public AbstractExpectationProvider(IExpectationRegion region) {
   super();
   Preconditions.checkPositionIndex(region.getOffset(), region.getDocument().length());
   Preconditions.checkPositionIndex(
       region.getOffset() + region.getLength(), region.getDocument().length());
   this.region = region;
 }
Example #2
0
 public void testCheckPositionIndex_withDesc_negative() {
   try {
     Preconditions.checkPositionIndex(-1, 1, "foo");
     fail();
   } catch (IndexOutOfBoundsException expected) {
     assertThat(expected).hasMessage("foo (-1) must not be negative");
   }
 }
Example #3
0
 public void testCheckPositionIndex_withDesc_tooHigh() {
   try {
     Preconditions.checkPositionIndex(2, 1, "foo");
     fail();
   } catch (IndexOutOfBoundsException expected) {
     assertThat(expected).hasMessage("foo (2) must not be greater than size (1)");
   }
 }
  public ListIterator<E> listIterator(final int start) {
    Preconditions.checkPositionIndex(start, size);

    return new ListIterator<E>() {
      int index = start;

      public boolean hasNext() {
        return index < size;
      }

      public boolean hasPrevious() {
        return index > 0;
      }

      public int nextIndex() {
        return index;
      }

      public int previousIndex() {
        return index - 1;
      }

      public E next() {
        E result;
        try {
          result = get(index);
        } catch (IndexOutOfBoundsException rethrown) {
          throw new NoSuchElementException();
        }
        index++;
        return result;
      }

      public E previous() {
        E result;
        try {
          result = get(index - 1);
        } catch (IndexOutOfBoundsException rethrown) {
          throw new NoSuchElementException();
        }
        index--;
        return result;
      }

      public void set(E o) {
        throw new UnsupportedOperationException();
      }

      public void add(E o) {
        throw new UnsupportedOperationException();
      }

      public void remove() {
        throw new UnsupportedOperationException();
      }
    };
  }
  /**
   * Returns the highest intensity value. Returns 0 if the list has no data points.
   *
   * @return a {@link java.lang.Float} object.
   * @param intensityValues an array of float.
   * @param size a {@link java.lang.Integer} object.
   * @param mzValues an array of double.
   * @param mzRange a {@link com.google.common.collect.Range} object.
   */
  public static @Nonnull Float getMaxIntensity(
      @Nonnull double mzValues[],
      @Nonnull float intensityValues[],
      @Nonnull Integer size,
      @Nonnull Range<Double> mzRange) {

    // Parameter check
    Preconditions.checkNotNull(mzValues);
    Preconditions.checkNotNull(intensityValues);
    Preconditions.checkNotNull(size);
    Preconditions.checkPositionIndex(size, mzValues.length);
    Preconditions.checkPositionIndex(size, intensityValues.length);
    Preconditions.checkNotNull(mzRange);

    Integer topIndex = getBasePeakIndex(mzValues, intensityValues, size, mzRange);
    if (topIndex == null) return 0f;
    return intensityValues[topIndex];
  }
Example #6
0
 public void testCheckPositionIndex_badSize() {
   try {
     Preconditions.checkPositionIndex(1, -1);
     fail();
   } catch (IllegalArgumentException expected) {
     // don't care what the message text is, as this is an invalid usage of
     // the Preconditions class, unlike all the other exceptions it throws
   }
 }
 /**
  * Returns the index of the first matching character in a character sequence, starting from a
  * given position, or {@code -1} if no character matches after that position.
  *
  * <p>The default implementation iterates over the sequence in forward order, beginning at {@code
  * start}, calling {@link #matches} for each character.
  *
  * @param sequence the character sequence to examine
  * @param start the first index to examine; must be nonnegative and no greater than {@code
  *     sequence.length()}
  * @return the index of the first matching character, guaranteed to be no less than {@code start},
  *     or {@code -1} if no character matches
  * @throws IndexOutOfBoundsException if start is negative or greater than {@code
  *     sequence.length()}
  */
 public int indexIn(CharSequence sequence, int start) {
   int length = sequence.length();
   Preconditions.checkPositionIndex(start, length);
   for (int i = start; i < length; i++) {
     if (matches(sequence.charAt(i))) {
       return i;
     }
   }
   return -1;
 }
  /**
   * Calculates the total ion current (=sum of all intensity values)
   *
   * @return a {@link java.lang.Float} object.
   * @param intensityValues an array of float.
   * @param size a {@link java.lang.Integer} object.
   * @param mzValues an array of double.
   * @param mzRange a {@link com.google.common.collect.Range} object.
   */
  public static @Nonnull Float getTIC(
      @Nonnull double mzValues[],
      @Nonnull float intensityValues[],
      @Nonnull Integer size,
      @Nonnull Range<Double> mzRange) {

    // Parameter check
    Preconditions.checkNotNull(mzValues);
    Preconditions.checkNotNull(intensityValues);
    Preconditions.checkNotNull(size);
    Preconditions.checkPositionIndex(size, mzValues.length);
    Preconditions.checkPositionIndex(size, intensityValues.length);
    Preconditions.checkNotNull(mzRange);

    float tic = 0f;
    for (int i = 0; i < size; i++) {
      if (mzRange.contains(mzValues[i])) tic += intensityValues[i];
    }
    return tic;
  }
  /**
   * Returns the index of the highest intensity value. Returns null if the list has no data points
   * or if no data point was found within the mz range.
   *
   * @param mzRange a {@link com.google.common.collect.Range} object.
   * @return a {@link java.lang.Integer} object.
   * @param mzValues an array of double.
   * @param intensityValues an array of float.
   * @param size a {@link java.lang.Integer} object.
   */
  public static @Nullable Integer getBasePeakIndex(
      @Nonnull double mzValues[],
      @Nonnull float intensityValues[],
      @Nonnull Integer size,
      @Nonnull Range<Double> mzRange) {

    // Parameter check
    Preconditions.checkNotNull(intensityValues);
    Preconditions.checkNotNull(mzValues);
    Preconditions.checkNotNull(size);
    Preconditions.checkPositionIndex(size, mzValues.length);
    Preconditions.checkPositionIndex(size, intensityValues.length);
    Preconditions.checkNotNull(mzRange);

    Integer topIndex = null;
    for (int i = 0; i < size; i++) {
      if ((topIndex == null || intensityValues[i] > intensityValues[topIndex])
          && mzRange.contains(mzValues[i])) topIndex = i;
    }
    return topIndex;
  }
  @SuppressWarnings("null")
  public static @Nonnull String msSpectrumToString(
      @Nonnull double mzValues[], @Nonnull float intensityValues[], @Nonnull Integer size) {

    // Parameter check
    Preconditions.checkNotNull(mzValues);
    Preconditions.checkNotNull(intensityValues);
    Preconditions.checkNotNull(size);
    Preconditions.checkPositionIndex(size, mzValues.length);
    Preconditions.checkPositionIndex(size, intensityValues.length);

    StringBuilder b = new StringBuilder();
    for (int i = 0; i < size; i++) {
      b.append(mzValues[i]);
      b.append(" ");
      b.append(intensityValues[i]);
      if (i < size - 1) b.append("\n");
    }

    return b.toString();
  }
  static <K, V> RegularImmutableBiMap<K, V> fromEntryArray(int n, Entry<K, V>[] entryArray) {
    checkPositionIndex(n, entryArray.length);
    int tableSize = Hashing.closedTableSize(n, MAX_LOAD_FACTOR);
    int mask = tableSize - 1;
    ImmutableMapEntry<K, V>[] keyTable = createEntryArray(tableSize);
    ImmutableMapEntry<K, V>[] valueTable = createEntryArray(tableSize);
    Entry<K, V>[] entries;
    if (n == entryArray.length) {
      entries = entryArray;
    } else {
      entries = createEntryArray(n);
    }
    int hashCode = 0;

    for (int i = 0; i < n; i++) {
      @SuppressWarnings("unchecked")
      Entry<K, V> entry = entryArray[i];
      K key = entry.getKey();
      V value = entry.getValue();
      checkEntryNotNull(key, value);
      int keyHash = key.hashCode();
      int valueHash = value.hashCode();
      int keyBucket = Hashing.smear(keyHash) & mask;
      int valueBucket = Hashing.smear(valueHash) & mask;

      ImmutableMapEntry<K, V> nextInKeyBucket = keyTable[keyBucket];
      checkNoConflictInKeyBucket(key, entry, nextInKeyBucket);
      ImmutableMapEntry<K, V> nextInValueBucket = valueTable[valueBucket];
      checkNoConflictInValueBucket(value, entry, nextInValueBucket);
      ImmutableMapEntry<K, V> newEntry;
      if (nextInValueBucket == null && nextInKeyBucket == null) {
        /*
         * TODO(user): consider using a NonTerminalImmutableMapEntry when nextInKeyBucket is
         * nonnull but nextInValueBucket is null.  This may save a few bytes on some platforms, but
         * 2-morphic call sites are often optimized much better than 3-morphic, so it'd require
         * benchmarking.
         */
        boolean reusable =
            entry instanceof ImmutableMapEntry && ((ImmutableMapEntry<K, V>) entry).isReusable();
        newEntry =
            reusable ? (ImmutableMapEntry<K, V>) entry : new ImmutableMapEntry<K, V>(key, value);
      } else {
        newEntry =
            new NonTerminalImmutableBiMapEntry<K, V>(
                key, value, nextInKeyBucket, nextInValueBucket);
      }
      keyTable[keyBucket] = newEntry;
      valueTable[valueBucket] = newEntry;
      entries[i] = newEntry;
      hashCode += keyHash ^ valueHash;
    }
    return new RegularImmutableBiMap<K, V>(keyTable, valueTable, entries, mask, hashCode);
  }
  /**
   * Calculates the total ion current (=sum of all intensity values)
   *
   * @return a {@link java.lang.Float} object.
   * @param intensityValues an array of float.
   * @param size a {@link java.lang.Integer} object.
   */
  public static @Nonnull Float getTIC(@Nonnull float intensityValues[], @Nonnull Integer size) {

    // Parameter check
    Preconditions.checkNotNull(intensityValues);
    Preconditions.checkNotNull(size);
    Preconditions.checkPositionIndex(size, intensityValues.length);

    float tic = 0f;
    for (int i = 0; i < size; i++) {
      tic += intensityValues[i];
    }
    return tic;
  }
  /**
   * Returns the m/z range of given data points. Can return null if the data point list is empty.
   *
   * @return a {@link com.google.common.collect.Range} object.
   * @param mzValues an array of double.
   * @param size a {@link java.lang.Integer} object.
   */
  @Nullable
  public static Range<Double> getMzRange(@Nonnull double mzValues[], @Nonnull Integer size) {

    // Parameter check
    Preconditions.checkNotNull(mzValues);
    Preconditions.checkNotNull(size);
    Preconditions.checkPositionIndex(size, mzValues.length);

    if (size == 0) return null;

    double min = mzValues[0];
    double max = mzValues[size - 1];
    return Range.closed(min, max);
  }
  /**
   * Returns the index of the highest intensity value. Returns null if the list has no data points.
   *
   * @return a {@link java.lang.Integer} object.
   * @param intensityValues an array of float.
   * @param size a {@link java.lang.Integer} object.
   */
  public static @Nullable Integer getBasePeakIndex(
      @Nonnull float intensityValues[], @Nonnull Integer size) {

    // Parameter check
    Preconditions.checkNotNull(intensityValues);
    Preconditions.checkNotNull(size);
    Preconditions.checkPositionIndex(size, intensityValues.length);

    Integer topIndex = null;
    for (int i = 0; i < size; i++) {
      if ((topIndex == null) || ((intensityValues[i] > intensityValues[topIndex]))) topIndex = i;
    }
    return topIndex;
  }
  public static void normalizeIntensity(
      @Nonnull float intensityValues[], @Nonnull Integer size, @Nonnull Float scale) {

    // Parameter check
    Preconditions.checkNotNull(intensityValues);
    Preconditions.checkNotNull(size);
    Preconditions.checkPositionIndex(size, intensityValues.length);
    Preconditions.checkNotNull(scale);

    final float max = getMaxIntensity(intensityValues, size);

    for (int i = 0; i < intensityValues.length; i++) {
      intensityValues[i] = intensityValues[i] / max * scale;
    }
  }
Example #16
0
  // Assumes input grouped on relevant pagesHashStrategy columns
  private static int findGroupEnd(
      PagesIndex pagesIndex, PagesHashStrategy pagesHashStrategy, int startPosition) {
    checkArgument(pagesIndex.getPositionCount() > 0, "Must have at least one position");
    checkPositionIndex(startPosition, pagesIndex.getPositionCount(), "startPosition out of bounds");

    // Short circuit if the whole page has the same value
    if (pagesIndex.positionEqualsPosition(
        pagesHashStrategy, startPosition, pagesIndex.getPositionCount() - 1)) {
      return pagesIndex.getPositionCount();
    }

    // TODO: do position binary search
    int endPosition = startPosition + 1;
    while ((endPosition < pagesIndex.getPositionCount())
        && pagesIndex.positionEqualsPosition(pagesHashStrategy, endPosition - 1, endPosition)) {
      endPosition++;
    }
    return endPosition;
  }
Example #17
0
  public void add(Slice key, Slice value) {
    Preconditions.checkNotNull(key, "key is null");
    Preconditions.checkNotNull(value, "value is null");
    Preconditions.checkState(!finished, "block is finished");
    Preconditions.checkPositionIndex(restartBlockEntryCount, blockRestartInterval);

    Preconditions.checkArgument(
        lastKey == null || comparator.compare(key, lastKey) > 0,
        "key %s must be greater than last key %s",
        key,
        lastKey);

    int sharedKeyBytes = 0;
    if (restartBlockEntryCount < blockRestartInterval) {
      sharedKeyBytes = calculateSharedBytes(key, lastKey);
    } else {
      // restart prefix compression
      restartPositions.add(block.size());
      restartBlockEntryCount = 0;
    }

    int nonSharedKeyBytes = key.length() - sharedKeyBytes;

    // write "<shared><non_shared><value_size>"
    VariableLengthQuantity.writeVariableLengthInt(sharedKeyBytes, block);
    VariableLengthQuantity.writeVariableLengthInt(nonSharedKeyBytes, block);
    VariableLengthQuantity.writeVariableLengthInt(value.length(), block);

    // write non-shared key bytes
    block.writeBytes(key, sharedKeyBytes, nonSharedKeyBytes);

    // write value bytes
    block.writeBytes(value, 0, value.length());

    // update last key
    lastKey = key;

    // update state
    entryCount++;
    restartBlockEntryCount++;
  }
Example #18
0
  /**
   * Returns a list iterator containing the elements in the specified range of {@code array} in
   * order, starting at the specified index.
   *
   * <p>The {@code Iterable} equivalent of this method is {@code
   * Arrays.asList(array).subList(offset, offset + length).listIterator(index)}.
   */
  static <T> UnmodifiableListIterator<T> forArray(
      final T[] array, final int offset, int length, int index) {
    checkArgument(length >= 0);
    int end = offset + length;

    // Technically we should give a slightly more descriptive error on overflow
    Preconditions.checkPositionIndexes(offset, end, array.length);
    Preconditions.checkPositionIndex(index, length);
    if (length == 0) {
      return emptyListIterator();
    }

    /*
     * We can't use call the two-arg constructor with arguments (offset, end)
     * because the returned Iterator is a ListIterator that may be moved back
     * past the beginning of the iteration.
     */
    return new AbstractIndexedListIterator<T>(length, index) {
      @Override
      protected T get(int index) {
        return array[offset + index];
      }
    };
  }
 public UnmodifiableListIterator<Object> listIterator(int paramInt) {
   Preconditions.checkPositionIndex(paramInt, 0);
   return Iterators.EMPTY_LIST_ITERATOR;
 }
Example #20
0
 @Override
 public void writeTo(OutputStream stream, long start, long end) throws IOException {
   Preconditions.checkPositionIndex(Ints.checkedCast(end), size);
   stream.write(bytes, Ints.checkedCast(start), Ints.checkedCast(end - start));
 }
Example #21
0
 private int reversePosition(int index) {
   int size = size();
   checkPositionIndex(index, size);
   return size - index;
 }
Example #22
0
 /**
  * Returns a new {@link ByteArrayDataInput} instance to read from the {@code bytes} array,
  * starting at the given position.
  *
  * @throws IndexOutOfBoundsException if {@code start} is negative or greater than the length of
  *     the array
  */
 public static ByteArrayDataInput newDataInput(byte[] bytes, int start) {
   checkPositionIndex(start, bytes.length);
   return new ByteArrayDataInputStream(bytes, start);
 }
Example #23
0
 public void testCheckPositionIndex_ok() {
   assertEquals(0, Preconditions.checkPositionIndex(0, 0));
   assertEquals(0, Preconditions.checkPositionIndex(0, 1));
   assertEquals(1, Preconditions.checkPositionIndex(1, 1));
 }
 public UnmodifiableListIterator<E> a(int paramInt)
 {
   Preconditions.checkPositionIndex(paramInt, 1);
   return new SingletonImmutableList.1(this, paramInt);
 }
 @Override
 public int indexIn(CharSequence sequence, int start) {
   int length = sequence.length();
   Preconditions.checkPositionIndex(start, length);
   return -1;
 }