예제 #1
0
 // Calls the Combiner object on each element to combine
 // it with a running result, which is finally returned:
 public static <T> T reduce(Iterable<T> seq, Combiner<T> combiner) {
   Iterator<T> it = seq.iterator();
   if (it.hasNext()) {
     T result = it.next();
     while (it.hasNext()) result = combiner.combine(result, it.next());
     return result;
   }
   // If seq is the empty list:
   return null; // Or throw exception
 }
예제 #2
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  /**
   * Remaps the stratifications from one stratification set to another, combining the values in V
   * according to the combiner function.
   *
   * <p>stratifierToReplace defines a set of states S1, while newStratifier defines a new set S2.
   * remappedStates is a map from all of S1 into at least some of S2. This function creates a new,
   * fully initialized manager where all of the data in this new manager is derived from the
   * original data in this object combined according to the mapping remappedStates. When multiple
   * elements of S1 can map to the same value in S2, these are sequentially combined by the function
   * combiner. Suppose for example at states s1, s2, and s3 all map to N1. Eventually the value
   * associated with state N1 would be
   *
   * <p>value(N1) = combine(value(s1), combine(value(s2), value(s3))
   *
   * <p>in some order for s1, s2, and s3, which is not defined. Note that this function only
   * supports combining one stratification at a time, but in principle a loop over stratifications
   * and this function could do the multi-dimensional collapse.
   *
   * @param stratifierToReplace
   * @param newStratifier
   * @param combiner
   * @param remappedStates
   * @return
   */
  public StratificationManager<K, V> combineStrats(
      final K stratifierToReplace,
      final K newStratifier,
      final Combiner<V> combiner,
      final Map<Object, Object> remappedStates) {
    // make sure the mapping is reasonable
    if (!newStratifier.getAllStates().containsAll(remappedStates.values()))
      throw new ReviewedGATKException(
          "combineStrats: remapped states contains states not found in newStratifer state set");

    if (!remappedStates.keySet().containsAll(stratifierToReplace.getAllStates()))
      throw new ReviewedGATKException(
          "combineStrats: remapped states missing mapping for some states");

    // the new strats are the old ones with the single replacement
    final List<K> newStrats = new ArrayList<K>(getStratifiers());
    final int stratOffset = newStrats.indexOf(stratifierToReplace);
    if (stratOffset == -1)
      throw new ReviewedGATKException(
          "Could not find strat to replace "
              + stratifierToReplace
              + " in existing strats "
              + newStrats);
    newStrats.set(stratOffset, newStratifier);

    // create an empty but fully initialized new manager
    final StratificationManager<K, V> combined = new StratificationManager<K, V>(newStrats);

    // for each key, get its state, update it according to the map, and update the combined manager
    for (int key = 0; key < size(); key++) {
      // the new state is just the old one with the replacement
      final List<Object> newStates = new ArrayList<Object>(getStatesForKey(key));
      final Object oldState = newStates.get(stratOffset);
      final Object newState = remappedStates.get(oldState);
      newStates.set(stratOffset, newState);

      // look up the new key given the new state
      final int combinedKey = combined.getKey(newStates);
      if (combinedKey == -1)
        throw new ReviewedGATKException(
            "Couldn't find key for states: " + Utils.join(",", newStates));

      // combine the old value with whatever new value is in combined already
      final V combinedValue = combiner.combine(combined.get(combinedKey), get(key));

      // update the value associated with combined key
      combined.set(combinedKey, combinedValue);
    }

    return combined;
  }
예제 #3
0
 /**
  * Write partial content, only
  *
  * @param out
  * @param start
  * @param finish
  * @throws IOException
  */
 public void writeContent(OutputStream out, long start, Long finish) throws IOException {
   Combiner combiner = new Combiner();
   List<String> fanoutCrcs = getFanout().getHashes();
   combiner.combine(fanoutCrcs, hashStore, blobStore, out, start, finish);
   out.flush();
 }