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.HiCGlobals;
  import juicebox.data.Block;
  import juicebox.data.ContactRecord;
  import juicebox.data.DatasetReader;
  import juicebox.data.MatrixZoomData;
  import juicebox.windowui.NormalizationHandler;
  import org.broad.igv.util.collections.LRUCache;
  
  import java.io.IOException;
  import java.util.Iterator;
  import java.util.List;
  
  public /**
   * Class for iterating over the contact records
   */
  class ContactRecordIterator implements Iterator<ContactRecord> {
      
      private final List<Integer> blockNumbers;
      private int blockIdx;
      private Iterator<ContactRecord> currentBlockIterator;
      private final DatasetReader reader;
      private final MatrixZoomData zd;
      private final LRUCache<String, Block> blockCache;
      
      /**
       * Initializes the iterator
       */
      ContactRecordIterator(DatasetReader reader, MatrixZoomData zd, LRUCache<String, Block> blockCache) {
          this.reader = reader;
          this.zd = zd;
          this.blockCache = blockCache;
          this.blockIdx = -1;
          this.blockNumbers = reader.getBlockNumbers(zd);
      }
  
      /**
       * Indicates whether or not there is another block waiting; checks current block
       * iterator and creates a new one if need be
       *
       * @return true if there is another block to be read
       */
      @Override
      public boolean hasNext() {
  
          if (currentBlockIterator != null && currentBlockIterator.hasNext()) {
              return true;
          } else {
              blockIdx++;
              if (blockNumbers != null && blockIdx < blockNumbers.size()) {
                  try {
                      int blockNumber = blockNumbers.get(blockIdx);
  
                      // Optionally check the cache
                      String key = zd.getBlockKey(blockNumber, NormalizationHandler.NONE);
                      Block nextBlock;
                      if (HiCGlobals.useCache && blockCache.containsKey(key)) {
                          nextBlock = blockCache.get(key);
                      } else {
                          nextBlock = reader.readNormalizedBlock(blockNumber, zd, NormalizationHandler.NONE);
                      }
                      currentBlockIterator = nextBlock.getContactRecords().iterator();
                      return true;
                  } catch (IOException e) {
                      System.err.println("Error fetching block " + e.getMessage());
                      return false;
                  }
              }
          }
  
          return false;
      }
  
      /**
       * Returns the next contact record
       *
       * @return The next contact record
       */
      @Override
      public ContactRecord next() {
          return currentBlockIterator == null ? null : currentBlockIterator.next();
      }
  
      /**
       * Not supported
       */
      @Override
      public void remove() {
          //Not supported
          throw new RuntimeException("remove() is not supported");
      }
  }
  