  import juicebox.windowui.HiCZoom;
  import juicebox.windowui.NormalizationType;
  
  /**
   * @author jrobinso
   *         Date: 2/10/13
   *         Time: 9:19 AM
   */
  public class NormalizationVector {
  
      private final NormalizationType type;
      private final int chrIdx;
      private final HiC.Unit unit;
      private final int resolution;
      private final ListOfDoubleArrays data;
      private boolean needsToBeScaledTo = false;
      
      public NormalizationVector(NormalizationType type, int chrIdx, HiC.Unit unit, int resolution, ListOfDoubleArrays data) {
          this.type = type;
          this.chrIdx = chrIdx;
          this.unit = unit;
          this.resolution = resolution;
          this.data = data;
      }
      
      public NormalizationVector(NormalizationType type, int chrIdx, HiC.Unit unit, int resolution, ListOfDoubleArrays data, boolean needsToBeScaledTo) {
          this(type, chrIdx, unit, resolution, data);
          this.needsToBeScaledTo = needsToBeScaledTo;
      }
  
      public static String getKey(NormalizationType type, int chrIdx, String unit, int resolution) {
          return type + "_" + chrIdx + "_" + unit + "_" + resolution;
      }
  
      public int getChrIdx() {
          return chrIdx;
      }
  
      public int getResolution() {
          return resolution;
      }
  
      public String getKey() {
          return NormalizationVector.getKey(type, chrIdx, unit.toString(), resolution);
      }
      
      public ListOfDoubleArrays getData() {
          return data;
      }
  
      public boolean doesItNeedToBeScaledTo() {
          return needsToBeScaledTo;
      }
  
      public NormalizationVector mmbaScaleToVector(Dataset ds) {
          Chromosome chromosome = ds.getChromosomeHandler().getChromosomeFromIndex(chrIdx);
          MatrixZoomData zd = HiCFileTools.getMatrixZoomData(ds, chromosome, chromosome, new HiCZoom(unit, resolution));
          if (zd == null) return null;
          return mmbaScaleToVector(zd.getIteratorContainer());
      }
  
      public NormalizationVector mmbaScaleToVector(IteratorContainer ic) {
  
          ListOfFloatArrays newNormVector = ZeroScale.scale(ic, data.convertToFloats(), getKey());
          if (newNormVector != null) {
              newNormVector = ZeroScale.normalizeVectorByScaleFactor(newNormVector, ic);
          }
          ListOfDoubleArrays newDoubleNormVector = newNormVector.convertToDoubles();
          return new NormalizationVector(type, chrIdx, unit, resolution, newDoubleNormVector);
      }
  }
  