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.iterator;
  
  import juicebox.data.ChromosomeHandler;
  import juicebox.data.ContactRecord;
  import juicebox.data.Dataset;
  import juicebox.data.basics.Chromosome;
  import juicebox.data.basics.ListOfFloatArrays;
  import juicebox.tools.dev.ParallelizedJuicerTools;
  import juicebox.windowui.HiCZoom;
  
  import java.util.Iterator;
  import java.util.List;
  import java.util.concurrent.atomic.AtomicInteger;
  
  
  public class GWIteratorContainer extends IteratorContainer {
  
      private final Dataset dataset;
      private final ChromosomeHandler handler;
      private final HiCZoom zoom;
      private final boolean includeIntra;
  
      public GWIteratorContainer(Dataset dataset, ChromosomeHandler handler,
                                 HiCZoom zoom, boolean includeIntra) {
          super(calculateMatrixSize(handler, zoom));
          this.dataset = dataset;
          this.handler = handler;
          this.zoom = zoom;
          this.includeIntra = includeIntra;
  
      }
  
      private static long calculateMatrixSize(ChromosomeHandler handler, HiCZoom zoom) {
          long totalSize = 0;
          for (Chromosome c1 : handler.getChromosomeArrayWithoutAllByAll()) {
              totalSize += (c1.getLength() / zoom.getBinSize()) + 1;
          }
          return totalSize;
      }
  
      @Override
      public Iterator<ContactRecord> getNewContactRecordIterator() {
          return new GenomeWideIterator(dataset, handler, zoom, includeIntra);
      }
  
      public List<Iterator<ContactRecord>> getAllFromFileContactRecordIterators() {
          return GenomeWideIterator.getAllFromFileIterators(dataset, handler, zoom, includeIntra);
      }
  
      @Override
      public ListOfFloatArrays sparseMultiply(ListOfFloatArrays vector, long vectorLength) {
          final ListOfFloatArrays totalSumVector = new ListOfFloatArrays(vectorLength);
  
          List<Iterator<ContactRecord>> allIterators = getAllFromFileContactRecordIterators();
  
          AtomicInteger index = new AtomicInteger(0);
          ParallelizedJuicerTools.launchParallelizedCode(numCPUMatrixThreads, () -> {
              int i = index.getAndIncrement();
              ListOfFloatArrays accumSumVector = new ListOfFloatArrays(vectorLength);
              while (i < allIterators.size()) {
                  accumSumVector.addValuesFrom(ZDIteratorContainer.matrixVectorMultiplyOnIterator(
                          allIterators.get(i), vector, vectorLength));
                  i = index.getAndIncrement();
              }
              synchronized (totalSumVector) {
                  totalSumVector.addValuesFrom(accumSumVector);
              }
          });
  
          allIterators.clear();
  
          return totalSumVector;
      }
  
      @Override
      public void clear() {
          // null, doesn't need to clean anything
      }
  }
  