Example usage for com.google.common.collect Range closed

Introduction

In this page you can find the example usage for com.google.common.collect Range closed.

Prototype

public static <C extends Comparable<?>> Range<C> closed(C lower, C upper) 

Source Link

Document

Returns a range that contains all values greater than or equal to lower and less than or equal to upper .

Usage

From source file:org.nmdp.ngs.tools.EvaluateScaffolds.java

@Override
public Integer call() throws Exception {
    PrintWriter writer = null;//  ww w  .j a v  a 2  s . c  o m
    try {
        writer = writer(evalFile);

        Sequence reference = readReference();
        List<Sequence> scaffolds = readScaffolds();

        writer.println("#reference length = " + reference.length());
        writer.println("#scaffold count = " + scaffolds.size());
        writer.println("#scaffold lengths = " + dumpLengths(scaffolds));

        RangeSet<Long> ranges = TreeRangeSet.create();
        for (HighScoringPair hsp : blastn(referenceFastaFile, scaffoldsFastaFile)) {
            if (reference.getName().equals(hsp.target())) {
                writer.println("#" + hsp.toString());
                if (hsp.targetStart() <= hsp.targetEnd()) { // strands match
                    ranges.add(Range.closed(hsp.targetStart(), hsp.targetEnd()));
                } else {
                    ranges.add(Range.closed(hsp.targetEnd(), hsp.targetStart()));
                }
            }
        }

        writer.println("#coalesced intervals = " + ranges);

        long breadthOfCoverage = 0;
        for (Range<Long> range : ranges.asRanges()) {
            breadthOfCoverage += ContiguousSet.create(range, DiscreteDomain.longs()).size();
        }
        double normalizedBreadthOfCoverage = (double) breadthOfCoverage / (double) reference.length();
        writer.println("#breadth-of-coverage = " + breadthOfCoverage);
        writer.println("#normalized breadth-of-coverage = " + normalizedBreadthOfCoverage);

        StringBuilder sb = new StringBuilder();
        sb.append(referenceFastaFile.getName());
        sb.append("\t");
        sb.append(scaffoldsFastaFile.getName());
        sb.append("\t");
        sb.append(reference.length());
        sb.append("\t");
        sb.append(scaffolds.size());
        sb.append("\t");
        sb.append(ranges.asRanges().size());
        sb.append("\t");
        sb.append(breadthOfCoverage);
        sb.append("\t");
        sb.append(normalizedBreadthOfCoverage);
        sb.append("\t");
        writer.println(sb.toString());

        return 0;
    } finally {
        try {
            writer.close();
        } catch (Exception e) {
            // ignore
        }
    }
}

---

From source file:org.jpmml.evaluator.DiscretizationUtil.java

static public Range<Double> toRange(Interval interval) {
    Double leftMargin = interval.getLeftMargin();
    Double rightMargin = interval.getRightMargin();

    // "The attributes leftMargin and rightMargin are optional but at least one value must be defined"
    if (leftMargin == null && rightMargin == null) {
        throw new InvalidFeatureException(interval);
    } // End if//  w  w  w  . j  a  v  a 2 s.  c  o  m

    if (leftMargin != null && rightMargin != null && (leftMargin).compareTo(rightMargin) > 0) {
        throw new InvalidFeatureException(interval);
    }

    Interval.Closure closure = interval.getClosure();
    switch (closure) {
    case OPEN_OPEN: {
        if (leftMargin == null) {
            return Range.lessThan(rightMargin);
        } else

        if (rightMargin == null) {
            return Range.greaterThan(leftMargin);
        }

        return Range.open(leftMargin, rightMargin);
    }
    case OPEN_CLOSED: {
        if (leftMargin == null) {
            return Range.atMost(rightMargin);
        } else

        if (rightMargin == null) {
            return Range.greaterThan(leftMargin);
        }

        return Range.openClosed(leftMargin, rightMargin);
    }
    case CLOSED_OPEN: {
        if (leftMargin == null) {
            return Range.lessThan(rightMargin);
        } else

        if (rightMargin == null) {
            return Range.atLeast(leftMargin);
        }

        return Range.closedOpen(leftMargin, rightMargin);
    }
    case CLOSED_CLOSED: {
        if (leftMargin == null) {
            return Range.atMost(rightMargin);
        } else

        if (rightMargin == null) {
            return Range.atLeast(leftMargin);
        }

        return Range.closed(leftMargin, rightMargin);
    }
    default:
        throw new UnsupportedFeatureException(interval, closure);
    }
}

---

From source file:io.horizondb.model.core.predicates.BetweenPredicate.java

/**    
 * {@inheritDoc}//from w  w w  . ja  v a2s  .com
 */
@Override
public Filter<Record> toFilter(TimeSeriesDefinition definition) {

    Range<Field> range = Range.closed(this.min, this.max);
    Filter<Field> fieldFilter = range(range, isTimestamp());

    if (this.notBetween) {
        fieldFilter = not(fieldFilter);
    }

    return toRecordFilter(definition, getFieldName(), fieldFilter);
}

---

From source file:org.robotframework.ide.eclipse.main.plugin.project.build.validation.RobotResourceFileValidator.java

private void reportProblem(final String declarationName, final AModelElement<?> element) {
    final RobotProblem problem = RobotProblem.causedBy(GeneralSettingsProblem.UNSUPPORTED_SETTING)
            .formatMessageWith(declarationName, "resource");
    final ProblemPosition position = new ProblemPosition(element.getBeginPosition().getLine(),
            Range.closed(element.getBeginPosition().getOffset(), element.getEndPosition().getOffset()));
    reporter.handleProblem(problem, file, position);
}

---

From source file:com.wealdtech.jackson.modules.DateTimeRangeDeserializer.java

public static Range<DateTime> deserialize(final String txt) throws IOException {
      final int txtLen = txt.length();

      final int firstDateChar;
      boolean lowerClosed;
      if (txt.charAt(0) == '[') {
          firstDateChar = 1;//  w ww.j  a  va2s .c  o  m
          lowerClosed = true;
      } else if (txt.charAt(0) == '(') {
          firstDateChar = 1;
          lowerClosed = false;
      } else if (txt.charAt(0) >= '0' && txt.charAt(0) <= '9') {
          // Lazy version
          firstDateChar = 0;
          lowerClosed = true;
      } else {
          throw new DataError.Bad("Unexpected first character in range \"" + txt + "\"");
      }

      boolean upperClosed;
      if (txt.charAt(txtLen - 1) == ']') {
          upperClosed = true;
      } else if (txt.charAt(txtLen - 1) == ')') {
          upperClosed = false;
      } else if (firstDateChar == 0) {
          upperClosed = false;
      } else {
          throw new DataError.Bad("Unexpected last character in range \"" + txt + "\"");
      }

      final Iterator<String> dateTimes;
      if (txt.indexOf(WEALD_SPLITTER_CHAR) != -1) {
          dateTimes = WEALD_SPLITTER.split(txt.substring(firstDateChar, txtLen - firstDateChar)).iterator();
      } else if (txt.indexOf(GUAVA_SPLITTER_CHAR) != -1) {
          dateTimes = GUAVA_SPLITTER.split(txt.substring(firstDateChar, txtLen - firstDateChar)).iterator();
      } else {
          throw new DataError.Bad("Cannot find a range separator in range \"" + txt + "\"");
      }
      String start = dateTimes.next();
      String end = dateTimes.next();

      boolean lowerBound;
      final DateTime lowerPoint;
      if (start.equals(NEGATIVE_INFINITY)) {
          lowerBound = false;
          lowerPoint = null;
      } else {
          lowerBound = true;
          lowerPoint = DateTimeDeserializer.deserialize(start);
      }

      boolean upperBound;
      final DateTime upperPoint;
      if (end.equals(POSITIVE_INFINITY)) {
          upperBound = false;
          upperPoint = null;
      } else {
          upperBound = true;
          upperPoint = DateTimeDeserializer.deserialize(end);
      }

      if (lowerBound == false && upperBound == false) {
          return Range.all();
      } else if (lowerBound == false) {
          // Upper present
          if (upperClosed == true) {
              return Range.lessThan(upperPoint);
          } else {
              return Range.atMost(upperPoint);
          }
      } else if (upperBound == false) {
          // Lower present
          if (lowerClosed == true) {
              return Range.atLeast(lowerPoint);
          } else {
              return Range.greaterThan(lowerPoint);
          }
      } else {
          // Both present
          if (lowerClosed == true) {
              if (upperClosed == true) {
                  return Range.closed(lowerPoint, upperPoint);
              } else {
                  return Range.closedOpen(lowerPoint, upperPoint);
              }
          } else {
              if (upperClosed == true) {
                  return Range.openClosed(lowerPoint, upperPoint);
              } else {
                  return Range.open(lowerPoint, upperPoint);
              }
          }
      }
  }

---

From source file:org.mskcc.shenkers.control.track.gene.GTFGeneModelProvider.java

@Override
public Iterable<GeneModel> query(String chr, int start, int end) {
    CloseableTribbleIterator<GTFContext> query = null;
    try {//from   w w w .j  a v  a2  s. com
        query = features.query(chr, start, end);

        Stream<GTFContext> filter = StreamSupport
                .stream(Spliterators.spliteratorUnknownSize(query, Spliterator.CONCURRENT), true)
                .filter(c -> c.getTranscriptId() != null);

        ImmutableListMultimap<String, GTFContext> transcript_id_multimap = Multimaps.index(filter.iterator(),
                GTFContext::getTranscriptId);

        Stream<GeneModel> map = transcript_id_multimap.keySet().stream().map(key -> {
            System.out.println(key);
            ImmutableListMultimap<String, GTFContext> transcript_features = Multimaps
                    .index(transcript_id_multimap.get(key), GTFContext::getFeature);
            Map<String, RangeSet<Integer>> collect = transcript_features.keySet().stream()
                    .collect(Collectors.toMap(s -> s, feature -> {
                        return transcript_features.get(feature).stream()
                                .map(c -> Range.closed(c.getStart(), c.getEnd()))
                                .collect(new RangeSetCollector());
                    }));

            GeneModel model = new GeneModel(collect.get("transcript").span(),
                    Optional.ofNullable(collect.get("exon")),
                    Optional.ofNullable(collect.get("CDS")).map(c -> c.span()));
            return model;
        });

        return map::iterator;
    } catch (IOException ex) {
        logger.error("exception reading gene models ", ex);
        throw new RuntimeException(ex);
    } finally {
        query.close();
    }
}

---

From source file:es.upv.grycap.coreutils.fiber.http.HttpDataFetcher.java

/**
 * Convenient constructor that allows creating a new instance of this class setting the value of the concurrency level.
 * Values above this {@link HttpDataFetcher#MAX_CONCURRENCY limit} will be trimmed.
 * @param concurrencyLevel - desired concurrency level
 *///from  w  w  w . ja v a 2  s  . com
public HttpDataFetcher(final int concurrencyLevel) {
    this.concurrencyLevel = Range.closed(1, MAX_CONCURRENCY).contains(concurrencyLevel) ? concurrencyLevel
            : MAX_CONCURRENCY;
    LOGGER.info(new StringBuilder("Concurrency level: ").append(this.concurrencyLevel).toString());
}

---

From source file:org.eclipse.m2m.internal.qvt.oml.tools.coverage.ui.TransformationCoverageModel.java

public RangeSet<Integer> getTouchedRanges() {
    if (touchedRanges == null) {
        touchedRanges = TreeRangeSet.create();
        for (NodeCoverageModel nodeModel : getTouchedExpressionNodes()) {
            touchedRanges.add(Range.closed(nodeModel.getStart(), nodeModel.getEnd() + 1));
        }//  w w  w.j a va2  s  .c om
        // Now remove untouched ranges
        for (Range<Integer> untouchedRange : getUntouchedRanges().asRanges()) {
            touchedRanges.remove(untouchedRange);
        }
    }
    return touchedRanges;
}

---

From source file:com.basistech.tclre.ColorMap.java

ColorMap(Compiler compiler) {
    map = TreeRangeMap.create();/*from  w  ww .j  a  va2  s.  c o m*/
    // the color map starts by assigning all characters to WHITE
    map.put(Range.closed(0, Character.MAX_CODE_POINT), Constants.WHITE);
    this.compiler = compiler;

    colorDescs = Lists.newArrayList();

    ColorDesc white = new ColorDesc(); // [WHITE]
    colorDescs.add(white);
    assert colorDescs.size() == 1;
    white.sub = Constants.NOSUB;
    white.setNChars(65536);
}

---

From source file:net.sf.mzmine.modules.visualization.twod.TwoDXYPlot.java

public boolean render(final Graphics2D g2, final Rectangle2D dataArea, int index, PlotRenderingInfo info,
        CrosshairState crosshairState) {

    // if this is not TwoDDataSet
    if (index != 0)
        return super.render(g2, dataArea, index, info, crosshairState);

    // prepare some necessary constants
    final int x = (int) dataArea.getX();
    final int y = (int) dataArea.getY();
    final int width = (int) dataArea.getWidth();
    final int height = (int) dataArea.getHeight();

    final double imageRTMin = (double) getDomainAxis().getRange().getLowerBound();
    final double imageRTMax = (double) getDomainAxis().getRange().getUpperBound();
    final double imageRTStep = (imageRTMax - imageRTMin) / width;
    final double imageMZMin = (double) getRangeAxis().getRange().getLowerBound();
    final double imageMZMax = (double) getRangeAxis().getRange().getUpperBound();
    final double imageMZStep = (imageMZMax - imageMZMin) / height;

    if ((zoomOutBitmap != null) && (imageRTMin == totalRTRange.lowerEndpoint())
            && (imageRTMax == totalRTRange.upperEndpoint()) && (imageMZMin == totalMZRange.lowerEndpoint())
            && (imageMZMax == totalMZRange.upperEndpoint()) && (zoomOutBitmap.getWidth() == width)
            && (zoomOutBitmap.getHeight() == height)) {
        g2.drawImage(zoomOutBitmap, x, y, null);
        return true;
    }/*w  w w.ja  v a 2 s  . c  o  m*/

    // Save current time
    Date renderStartTime = new Date();

    // prepare a double array of summed intensities
    double values[][] = new double[width][height];
    maxValue = 0; // now this is an instance variable

    for (int i = 0; i < width; i++)
        for (int j = 0; j < height; j++) {

            double pointRTMin = imageRTMin + (i * imageRTStep);
            double pointRTMax = pointRTMin + imageRTStep;
            double pointMZMin = imageMZMin + (j * imageMZStep);
            double pointMZMax = pointMZMin + imageMZStep;

            double lv = dataset.upperEndpointIntensity(Range.closed(pointRTMin, pointRTMax),
                    Range.closed(pointMZMin, pointMZMax), plotMode);

            if (logScale) {
                lv = Math.log10(lv);
                if (lv < 0 || Double.isInfinite(lv))
                    lv = 0;
                values[i][j] = lv;
                // values[r.nextInt(width)][r.nextInt(height)] = lv;
            } else {
                values[i][j] = lv;
            }

            if (lv > maxValue)
                maxValue = lv;

        }

    // This should never happen, but just for correctness
    if (maxValue == 0)
        return false;

    // Normalize all values
    for (int i = 0; i < width; i++)
        for (int j = 0; j < height; j++) {
            values[i][j] /= maxValue;
        }

    // prepare a bitmap of required size
    BufferedImage image = new BufferedImage(width, height, BufferedImage.TYPE_INT_ARGB);

    // draw image points
    for (int i = 0; i < width; i++)
        for (int j = 0; j < height; j++) {
            Color pointColor = paletteType.getColor(values[i][j]);
            image.setRGB(i, height - j - 1, pointColor.getRGB());
        }

    // if we are zoomed out, save the values
    if ((imageRTMin == totalRTRange.lowerEndpoint()) && (imageRTMax == totalRTRange.upperEndpoint())
            && (imageMZMin == totalMZRange.lowerEndpoint()) && (imageMZMax == totalMZRange.upperEndpoint())) {
        zoomOutBitmap = image;
    }

    // Paint image
    g2.drawImage(image, x, y, null);

    Date renderFinishTime = new Date();

    logger.finest("Finished rendering 2D visualizer, "
            + (renderFinishTime.getTime() - renderStartTime.getTime()) + " ms");

    return true;

}

---

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