Java Code Examples for com.google.common.collect.Range#encloses()

@MethodParser("random")
public RandomFilter parseRandom(Element el) throws InvalidXMLException {
  Node node = new Node(el);
  Range<Double> chance;
  try {
    chance = Range.closedOpen(0d, XMLUtils.parseNumber(node, Double.class));
  } catch (InvalidXMLException e) {
    chance = XMLUtils.parseNumericRange(node, Double.class);
  }

  Range<Double> valid = Range.closed(0d, 1d);
  if (valid.encloses(chance)) {
    return new RandomFilter(chance);
  } else {
    double lower = chance.hasLowerBound() ? chance.lowerEndpoint() : Double.NEGATIVE_INFINITY;
    double upper = chance.hasUpperBound() ? chance.upperEndpoint() : Double.POSITIVE_INFINITY;
    double invalid;
    if (!valid.contains(lower)) {
      invalid = lower;
    } else {
      invalid = upper;
    }

    throw new InvalidXMLException("chance value (" + invalid + ") is not between 0 and 1", el);
  }
}
 

static int moveDelta(Range<Integer> container, Range<Integer> range) {
  if (container.encloses(range)) return 0;
  if (container.upperEndpoint() - container.lowerEndpoint() < range.upperEndpoint() - range.lowerEndpoint()) {
    return container.lowerEndpoint() - range.lowerEndpoint();
  }

  if (container.contains(range.upperEndpoint())) {
    return container.lowerEndpoint() - range.lowerEndpoint();
  }

  if (container.contains(range.lowerEndpoint())) {
    return container.upperEndpoint() - range.upperEndpoint();
  }

  if (container.upperEndpoint() < range.lowerEndpoint()) {
    return container.upperEndpoint() - range.upperEndpoint();
  } else if (container.lowerEndpoint() > range.upperEndpoint()) {
    return container.lowerEndpoint() - range.lowerEndpoint();
  } else {
    throw new IllegalStateException("This can't happen");
  }
}
 

/** Weakens a term so that it checks only what is not implied by predicates.
 *
 * <p>The term is broken into "ref comparison constant",
 * for example "$0 &lt; 5".
 *
 * <p>Examples:
 * <ul>
 *
 * <li>{@code residue($0 < 10, [$0 < 5])} returns {@code true}
 *
 * <li>{@code residue($0 < 10, [$0 < 20, $0 > 0])} returns {@code $0 < 10}
 * </ul>
 */
private <C extends Comparable<C>> Range<C> residue(RexNode ref, Range<C> r0, List<RexNode> predicates,
        Class<C> clazz) {
    for (RexNode predicate : predicates) {
        switch (predicate.getKind()) {
        case EQUALS:
        case LESS_THAN:
        case LESS_THAN_OR_EQUAL:
        case GREATER_THAN:
        case GREATER_THAN_OR_EQUAL:
            final RexCall call = (RexCall) predicate;
            if (call.getOperands().get(0).equals(ref) && call.getOperands().get(1) instanceof RexLiteral) {
                final RexLiteral literal = (RexLiteral) call.getOperands().get(1);
                final C c1 = literal.getValueAs(clazz);
                final Range<C> r1 = range(predicate.getKind(), c1);
                if (r0.encloses(r1)) {
                    // Given these predicates, term is always satisfied.
                    // e.g. r0 is "$0 < 10", r1 is "$0 < 5"
                    return Range.all();
                }
                if (r0.isConnected(r1)) {
                    return r0.intersection(r1);
                }
                // Ranges do not intersect. Return null meaning the empty range.
                return null;
            }
        }
    }
    return r0;
}
 

/** Weakens a term so that it checks only what is not implied by predicates.
 *
 * <p>The term is broken into "ref comparison constant",
 * for example "$0 &lt; 5".
 *
 * <p>Examples:
 * <ul>
 *
 * <li>{@code residue($0 < 10, [$0 < 5])} returns {@code true}
 *
 * <li>{@code residue($0 < 10, [$0 < 20, $0 > 0])} returns {@code $0 < 10}
 * </ul>
 */
private <C extends Comparable<C>> Range<C> residue(RexNode ref, Range<C> r0,
    List<RexNode> predicates, Class<C> clazz) {
  for (RexNode predicate : predicates) {
    switch (predicate.getKind()) {
    case EQUALS:
    case LESS_THAN:
    case LESS_THAN_OR_EQUAL:
    case GREATER_THAN:
    case GREATER_THAN_OR_EQUAL:
      final RexCall call = (RexCall) predicate;
      if (call.operands.get(0).equals(ref)
          && call.operands.get(1) instanceof RexLiteral) {
        final RexLiteral literal = (RexLiteral) call.operands.get(1);
        final C c1 = literal.getValueAs(clazz);
        final Range<C> r1 = range(predicate.getKind(), c1);
        if (r0.encloses(r1)) {
          // Given these predicates, term is always satisfied.
          // e.g. r0 is "$0 < 10", r1 is "$0 < 5"
          return Range.all();
        }
        if (r0.isConnected(r1)) {
          return r0.intersection(r1);
        }
        // Ranges do not intersect. Return null meaning the empty range.
        return null;
      }
    }
  }
  return r0;
}
 

@MethodParser("random")
public Filter parseRandom(Element el) throws InvalidXMLException {
    Node node = new Node(el);
    Range<Double> chance;
    try {
        chance = Range.closedOpen(0d, XMLUtils.parseNumber(node, Double.class));
    } catch(InvalidXMLException e) {
        chance = XMLUtils.parseNumericRange(node, Double.class);
    }

    Range<Double> valid = Range.closed(0d, 1d);
    if (valid.encloses(chance)) {
        return proto.isNoOlderThan(ProtoVersions.EVENT_QUERIES) ? new RandomFilter(chance)
                                                                : new LegacyRandomFilter(chance);
    } else {
        double lower = chance.hasLowerBound() ? chance.lowerEndpoint() : Double.NEGATIVE_INFINITY;
        double upper = chance.hasUpperBound() ? chance.upperEndpoint() : Double.POSITIVE_INFINITY;
        double invalid;
        if(!valid.contains(lower)) {
            invalid = lower;
        } else {
            invalid = upper;
        }

        throw new InvalidXMLException("chance value (" + invalid + ") is not between 0 and 1", el);
    }
}
 

public boolean matches(FileSystem fs, FileAttributes attributes) throws IOException{
  if (ranges.isEmpty() || attributes.isDirectory()) {
    return false;
  }
  // walk all the way down in the symlinks until a hard entry is reached
  FileAttributes current = attributes;
  while (current.isSymbolicLink()) {
    current = fs.getFileAttributes(attributes.getSymbolicLink());
  }
  // if hard entry is not a file nor can it be a symlink then it is not readable simply deny matching.
  if (!current.isRegularFile()) {
    return false;
  }

  final Range<Long> fileRange = Range.closedOpen( 0L, attributes.size());

  try (FSInputStream is = fs.open(attributes.getPath())) {
    for(RangeMagics rMagic : ranges) {
      Range<Long> r = rMagic.range;
      if (!fileRange.encloses(r)) {
        continue;
      }
      int len = (int) (r.upperEndpoint() - r.lowerEndpoint());
      byte[] bytes = new byte[len];
      is.setPosition(r.lowerEndpoint());
      IOUtils.readFully(is, bytes);
      for (byte[] magic : rMagic.magics) {
        if (Arrays.equals(magic, bytes)) {
          return true;
        }
      }
    }
  }
  return false;
}
 

private void addFieldstoTree() {

			if (!fieldLineRanges.isEmpty()) {

				final Table<FieldDeclaration, ASTNode, ArrayList<String>> fieldNodes = HashBasedTable.create();

				// Conflate field node ranges
				for (final Range<Integer> lineRange : fieldLineRanges.asRanges()) {

					// Bizarrely RangeSet uses closedOpen ranges
					final int startLine = lineRange.lowerEndpoint();
					final int endLine = lineRange.upperEndpoint() - 1;

					// Add ranges to allFolds along with first
					// non-empty line of comment
					final Integer startChar = lineToFieldRanges.get(startLine).lowerEndpoint();
					final Integer endChar = lineToFieldRanges.get(endLine).upperEndpoint();
					final Range<Integer> conflatedRange = Range.closed(startChar, endChar);
					allFolds.add(conflatedRange);

					// Get tokens in conflated range
					final ArrayList<String> tokens = Lists.newArrayList();
					for (final Range<Integer> range : fieldIdentifiers.keySet()) {
						if (conflatedRange.encloses(range))
							tokens.addAll(fieldIdentifiers.get(range));
					}

					// Create single block node and add tokens
					final VariableDeclarationFragment fragment = cu.getAST().newVariableDeclarationFragment();
					final FieldDeclaration node = cu.getAST().newFieldDeclaration(fragment);
					final ASTNode parent = fieldLineParentNodes.get(startLine);
					node.setSourceRange(startChar, endChar - startChar + 1);
					fieldNodes.put(node, parent, tokens);
				}

				// Add conflated field nodes to tree
				tree.addNodes(fieldNodes);
			}
		}
 

/** Weakens a term so that it checks only what is not implied by predicates.
 *
 * <p>The term is broken into "ref comparison constant",
 * for example "$0 &lt; 5".
 *
 * <p>Examples:
 * <ul>
 *
 * <li>{@code residue($0 < 10, [$0 < 5])} returns {@code true}
 *
 * <li>{@code residue($0 < 10, [$0 < 20, $0 > 0])} returns {@code $0 < 10}
 * </ul>
 */
private <C extends Comparable<C>> Range<C> residue(RexNode ref, Range<C> r0,
    List<RexNode> predicates, Class<C> clazz) {
  Range<C> result = r0;
  for (RexNode predicate : predicates) {
    switch (predicate.getKind()) {
    case EQUALS:
    case LESS_THAN:
    case LESS_THAN_OR_EQUAL:
    case GREATER_THAN:
    case GREATER_THAN_OR_EQUAL:
      final RexCall call = (RexCall) predicate;
      if (call.operands.get(0).equals(ref)
          && call.operands.get(1) instanceof RexLiteral) {
        final RexLiteral literal = (RexLiteral) call.operands.get(1);
        final C c1 = literal.getValueAs(clazz);
        final Range<C> r1 = range(predicate.getKind(), c1);
        if (result.encloses(r1)) {
          // Given these predicates, term is always satisfied.
          // e.g. r0 is "$0 < 10", r1 is "$0 < 5"
          result = Range.all();
          continue;
        }
        if (result.isConnected(r1)) {
          result = result.intersection(r1);
          continue;
        }
        // Ranges do not intersect. Return null meaning the empty range.
        return null;
      }
    }
  }
  return result;
}
 

void updateTitle() {

    NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
    NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
    NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

    StringBuffer mainTitle = new StringBuffer();
    StringBuffer subTitle = new StringBuffer();

    // If all data files have m/z range less than or equal to range of
    // the plot (mzMin, mzMax), then call this TIC, otherwise XIC
    Set<RawDataFile> fileSet = ticDataSets.keySet();
    String ticOrXIC = "TIC";

    // Enlarge range a bit to avoid rounding errors
    Range<Double> mzRange2 = Range.range(mzRange.lowerEndpoint() - 1, BoundType.CLOSED,
        mzRange.upperEndpoint() + 1, BoundType.CLOSED);
    for (RawDataFile df : fileSet) {
      if (!mzRange2.encloses(df.getDataMZRange())) {
        ticOrXIC = "XIC";
        break;
      }
    }

    if (plotType == TICPlotType.BASEPEAK) {
      if (ticOrXIC.equals("TIC")) {
        mainTitle.append("Base peak chromatogram");
      } else {
        mainTitle.append("XIC (base peak)");
      }
    } else {
      if (ticOrXIC.equals("TIC")) {
        mainTitle.append("TIC");
      } else {
        mainTitle.append("XIC");
      }
    }

    mainTitle.append(", m/z: " + mzFormat.format(mzRange.lowerEndpoint()) + " - "
        + mzFormat.format(mzRange.upperEndpoint()));

    CursorPosition pos = getCursorPosition();

    if (pos != null) {
      subTitle.append("Selected scan #");
      subTitle.append(pos.getScanNumber());
      if (ticDataSets.size() > 1) {
        subTitle.append(" (" + pos.getDataFile() + ")");
      }
      subTitle.append(", RT: " + rtFormat.format(pos.getRetentionTime()));
      if (plotType == TICPlotType.BASEPEAK) {
        subTitle.append(", base peak: " + mzFormat.format(pos.getMzValue()) + " m/z");
      }
      subTitle.append(", IC: " + intensityFormat.format(pos.getIntensityValue()));
    }

    // update window title
    RawDataFile files[] = ticDataSets.keySet().toArray(new RawDataFile[0]);
    Arrays.sort(files, new SimpleSorter());
    String dataFileNames = Joiner.on(",").join(files);
    setTitle("Chromatogram: [" + dataFileNames + "; " + mzFormat.format(mzRange.lowerEndpoint())
        + " - " + mzFormat.format(mzRange.upperEndpoint()) + " m/z" + "]");

    // update plot title
    ticPlot.setTitle(mainTitle.toString(), subTitle.toString());

  }
 

protected List<FileDownloadRequestChain> getFileDownloadRequestChains(ConcurrentMap<String, DownloadRequestContext> contextMap)
    throws IOException
{
  List<FileDownloadRequestChain> readRequestChainList = new ArrayList<FileDownloadRequestChain>();
  for (Map.Entry<String, DownloadRequestContext> entry : contextMap.entrySet()) {
    Path path = new Path(entry.getKey());
    DownloadRequestContext context = entry.getValue();

    FileSystem fs = FileSystem.get(path.toUri(), conf);
    fs.initialize(path.toUri(), conf);

    String localPath = CacheUtil.getLocalPath(entry.getKey(), conf);
    log.debug("Processing Request for File : " + path.toString() + " LocalFile : " + localPath);
    ByteBuffer directWriteBuffer = bufferPool.getBuffer(diskReadBufferSize);

    FileDownloadRequestChain requestChain = new FileDownloadRequestChain(bookKeeper, fs, localPath,
        directWriteBuffer, conf, context.getRemoteFilePath(), context.getFileSize(),
        context.getLastModifiedTime());

    Range<Long> previousRange = null;
    for (Range<Long> range : context.getRanges().asRanges()) {
      // align range to block boundary
      long startBlock = toStartBlock(range.lowerEndpoint(), conf);
      long endBlock = toEndBlock(range.upperEndpoint(), conf);

      // We can get cases where multiple reads are part of same Block
      Range<Long> currentRange = Range.closedOpen(startBlock, endBlock);
      if (previousRange != null && previousRange.encloses(currentRange)) {
        // already covered in previous request
        continue;
      }

      previousRange = currentRange;

      // Avoid duplicate warm-ups
      List<BlockLocation> blockLocations = null;

      try {
        blockLocations = bookKeeper.getCacheStatus(
                new CacheStatusRequest(
                        context.getRemoteFilePath(),
                        context.getFileSize(),
                        context.getLastModifiedTime(),
                        startBlock,
                        endBlock));
      }
      catch (Exception e) {
        log.warn("Error communicating with bookKeeper", e);
        // Exception is not expected as RemoteFetchProcessor ensures to not start processing until BookKeeper has initialized
        // recover from this, requeue the requests for this file and continue with next file
        remoteFetchProcessor.addToProcessQueueSafe(context.getRemoteFilePath(), context.getRanges().asRanges(), context.getFileSize(), context.getLastModifiedTime());
        requestChain = null;
        break;
      }

      for (int i = 0; i < blockLocations.size(); i++) {
        if (!blockLocations.get(i).getLocation().equals(Location.LOCAL)) {
          continue;
        }

        long block = startBlock + i;
        long startPosition = toBlockStartPosition(block, conf);
        long endPosition = Math.min(toBlockStartPosition(block + 1, conf), context.getFileSize());
        ReadRequest readRequest = new ReadRequest(startPosition, endPosition, startPosition, endPosition, null, 0, context.getFileSize());
        requestChain.addReadRequest(readRequest);
      }
    }

    if (requestChain != null) {
      log.debug("Request added for file: " + requestChain.getRemotePath() + " Number of Requests : " +
              requestChain.getReadRequests().size());

      readRequestChainList.add(requestChain);
    }
  }

  return readRequestChainList;
}
 

void updateTitle() {

    NumberFormat rtFormat = MZmineCore.getConfiguration().getRTFormat();
    NumberFormat mzFormat = MZmineCore.getConfiguration().getMZFormat();
    NumberFormat intensityFormat = MZmineCore.getConfiguration().getIntensityFormat();

    StringBuffer mainTitle = new StringBuffer();
    StringBuffer subTitle = new StringBuffer();

    // If all data files have m/z range less than or equal to range of
    // the plot (mzMin, mzMax), then call this TIC, otherwise XIC
    Set<RawDataFile> fileSet = ticDataSets.keySet();
    String ticOrXIC = "TIC";

    // Enlarge range a bit to avoid rounding errors
    Range<Double> mzRange2 = Range.range(mzRange.lowerEndpoint() - 1, BoundType.CLOSED,
        mzRange.upperEndpoint() + 1, BoundType.CLOSED);
    for (RawDataFile df : fileSet) {
      if (!mzRange2.encloses(df.getDataMZRange())) {
        ticOrXIC = "XIC";
        break;
      }
    }

    if (plotType == TICPlotType.BASEPEAK) {
      if (ticOrXIC.equals("TIC")) {
        mainTitle.append("Base peak chromatogram");
      } else {
        mainTitle.append("XIC (base peak)");
      }
    } else {
      if (ticOrXIC.equals("TIC")) {
        mainTitle.append("TIC");
      } else {
        mainTitle.append("XIC");
      }
    }

    mainTitle.append(", m/z: " + mzFormat.format(mzRange.lowerEndpoint()) + " - "
        + mzFormat.format(mzRange.upperEndpoint()));

    CursorPosition pos = getCursorPosition();

    if (pos != null) {
      subTitle.append("Selected scan #");
      subTitle.append(pos.getScanNumber());
      if (ticDataSets.size() > 1) {
        subTitle.append(" (" + pos.getDataFile() + ")");
      }
      subTitle.append(", RT: " + rtFormat.format(pos.getRetentionTime()));
      if (plotType == TICPlotType.BASEPEAK) {
        subTitle.append(", base peak: " + mzFormat.format(pos.getMzValue()) + " m/z");
      }
      subTitle.append(", IC: " + intensityFormat.format(pos.getIntensityValue()));
    }

    // update window title
    RawDataFile files[] = ticDataSets.keySet().toArray(new RawDataFile[0]);
    Arrays.sort(files, new SimpleSorter());
    String dataFileNames = Joiner.on(",").join(files);
    setTitle("Chromatogram: [" + dataFileNames + "; " + mzFormat.format(mzRange.lowerEndpoint())
        + " - " + mzFormat.format(mzRange.upperEndpoint()) + " m/z" + "]");

    // update plot title
    ticPlot.setTitle(mainTitle.toString(), subTitle.toString());

  }