Examples with Function java.util.function.Function used on opensource projects

Example 81 with Function

use of java.util.function.Function in project gatk-protected by broadinstitute.

the class CNLOHCaller method calcNewRhos.

private double[] calcNewRhos(final List<ACNVModeledSegment> segments, final List<double[][][]> responsibilitiesBySeg, final double lambda, final double[] rhos, final int[] mVals, final int[] nVals, final JavaSparkContext ctx) {
    // Since, we pass in the entire responsibilities matrix, we need the correct index for each rho.  That, and the
    //  fact that this is a univariate objective function, means we need to create an instance for each rho.  And
    //  then we blast across Spark.
    final List<Pair<? extends Function<Double, Double>, SearchInterval>> objectives = IntStream.range(0, rhos.length).mapToObj(i -> new Pair<>(new Function<Double, Double>() {

        @Override
        public Double apply(Double rho) {
            return calculateESmnObjective(rho, segments, responsibilitiesBySeg, mVals, nVals, lambda, i);
        }
    }, new SearchInterval(0.0, 1.0, rhos[i]))).collect(Collectors.toList());
    final JavaRDD<Pair<? extends Function<Double, Double>, SearchInterval>> objectivesRDD = ctx.parallelize(objectives);
    final List<Double> resultsAsDouble = objectivesRDD.map(objective -> optimizeIt(objective.getFirst(), objective.getSecond())).collect();
    return resultsAsDouble.stream().mapToDouble(Double::doubleValue).toArray();
}

Example 82 with Function

use of java.util.function.Function in project gatk by broadinstitute.

the class GatherVcfs method getReaderFromVCFUri.

private static FeatureReader<VariantContext> getReaderFromVCFUri(final Path variantPath, final int cloudPrefetchBuffer) {
    final String variantURI = variantPath.toUri().toString();
    final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Function.identity());
    return AbstractFeatureReader.getFeatureReader(variantURI, null, new VCFCodec(), false, cloudWrapper, Function.identity());
}

Example 83 with Function

use of java.util.function.Function in project Gargoyle by callakrsos.

the class FileSearcher method listClases.

public static List<ProjectInfo> listClases(String classDirName) throws Exception {
    File file = new File(classDirName);
    // 기본적인 파일의 존재유무 및 디렉토리인지 체크.
    if (!file.exists())
        throw new FileNotFoundException(file + " Not found!");
    //
    if (!file.isDirectory())
        throw new IllegalArgumentException("only directory.");
    /*
		 * 디렉토리안에 클래스패스 정보가 존재하는지 확인하고 존재한다면 classpath에 기술된 정보 기준으로 클래스 파일을
		 * 로드한다. 프로그램내에서 workspace를 선택한 경우일수있고, 프로젝트를 선택한 두가지의 경우가 있기때문에 두가지의
		 * 케이스를 고려한 로직이 들어간다.
		 */
    /*
		 * 일단 워크스페이스를 선택한경우라고 가정하고 워크스페이스내에 폴더들을 순차적으로 돌아보면서 classpath의 존재유무를 찾고
		 * 존재하는케이스는 따로 모아놓는다. 파일레벨은 워크스페이스(0레벨)-프로젝트(1레벨)로 가정하여 1레벨까지만 이동한다.
		 */
    List<File> listFiles = findClassPaths(file);
    /*
		 * classpath파일을 찾은경우 그 파일path를 기준으로 클래스들을 로딩한다.
		 */
    List<ProjectInfo> allClasses = new ArrayList<>();
    if (listFiles != null && !listFiles.isEmpty())
        LOGGER.debug(" im will working...");
    long startTime = System.currentTimeMillis();
    int searchedDirCount = 0;
    StringBuffer srchedDirNames = new StringBuffer();
    for (File f : listFiles) {
        try {
            ClassPath parsingClassPath = parsingClassPath(f.getAbsolutePath());
            // 프로젝트파일.
            File projectFile = f.getParentFile();
            // output 속성값의 존재유무만 확인하여 컴파일되는 경로를 찾는다.
            List<ProjectInfo> collect = parsingClassPath.toStream().filter(entry -> {
                boolean notEmpty = ValueUtil.isNotEmpty(entry.getOutput());
                LOGGER.debug(String.format("srch entry path : %s is Traget %b ", entry.getPath(), notEmpty));
                return notEmpty;
            }).map(pram -> pram.getOutput()).distinct().parallel().flatMap(new Function<String, Stream<ProjectInfo>>() {

                @Override
                public Stream<ProjectInfo> apply(String entry) {
                    LOGGER.debug(String.format("entry : %s", entry));
                    File compiledFilePath = new File(projectFile, entry);
                    int length = compiledFilePath.getAbsolutePath().length() + 1;
                    List<String> findClases = findClases(projectFile.getAbsolutePath(), compiledFilePath, length);
                    LOGGER.debug(compiledFilePath.toString());
                    LOGGER.debug(findClases.toString());
                    LOGGER.debug(String.valueOf(findClases.size()));
                    ProjectInfo classInfo = new ProjectInfo();
                    classInfo.setProjectName(projectFile.getName());
                    classInfo.setProjectDir(compiledFilePath.getAbsolutePath());
                    classInfo.setClasses(findClases);
                    return Stream.of(classInfo);
                }
            }).collect(Collectors.toList());
            allClasses.addAll(collect);
            searchedDirCount++;
            srchedDirNames.append(f.getAbsolutePath()).append(SystemUtils.LINE_SEPARATOR);
        } catch (SAXParseException e) {
            LOGGER.error(String.format("정상적인 XML 형태가 아님. 파일명 :  %s", f.getAbsolutePath()));
            LOGGER.error(String.format("%d 행 :: %d 열", e.getLineNumber(), e.getColumnNumber()));
        }
    }
    long endTime = System.currentTimeMillis();
    long costMillisend = endTime - startTime;
    LOGGER.debug(String.format("Total Cost time : %s (ms) searched Directory Count : %d ", costMillisend, searchedDirCount));
    LOGGER.debug(String.format("Searched Dirs info \n%s", srchedDirNames.toString()));
    return allClasses;
}

Example 84 with Function

use of java.util.function.Function in project gatk by broadinstitute.

the class AlleleFractionSegmenter method relearnAdditionalParameters.

@Override
protected void relearnAdditionalParameters(final ExpectationStep eStep) {
    final Function<AlleleFractionGlobalParameters, Double> emissionLogLikelihood = params -> {
        double logLikelihood = 0.0;
        for (int position = 0; position < numPositions(); position++) {
            for (int state = 0; state < numStates(); state++) {
                final double eStepPosterior = eStep.pStateAtPosition(state, position);
                logLikelihood += eStepPosterior < NEGLIGIBLE_POSTERIOR_FOR_M_STEP ? 0 : eStepPosterior * AlleleFractionHMM.logEmissionProbability(data.get(position), getState(state), params, allelicPoN);
            }
        }
        return logLikelihood;
    };
    final Function<Double, Double> meanBiasObjective = mean -> emissionLogLikelihood.apply(globalParameters.copyWithNewMeanBias(mean));
    final double newMeanBias = OptimizationUtils.argmax(meanBiasObjective, 0, AlleleFractionInitializer.MAX_REASONABLE_MEAN_BIAS, globalParameters.getMeanBias(), RELATIVE_TOLERANCE_FOR_OPTIMIZATION, ABSOLUTE_TOLERANCE_FOR_OPTIMIZATION, MAX_EVALUATIONS_FOR_OPTIMIZATION);
    final Function<Double, Double> biasVarianceObjective = variance -> emissionLogLikelihood.apply(globalParameters.copyWithNewBiasVariance(variance));
    final double newBiasVariance = OptimizationUtils.argmax(biasVarianceObjective, 0, AlleleFractionInitializer.MAX_REASONABLE_BIAS_VARIANCE, globalParameters.getBiasVariance(), RELATIVE_TOLERANCE_FOR_OPTIMIZATION, ABSOLUTE_TOLERANCE_FOR_OPTIMIZATION, MAX_EVALUATIONS_FOR_OPTIMIZATION);
    final Function<Double, Double> outlierProbabilityObjective = pOutlier -> emissionLogLikelihood.apply(globalParameters.copyWithNewOutlierProbability(pOutlier));
    final double newOutlierProbability = OptimizationUtils.argmax(outlierProbabilityObjective, 0, AlleleFractionInitializer.MAX_REASONABLE_OUTLIER_PROBABILITY, globalParameters.getOutlierProbability(), RELATIVE_TOLERANCE_FOR_OPTIMIZATION, ABSOLUTE_TOLERANCE_FOR_OPTIMIZATION, MAX_EVALUATIONS_FOR_OPTIMIZATION);
    globalParameters = new AlleleFractionGlobalParameters(newMeanBias, newBiasVariance, newOutlierProbability);
    logger.info(String.format("Global allelic bias parameters learned.  Mean allelic bias: %f, variance of allelic bias: %f, outlier probability: %f.", newMeanBias, newBiasVariance, newOutlierProbability));
}

Example 85 with Function

use of java.util.function.Function in project gatk by broadinstitute.

the class GenomicsDBImport method getReaderFromVCFUri.

/**
     * Creates a feature reader object from a given VCF URI (can also be
     * a local file path) and returns it
     * @param variantPath  URI or file path
     * @return  Feature reader
     */
private AbstractFeatureReader<VariantContext, LineIterator> getReaderFromVCFUri(final String variantPath) {
    final String variantURI = IOUtils.getPath(variantPath).toAbsolutePath().toUri().toString();
    final Function<SeekableByteChannel, SeekableByteChannel> cloudWrapper = (cloudPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudPrefetchBuffer, is) : Function.identity());
    final Function<SeekableByteChannel, SeekableByteChannel> cloudIndexWrapper = (cloudIndexPrefetchBuffer > 0 ? is -> SeekableByteChannelPrefetcher.addPrefetcher(cloudIndexPrefetchBuffer, is) : Function.identity());
    return AbstractFeatureReader.getFeatureReader(variantURI, null, new VCFCodec(), true, cloudWrapper, cloudIndexWrapper);
}