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

Example 86 with Function

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

the class XHMMModelUnitTest method testLogEmissionProbability.

@Test(dataProvider = "testData", dependsOnMethods = "testInstantiation")
public void testLogEmissionProbability(final double eventStartProbability, final double meanEventSize, final double deletionMean, final double duplicationMean) {
    final XHMMModel model = new XHMMModel(eventStartProbability, meanEventSize, deletionMean, duplicationMean);
    final Target target = new Target("NAME");
    final double logDenominator = Math.log(Math.sqrt(2 * Math.PI));
    final Function<Double, Double> neutralEmission = x -> -.5 * (x * x) - logDenominator;
    final Function<Double, Double> deletionEmission = x -> -.5 * Math.pow(x - deletionMean, 2) - logDenominator;
    final Function<Double, Double> duplicationEmission = x -> -.5 * Math.pow(x - duplicationMean, 2) - logDenominator;
    for (final double coverage : TEST_COVERAGE_VALUES) {
        final double neutralObserved = model.logEmissionProbability(new XHMMEmissionData(coverage), CopyNumberTriState.NEUTRAL, target);
        final double deletionObserved = model.logEmissionProbability(new XHMMEmissionData(coverage), CopyNumberTriState.DELETION, target);
        final double duplicationObserved = model.logEmissionProbability(new XHMMEmissionData(coverage), CopyNumberTriState.DUPLICATION, target);
        final double neutralExpected = neutralEmission.apply(coverage);
        final double deletionExpected = deletionEmission.apply(coverage);
        final double duplicationExpected = duplicationEmission.apply(coverage);
        Assert.assertEquals(neutralObserved, neutralExpected, "neutral emission for " + coverage);
        Assert.assertEquals(deletionObserved, deletionExpected);
        Assert.assertEquals(duplicationObserved, duplicationExpected);
    }
}

Example 87 with Function

use of java.util.function.Function in project gatk-protected 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 88 with Function

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

the class DbUtil method getTransactionedScope.

public static <T> int getTransactionedScope(Connection con, T userObj, Function<T, List<String>> sqlConverter, Consumer<Exception> exceptionHandler) throws Exception {
    int result = -1;
    try {
        LOGGER.debug("is AutoCommit ? : {}", con.getAutoCommit());
        con.setAutoCommit(false);
        List<String> apply = sqlConverter.apply(userObj);
        Statement createStatement = con.createStatement();
        for (String sql : apply) {
            /*
				 * sqlite에서 공백이 포함된 sql은 add한경우 에러.
				 * 확인해보니 isEmpty함수에 이상이 있는듯하여 수정.
				 */
            if (ValueUtil.isEmpty(sql))
                continue;
            LOGGER.debug(sql);
            createStatement.addBatch(sql);
        }
        int[] executeBatch = createStatement.executeBatch();
        con.commit();
        result = (int) IntStream.of(executeBatch).filter(v -> v == 0).count();
    } catch (Exception e) {
        con.rollback();
        exceptionHandler.accept(e);
        result = -1;
    } finally {
        con.commit();
        close(con);
    }
    return result;
}

Example 89 with Function

use of java.util.function.Function in project gatk 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 90 with Function

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

the class DaoWizardViewController method btnExecOnMouseClick.

/**
	 * 텍스트에 기술된 SQL문을 실행한다. 기본적으로 ROWNUM 기술문을 100개를 감싸서 SQL을 조회한다.
	 *
	 * @작성자 : KYJ
	 * @작성일 : 2015. 10. 21.
	 */
@FXML
public void btnExecOnMouseClick(MouseEvent e) {
    LOGGER.debug("event] btnExecOnMouseClick");
    String velocitySQL = txtSql.getText().trim();
    if (velocitySQL == null || velocitySQL.isEmpty())
        return;
    LOGGER.debug(String.format("velocitySQL : %s", velocitySQL));
    // 파라미터 컬럼값 반환받는다.
    ObservableList<TbpSysDaoFieldsDVO> items = tbParams.getItems();
    Map<String, TbpSysDaoColumnsDVO> unmapping = this.tbMappings.getItems().stream().filter(v -> {
        String lockYn = v.getLockYn();
        if ("Y".equals(lockYn))
            return true;
        return false;
    }).collect(Collectors.toMap(TbpSysDaoColumnsDVO::getColumnName, v -> v));
    Map<String, Object> paramMap = items.stream().filter(vo -> vo.getTestValue() != null && !vo.getTestValue().isEmpty()).collect(Collectors.toMap(TbpSysDaoFieldsDVO::getFieldName, new Function<TbpSysDaoFieldsDVO, Object>() {

        @Override
        public Object apply(TbpSysDaoFieldsDVO t) {
            if ("Arrays".equals(t.getType())) {
                String pattern = "'[^']{0,}'";
                List<String> regexMatchs = ValueUtil.regexMatchs(pattern, t.getTestValue(), str -> {
                    return str.substring(1, str.length() - 1);
                });
                return regexMatchs;
            }
            return t.getTestValue();
        }
    }));
    SimpleSQLResultView simpleSQLResultView = new SimpleSQLResultView(velocitySQL, paramMap);
    try {
        simpleSQLResultView.show();
        List<TableModelDVO> columns = simpleSQLResultView.getColumns();
        List<TbpSysDaoColumnsDVO> resultList = columns.stream().map(vo -> {
            TbpSysDaoColumnsDVO dvo = new TbpSysDaoColumnsDVO();
            dvo.setColumnName(vo.getDatabaseColumnName());
            String databaseTypeName = vo.getDatabaseTypeName();
            dvo.setColumnType(databaseTypeName);
            if (unmapping.containsKey(vo.getDatabaseColumnName())) {
                TbpSysDaoColumnsDVO tmp = unmapping.get(vo.getDatabaseColumnName());
                dvo.setProgramType(tmp.getProgramType());
                dvo.setLockYn(tmp.getLockYn());
            } else {
                String programType = DatabaseTypeMappingResourceLoader.getInstance().get(databaseTypeName);
                dvo.setProgramType(programType);
            }
            return dvo;
        }).collect(Collectors.toList());
        // if (!this.tbMappings.getItems().isEmpty())
        if (!resultList.isEmpty()) {
            try {
                this.tbMappings.getItems().clear();
                getSelectedMethodItem().getTbpSysDaoColumnsDVOList().clear();
                this.tbMappings.getItems().addAll(resultList);
                getSelectedMethodItem().getTbpSysDaoColumnsDVOList().addAll(resultList);
            } catch (NullPointerException n) {
                DialogUtil.showMessageDialog("메소드를 선택해주세요.");
            }
        }
    } catch (IOException e1) {
        LOGGER.error(ValueUtil.toString(e1));
        DialogUtil.showExceptionDailog(e1);
    }
}