Examples with Fraction org.apache.commons.lang3.math.Fraction used on opensource projects

Example 11 with Fraction

use of org.apache.commons.lang3.math.Fraction in project pcgen by PCGen.

the class PCGenTaskExecutor method progressChanged.

@Override
public void progressChanged(PCGenTaskEvent event) {
    if (currentTask.getMaximum() == 0) {
        return;
    }
    Fraction progress = Fraction.getFraction(currentTask.getProgress(), currentTask.getMaximum());
    progress = progress.multiplyBy(progressMultiplier);
    progress = baseProgress.add(progress);
    setValues(currentTask.getMessage(), progress.getNumerator(), progress.getDenominator());
}

Example 12 with Fraction

use of org.apache.commons.lang3.math.Fraction in project gatk by broadinstitute.

the class PerformJointSegmentation method doWork.

@Override
public Object doWork() {
    ParamUtils.isPositive(initialNumAFStates, "Must have at least one allele-fraction state.");
    ParamUtils.isPositive(initialNumCRStates, "Must have at least one copy-ratio state.");
    final AllelicPanelOfNormals allelicPoN = allelicPoNFile != null ? AllelicPanelOfNormals.read(allelicPoNFile) : AllelicPanelOfNormals.EMPTY_PON;
    final AllelicCountCollection acc = new AllelicCountCollection(snpCountsFile);
    final ReadCountCollection rcc;
    try {
        rcc = ReadCountCollectionUtils.parse(new File(coverageFile));
    } catch (final IOException ex) {
        throw new UserException.BadInput("could not read input file");
    }
    final JointAFCRSegmenter jointSegmenter = JointAFCRSegmenter.createJointSegmenter(initialNumCRStates, rcc, initialNumAFStates, acc, allelicPoN);
    final List<Pair<SimpleInterval, AFCRHiddenState>> segmentation = jointSegmenter.findSegments();
    final List<ACNVModeledSegment> segments = segmentation.stream().map(pair -> new ACNVModeledSegment(pair.getLeft(), errorlessPosterior(pair.getRight().getLog2CopyRatio()), errorlessPosterior(pair.getRight().getMinorAlleleFraction()))).collect(Collectors.toList());
    //TODO: make more reasonable output for ACNV 2.0
    SegmentUtils.writeACNVModeledSegmentFile(outputSegmentsFile, segments, new Genome(rcc, acc.getCounts()));
    return "SUCCESS";
}

Example 13 with Fraction

use of org.apache.commons.lang3.math.Fraction in project gatk-protected by broadinstitute.

the class AllelicPanelOfNormalsCreator method create.

/**
     * Creates an {@link AllelicPanelOfNormals} given a site-frequency threshold;
     * sites appearing in strictly less than this fraction of samples will not be included in the panel of normals.
     * @param siteFrequencyThreshold    site-frequency threshold
     * @return                          an {@link AllelicPanelOfNormals} containing sites
     *                                  above the site-frequency threshold
     */
public AllelicPanelOfNormals create(final double siteFrequencyThreshold) {
    logger.info("Creating allelic panel of normals...");
    //used to filter on frequency
    final Map<SimpleInterval, MutableInt> numberOfSamplesMap = new HashMap<>();
    //store only the total counts (smaller memory footprint)
    final Map<SimpleInterval, AllelicCount> totalCountsMap = new HashMap<>();
    int pulldownFileCounter = 1;
    final int totalNumberOfSamples = pulldownFiles.size();
    for (final File pulldownFile : pulldownFiles) {
        logger.info("Processing pulldown file " + pulldownFileCounter++ + "/" + totalNumberOfSamples + " (" + pulldownFile + ")...");
        final AllelicCountCollection pulldownCounts = new AllelicCountCollection(pulldownFile);
        for (final AllelicCount count : pulldownCounts.getCounts()) {
            //update the sum of ref and alt counts at each site
            final SimpleInterval site = count.getInterval();
            final AllelicCount currentCountAtSite = totalCountsMap.getOrDefault(site, new AllelicCount(site, 0, 0));
            final AllelicCount updatedCountAtSite = new AllelicCount(site, currentCountAtSite.getRefReadCount() + count.getRefReadCount(), currentCountAtSite.getAltReadCount() + count.getAltReadCount());
            totalCountsMap.put(site, updatedCountAtSite);
            //update the number of samples seen possessing each site
            final MutableInt numberOfSamplesAtSite = numberOfSamplesMap.get(site);
            if (numberOfSamplesAtSite == null) {
                numberOfSamplesMap.put(site, new MutableInt(1));
            } else {
                numberOfSamplesAtSite.increment();
            }
        }
    }
    logger.info("Total number of unique sites present in samples: " + totalCountsMap.size());
    //filter out sites that appear at a frequency strictly less than the provided threshold
    final AllelicCountCollection totalCounts = new AllelicCountCollection();
    numberOfSamplesMap.entrySet().stream().filter(e -> e.getValue().doubleValue() / totalNumberOfSamples >= siteFrequencyThreshold).map(e -> totalCountsMap.get(e.getKey())).forEach(totalCounts::add);
    logger.info(String.format("Number of unique sites present in samples above site frequency = %4.3f: %d", siteFrequencyThreshold, totalCounts.getCounts().size()));
    return new AllelicPanelOfNormals(totalCounts);
}

Example 14 with Fraction

use of org.apache.commons.lang3.math.Fraction in project gatk-protected by broadinstitute.

the class PerformJointSegmentation method doWork.

@Override
public Object doWork() {
    ParamUtils.isPositive(initialNumAFStates, "Must have at least one allele-fraction state.");
    ParamUtils.isPositive(initialNumCRStates, "Must have at least one copy-ratio state.");
    final AllelicPanelOfNormals allelicPoN = allelicPoNFile != null ? AllelicPanelOfNormals.read(allelicPoNFile) : AllelicPanelOfNormals.EMPTY_PON;
    final AllelicCountCollection acc = new AllelicCountCollection(snpCountsFile);
    final ReadCountCollection rcc;
    try {
        rcc = ReadCountCollectionUtils.parse(new File(coverageFile));
    } catch (final IOException ex) {
        throw new UserException.BadInput("could not read input file");
    }
    final JointAFCRSegmenter jointSegmenter = JointAFCRSegmenter.createJointSegmenter(initialNumCRStates, rcc, initialNumAFStates, acc, allelicPoN);
    final List<Pair<SimpleInterval, AFCRHiddenState>> segmentation = jointSegmenter.findSegments();
    final List<ACNVModeledSegment> segments = segmentation.stream().map(pair -> new ACNVModeledSegment(pair.getLeft(), errorlessPosterior(pair.getRight().getLog2CopyRatio()), errorlessPosterior(pair.getRight().getMinorAlleleFraction()))).collect(Collectors.toList());
    //TODO: make more reasonable output for ACNV 2.0
    SegmentUtils.writeACNVModeledSegmentFile(outputSegmentsFile, segments, new Genome(rcc, acc.getCounts()));
    return "SUCCESS";
}

Example 15 with Fraction

use of org.apache.commons.lang3.math.Fraction in project opencast by opencast.

the class AnalyzeTracksWorkflowOperationHandler method start.

@Override
public WorkflowOperationResult start(WorkflowInstance workflowInstance, JobContext context) throws WorkflowOperationException {
    logger.info("Running analyze-tracks workflow operation on workflow {}", workflowInstance.getId());
    final MediaPackage mediaPackage = workflowInstance.getMediaPackage();
    final String sourceFlavor = getConfig(workflowInstance, OPT_SOURCE_FLAVOR);
    Map<String, String> properties = new HashMap<>();
    final MediaPackageElementFlavor flavor = MediaPackageElementFlavor.parseFlavor(sourceFlavor);
    final Track[] tracks = mediaPackage.getTracks(flavor);
    if (tracks.length <= 0) {
        if (BooleanUtils.toBoolean(getConfig(workflowInstance, OPT_FAIL_NO_TRACK, "false"))) {
            throw new WorkflowOperationException("No matching tracks for flavor " + sourceFlavor);
        }
        logger.info("No tracks with specified flavors ({}) to analyse.", sourceFlavor);
        return createResult(mediaPackage, properties, Action.CONTINUE, 0);
    }
    List<Fraction> aspectRatios = getAspectRatio(getConfig(workflowInstance, OPT_VIDEO_ASPECT, ""));
    for (Track track : tracks) {
        final String varName = toVariableName(track.getFlavor());
        properties.put(varName + "_media", "true");
        properties.put(varName + "_video", Boolean.toString(track.hasVideo()));
        properties.put(varName + "_audio", Boolean.toString(track.hasAudio()));
        // Check resolution
        if (track.hasVideo()) {
            for (VideoStream video : ((TrackImpl) track).getVideo()) {
                // Set resolution variables
                properties.put(varName + "_resolution_x", video.getFrameWidth().toString());
                properties.put(varName + "_resolution_y", video.getFrameHeight().toString());
                Fraction trackAspect = Fraction.getReducedFraction(video.getFrameWidth(), video.getFrameHeight());
                properties.put(varName + "_aspect", trackAspect.toString());
                properties.put(varName + "_framerate", video.getFrameRate().toString());
                // Check if we should fall back to nearest defined aspect ratio
                if (!aspectRatios.isEmpty()) {
                    trackAspect = getNearestAspectRatio(trackAspect, aspectRatios);
                    properties.put(varName + "_aspect_snap", trackAspect.toString());
                }
            }
        }
    }
    logger.info("Finished analyze-tracks workflow operation adding the properties: {}", properties);
    return createResult(mediaPackage, properties, Action.CONTINUE, 0);
}