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.Block;
  import juicebox.data.ContactRecord;
  import juicebox.data.DatasetReader;
  import juicebox.data.MatrixZoomData;
  import juicebox.data.basics.ListOfDoubleArrays;
  import juicebox.data.basics.ListOfFloatArrays;
  import org.broad.igv.util.collections.LRUCache;
  
  import java.util.Iterator;
  
  public class ZDIteratorContainer extends IteratorContainer {
  
      private final LRUCache<String, Block> blockCache;
      private final DatasetReader reader;
      private final MatrixZoomData zd;
  
      public ZDIteratorContainer(DatasetReader reader, MatrixZoomData zd, LRUCache<String, Block> blockCache) {
          super(zd.getXGridAxis().getBinCount());
          this.reader = reader;
          this.zd = zd;
          this.blockCache = blockCache;
      }
  
      @Override
      public Iterator<ContactRecord> getNewContactRecordIterator() {
          return new ContactRecordIterator(reader, zd, blockCache);
      }
  
      public static ListOfFloatArrays matrixVectorMultiplyOnIterator(Iterator<ContactRecord> iterator,
                                                                     ListOfFloatArrays vector, long vectorLength) {
          ListOfDoubleArrays sumVector = new ListOfDoubleArrays(vectorLength);
          while (iterator.hasNext()) {
              ContactRecord cr = iterator.next();
              ListIteratorContainer.matrixVectorMult(vector, sumVector, cr);
          }
          return sumVector.convertToFloats();
      }
  
      @Override
      public ListOfFloatArrays sparseMultiply(ListOfFloatArrays vector, long vectorLength) {
          return matrixVectorMultiplyOnIterator(getNewContactRecordIterator(), vector, vectorLength);
      }
  
      @Override
      public void clear() {
          //blockCache.clear();
      }
  }
  