content: /*
   * The MIT License (MIT)
   *
   * Copyright (c) 2011-2020 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 NONINFRINGEMENT. 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 htsjdk.tribble.util.LittleEndianInputStream;
  import juicebox.tools.utils.original.IndexEntry;
  
  import java.io.IOException;
  import java.util.ArrayList;
  import java.util.HashMap;
  import java.util.List;
  import java.util.Map;
  
  public class BlockIndex {
      protected final Map<Integer, IndexEntry> blockIndex;
      protected final int numBlocks;
  
      public BlockIndex(int nBlocks) {
          numBlocks = nBlocks;
          blockIndex = new HashMap<>(nBlocks);
      }
  
      public void populateBlocks(LittleEndianInputStream dis) throws IOException {
          for (int b = 0; b < numBlocks; b++) {
              int blockNumber = dis.readInt();
              long filePosition = dis.readLong();
              int blockSizeInBytes = dis.readInt();
              blockIndex.put(blockNumber, new IndexEntry(filePosition, blockSizeInBytes));
          }
      }
  
      public List<Integer> getBlockNumbers() {
          return new ArrayList<>(blockIndex.keySet());
      }
  
      public Integer getBlockSize(int num) {
          if (blockIndex.containsKey(num)) {
              return blockIndex.get(num).size;
          } else {
              return null;
          }
      }
  
      public IndexEntry getBlock(int blockNumber) {
          return blockIndex.get(blockNumber);
      }
  }
  