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

Example 46 with BiFunction

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

the class CoverageModelEMWorkspace method getCopyRatioSegmentsSpark.

/**
     * Fetch copy ratio segments from compute blocks (Spark implementation)
     *
     * @return a list of {@link CopyRatioHMMResults}
     */
private List<List<HiddenStateSegmentRecord<STATE, Target>>> getCopyRatioSegmentsSpark() {
    /* local final member variables for lambda capture */
    final List<Target> processedTargetList = new ArrayList<>();
    processedTargetList.addAll(this.processedTargetList);
    final List<SexGenotypeData> processedSampleSexGenotypeData = new ArrayList<>();
    processedSampleSexGenotypeData.addAll(this.processedSampleSexGenotypeData);
    final List<String> processedSampleNameList = new ArrayList<>();
    processedSampleNameList.addAll(this.processedSampleNameList);
    final INDArray sampleReadDepths = Transforms.exp(sampleMeanLogReadDepths, true);
    final CopyRatioExpectationsCalculator<CoverageModelCopyRatioEmissionData, STATE> copyRatioExpectationsCalculator = this.copyRatioExpectationsCalculator;
    final BiFunction<SexGenotypeData, Target, STATE> referenceStateFactory = this.referenceStateFactory;
    return fetchCopyRatioEmissionDataSpark().mapPartitionsToPair(it -> {
        final List<Tuple2<Integer, CopyRatioHMMResults<CoverageModelCopyRatioEmissionData, STATE>>> newPartitionData = new ArrayList<>();
        while (it.hasNext()) {
            final Tuple2<Integer, List<CoverageModelCopyRatioEmissionData>> prevDatum = it.next();
            final int sampleIndex = prevDatum._1;
            final CopyRatioCallingMetadata copyRatioCallingMetadata = CopyRatioCallingMetadata.builder().sampleName(processedSampleNameList.get(sampleIndex)).sampleSexGenotypeData(processedSampleSexGenotypeData.get(sampleIndex)).sampleCoverageDepth(sampleReadDepths.getDouble(sampleIndex)).emissionCalculationStrategy(EmissionCalculationStrategy.HYBRID_POISSON_GAUSSIAN).build();
            newPartitionData.add(new Tuple2<>(sampleIndex, copyRatioExpectationsCalculator.getCopyRatioHMMResults(copyRatioCallingMetadata, processedTargetList, prevDatum._2)));
        }
        return newPartitionData.iterator();
    }, true).mapPartitionsToPair(it -> {
        final List<Tuple2<Integer, List<HiddenStateSegmentRecord<STATE, Target>>>> newPartitionData = new ArrayList<>();
        while (it.hasNext()) {
            final Tuple2<Integer, CopyRatioHMMResults<CoverageModelCopyRatioEmissionData, STATE>> prevDatum = it.next();
            final int sampleIndex = prevDatum._1;
            final CopyRatioHMMResults<CoverageModelCopyRatioEmissionData, STATE> result = prevDatum._2;
            final HMMSegmentProcessor<CoverageModelCopyRatioEmissionData, STATE, Target> processor = new HMMSegmentProcessor<>(Collections.singletonList(result.getMetaData().getSampleName()), Collections.singletonList(result.getMetaData().getSampleSexGenotypeData()), referenceStateFactory, Collections.singletonList(new HashedListTargetCollection<>(processedTargetList)), Collections.singletonList(result.getForwardBackwardResult()), Collections.singletonList(result.getViterbiResult()));
            newPartitionData.add(new Tuple2<>(sampleIndex, processor.getSegmentsAsList()));
        }
        return newPartitionData.iterator();
    }).collect().stream().sorted(Comparator.comparingInt(t -> t._1)).map(t -> t._2).collect(Collectors.toList());
}

Example 47 with BiFunction

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

the class ReadCountRecordUnitTest method testAppendCountsToBeyondEnd.

@Test(dataProvider = "testNonZeroCountsData", dependsOnMethods = "testAppendCountsTo", expectedExceptions = IllegalStateException.class)
public void testAppendCountsToBeyondEnd(@SuppressWarnings("unused") final String testName, final BiFunction<Target, double[], ? extends ReadCountRecord> constructor, final int size) {
    final double[] counts = generateCounts(size);
    final ReadCountRecord record = constructor.apply(TEST_TARGET, counts);
    final List<String> columnNames = Stream.concat(Stream.concat(IntStream.range(0, 10).mapToObj(i -> "pre-padding_" + i), IntStream.range(0, counts.length).mapToObj(i -> "column_" + i)), IntStream.range(0, 10).mapToObj(i -> "post-padding_" + i)).collect(Collectors.toList());
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    final DataLine dataLine = new DataLine(columns, RuntimeException::new);
    final double[] copiedCounts = new double[counts.length + 20];
    Arrays.fill(copiedCounts, -11);
    dataLine.seek(columnNames.size());
    record.appendCountsTo(dataLine);
}

Example 48 with BiFunction

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

the class ReadCountRecordUnitTest method testAppendCountsTo.

@Test(dataProvider = "testData", dependsOnMethods = "testCreation")
public void testAppendCountsTo(@SuppressWarnings("unused") final String testName, final BiFunction<Target, double[], ? extends ReadCountRecord> constructor, final int size) {
    final double[] counts = generateCounts(size);
    final boolean round = testName.equals("long[]");
    final ReadCountRecord record = constructor.apply(TEST_TARGET, counts);
    final List<String> columnNames = Stream.concat(Stream.concat(IntStream.range(0, 10).mapToObj(i -> "pre-padding_" + i), IntStream.range(0, counts.length).mapToObj(i -> "column_" + i)), IntStream.range(0, 10).mapToObj(i -> "post-padding_" + i)).collect(Collectors.toList());
    final TableColumnCollection columns = new TableColumnCollection(columnNames);
    final DataLine dataLine = new DataLine(columns, RuntimeException::new);
    final double[] copiedCounts = new double[counts.length + 20];
    Arrays.fill(copiedCounts, -11);
    for (int i = 0; i < 10 + 10 + counts.length; i++) {
        dataLine.append("-11");
    }
    dataLine.seek(10);
    record.appendCountsTo(dataLine);
    // Check the copied values.
    if (!round) {
        for (int i = 0; i < counts.length; i++) {
            Assert.assertEquals(dataLine.getDouble(10 + i), counts[i], 0.0);
        }
    } else {
        for (int i = 0; i < counts.length; i++) {
            Assert.assertEquals(dataLine.getDouble(10 + i), Math.round(counts[i]), 0.00001);
        }
    }
    // Check that the padding remains intact:
    for (int i = 0; i < 10; i++) {
        Assert.assertEquals(dataLine.get(i), "-11");
    }
    for (int i = counts.length + 10; i < copiedCounts.length; i++) {
        Assert.assertEquals(dataLine.get(i), "-11");
    }
}

Example 49 with BiFunction

use of java.util.function.BiFunction in project samza by apache.

the class StreamGraphImpl method getIntermediateStream.

/**
   * Internal helper for {@link MessageStreamImpl} to add an intermediate {@link MessageStream} to the graph.
   * An intermediate {@link MessageStream} is both an output and an input stream.
   *
   * @param streamName the name of the stream to be created. Will be prefixed with job name and id to generate the
   *                   logical streamId.
   * @param keyExtractor the {@link Function} to extract the outgoing key from the intermediate message
   * @param msgExtractor the {@link Function} to extract the outgoing message from the intermediate message
   * @param msgBuilder the {@link BiFunction} to convert the incoming key and message to a message
   *                   in the intermediate {@link MessageStream}
   * @param <K> the type of key in the intermediate message
   * @param <V> the type of message in the intermediate message
   * @param <M> the type of messages in the intermediate {@link MessageStream}
   * @return  the intermediate {@link MessageStreamImpl}
   */
<K, V, M> MessageStreamImpl<M> getIntermediateStream(String streamName, Function<? super M, ? extends K> keyExtractor, Function<? super M, ? extends V> msgExtractor, BiFunction<? super K, ? super V, ? extends M> msgBuilder) {
    String streamId = String.format("%s-%s-%s", config.get(JobConfig.JOB_NAME()), config.get(JobConfig.JOB_ID(), "1"), streamName);
    if (msgBuilder == null) {
        throw new IllegalArgumentException("msgBuilder cannot be null for an intermediate stream");
    }
    if (keyExtractor == null) {
        throw new IllegalArgumentException("keyExtractor can't be null for an output stream.");
    }
    if (msgExtractor == null) {
        throw new IllegalArgumentException("msgExtractor can't be null for an output stream.");
    }
    StreamSpec streamSpec = runner.getStreamSpec(streamId);
    IntermediateStreamInternalImpl<K, V, M> intStream = (IntermediateStreamInternalImpl<K, V, M>) inStreams.computeIfAbsent(streamSpec, k -> new IntermediateStreamInternalImpl<>(this, streamSpec, (Function<M, K>) keyExtractor, (Function<M, V>) msgExtractor, (BiFunction<K, V, M>) msgBuilder));
    outStreams.putIfAbsent(streamSpec, intStream);
    return intStream;
}

Example 50 with BiFunction

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

the class RequestUtil method request200.

public static <T> T request200(URL url, byte[] out, BiFunction<InputStream, Charset, T> response, boolean autoClose) throws Exception {
    URLConnection openConnection = url.openConnection();
    HttpURLConnection conn = (HttpURLConnection) openConnection;
    InputStream is = null;
    T result = null;
    try {
        conn.setDefaultUseCaches(true);
        conn.setUseCaches(true);
        conn.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows NT 6.1; WOW64; rv:12.0) Gecko/20100101 Firefox/12.0");
        conn.setRequestProperty("Accept-Encoding", "UTF-8");
        // conn.setRequestProperty("Connection", "keep-alive");
        conn.setRequestProperty("Accept", "application/json");
        conn.setRequestProperty("Accept-Charset", "UTF-8");
        conn.setRequestProperty("Accept-Encoding", "UTF-8");
        conn.setRequestProperty("Accept-Language", "KR");
        conn.setConnectTimeout(6000);
        conn.setReadTimeout(6000);
        if (out != null) {
            conn.setDoOutput(true);
            OutputStream stream = conn.getOutputStream();
            stream.write(out);
        }
        conn.connect();
        is = conn.getInputStream();
        String contentType = conn.getContentType();
        String contentEncoding = conn.getContentEncoding();
        //			int contentLength = conn.getContentLength();
        Map<String, List<String>> headerFields = conn.getHeaderFields();
        try {
            Optional<String> findAny = headerFields.keySet().stream().filter(f -> f != null).filter(str -> {
                if ("Accept-Encoding".equals(str))
                    return true;
                return str.toLowerCase().indexOf("charset") >= 0;
            }).findAny();
            if (findAny.isPresent()) {
                String wow = findAny.get();
                List<String> list = headerFields.get(wow);
                wow = list.get(0);
                if (Charset.isSupported(wow)) {
                    contentEncoding = wow;
                }
            }
        } catch (IllegalArgumentException e) {
            e.printStackTrace();
        }
        //			String charset = "UTF-8";
        if (ValueUtil.isEmpty(contentEncoding)) {
            if (contentType != null) {
                Optional<String> map = Stream.of(contentType.split(";")).filter(txt -> txt.toLowerCase().contains("charset")).findFirst().map(v -> {
                    return v.substring(v.indexOf("=") + 1);
                });
                if (map.isPresent())
                    contentEncoding = map.get();
                else {
                    String headerField = conn.getHeaderField("Accept-Charset");
                    if (ValueUtil.isNotEmpty(headerField))
                        contentEncoding = headerField;
                }
            }
        }
        if (ValueUtil.isEmpty(contentEncoding)) {
            contentEncoding = "UTF-8";
            LOGGER.debug("force encoding 'UTF-8' -  what is encoding ?????  ########################################");
        }
        LOGGER.debug("code : [{}] [{}] URL : {} ,  ", conn.getResponseCode(), contentEncoding, url.toString());
        if (200 == conn.getResponseCode()) {
            result = response.apply(is, Charset.forName(contentEncoding));
        }
    } finally {
        if (autoClose) {
            if (is != null)
                is.close();
            if (conn != null)
                conn.disconnect();
        }
    }
    return result;
}