Source:
private static HyperparameterValues parseGlobalHyperparameterValues(final File inputFile) { try { final List<String> commentLines = FileUtils.readLines(inputFile).stream().filter(l -> l.contains(TableUtils.COMMENT_PREFIX)).collect(Collectors.toList()); final List<String> globalAlphaCommentLines = commentLines.stream().filter(l -> l.contains(GLOBAL_ALPHA_COMMENT_STRING)).collect(Collectors.toList()); final List<String> globalBetaCommentLines = commentLines.stream().filter(l -> l.contains(GLOBAL_BETA_COMMENT_STRING)).collect(Collectors.toList()); if (globalAlphaCommentLines.size() != 1 || globalBetaCommentLines.size() != 1) { throw new UserException.BadInput("MLE global hyperparameter values for allelic panel of normals were not specified correctly in comment lines of file " + inputFile.getAbsolutePath() + "."); } final double globalAlpha = Double.valueOf(globalAlphaCommentLines.get(0).replace(TableUtils.COMMENT_PREFIX + GLOBAL_ALPHA_COMMENT_STRING, "")); final double globalBeta = Double.valueOf(globalBetaCommentLines.get(0).replace(TableUtils.COMMENT_PREFIX + GLOBAL_BETA_COMMENT_STRING, "")); ParamUtils.isPositive(globalAlpha, "MLE global hyperparameter alpha must be positive."); ParamUtils.isPositive(globalBeta, "MLE global hyperparameter alpha must be positive."); return new HyperparameterValues(globalAlpha, globalBeta); } catch (final IOException | UncheckedIOException e) { throw new UserException.CouldNotReadInputFile(inputFile, e); } catch (final NumberFormatException e) { throw new UserException.BadInput("MLE global hyperparameter values for allelic panel of normals were not specified correctly in comment lines of file " + inputFile.getAbsolutePath() + "."); } }

Target:
private static HyperparameterValues parseGlobalHyperparameterValues(final File inputFile) { try { final List<String> commentLines = FileUtils.readLines(inputFile).stream() .filter(l -> l.contains(TableUtils.COMMENT_PREFIX)).collect(Collectors.toList()); final List<String> globalAlphaCommentLines = commentLines.stream() .filter(l -> l.contains(GLOBAL_ALPHA_COMMENT_STRING)).collect(Collectors.toList()); final List<String> globalBetaCommentLines = commentLines.stream() .filter(l -> l.contains(GLOBAL_BETA_COMMENT_STRING)).collect(Collectors.toList()); if (globalAlphaCommentLines.size() != 1 || globalBetaCommentLines.size() != 1) { throw new UserException.BadInput("MLE global hyperparameter values for allelic panel of normals " + "were not specified correctly in comment lines of file " + inputFile.getAbsolutePath() + "."); } final double globalAlpha = Double.valueOf(globalAlphaCommentLines.get(0) .replace(TableUtils.COMMENT_PREFIX + GLOBAL_ALPHA_COMMENT_STRING, "")); final double globalBeta = Double.valueOf(globalBetaCommentLines.get(0) .replace(TableUtils.COMMENT_PREFIX + GLOBAL_BETA_COMMENT_STRING, "")); ParamUtils.isPositive(globalAlpha, "MLE global hyperparameter alpha must be positive."); ParamUtils.isPositive(globalBeta, "MLE global hyperparameter alpha must be positive."); return new HyperparameterValues(globalAlpha, globalBeta); } catch (final IOException | UncheckedIOException e) { throw new UserException.CouldNotReadInputFile(inputFile, e); } catch (final NumberFormatException e) { throw new UserException.BadInput("MLE global hyperparameter values for allelic panel of normals " + "were not specified correctly in comment lines of file " + inputFile.getAbsolutePath() + "."); } }