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.ContactRecord;
  import juicebox.data.basics.ListOfDoubleArrays;
  import juicebox.data.basics.ListOfFloatArrays;
  import juicebox.tools.dev.ParallelizedJuicerTools;
  
  import java.util.Iterator;
  import java.util.List;
  import java.util.concurrent.atomic.AtomicInteger;
  
  public class ListOfListIteratorContainer extends IteratorContainer {
  
      private final BigContactRecordList allContactRecords;
  
      public ListOfListIteratorContainer(BigContactRecordList allContactRecords, long matrixSize,
                                         long totalNumberOfContacts) {
          super(matrixSize);
          setNumberOfContactRecords(totalNumberOfContacts);
          this.allContactRecords = allContactRecords;
      }
  
      @Override
      public Iterator<ContactRecord> getNewContactRecordIterator() {
          return new ListOfListIterator(allContactRecords);
      }
  
      @Override
      public boolean getIsThereEnoughMemoryForNormCalculation() {
          // float is 4 bytes; one for each row (row sums)
          // 12 bytes (2 ints, 1 float) for contact record
          return 4 * getMatrixSize() + 12 * getNumberOfContactRecords() < Runtime.getRuntime().maxMemory();
      }
  
      @Override
      public ListOfFloatArrays sparseMultiply(ListOfFloatArrays vector, long vectorLength) {
  
          if (allContactRecords.getNumLists() < numCPUMatrixThreads) {
              final ListOfFloatArrays totalSumVector = new ListOfFloatArrays(vectorLength);
              for (int k = 0; k < allContactRecords.getNumLists(); k++) {
                  List<ContactRecord> contactRecords = allContactRecords.getSubList(k);
                  totalSumVector.addValuesFrom(ListIteratorContainer.sparseMultiplyByListContacts(
                          contactRecords, vector, vectorLength, numCPUMatrixThreads));
              }
              return totalSumVector;
          }
  
          return sparseMultiplyAcrossLists(vector, vectorLength);
      }
  
      @Override
      public void clear() {
          allContactRecords.clear();
      }
  
      private ListOfFloatArrays sparseMultiplyAcrossLists(ListOfFloatArrays vector, long vectorLength) {
          final ListOfDoubleArrays totalSumVector = new ListOfDoubleArrays(vectorLength);
  
          AtomicInteger index = new AtomicInteger(0);
          ParallelizedJuicerTools.launchParallelizedCode(numCPUMatrixThreads, () -> {
              int sIndx = index.getAndIncrement();
              ListOfDoubleArrays sumVector = new ListOfDoubleArrays(vectorLength);
              while (sIndx < allContactRecords.getNumLists()) {
                  for (ContactRecord cr : allContactRecords.getSubList(sIndx)) {
                      ListIteratorContainer.matrixVectorMult(vector, sumVector, cr);
                  }
                  sIndx = index.getAndIncrement();
              }
  
              synchronized (totalSumVector) {
                  totalSumVector.addValuesFrom(sumVector);
              }
          });
  
          return totalSumVector.convertToFloats();
      }
  }
  