Examples with Parameter com.beust.jcommander.Parameter used on opensource projects

Example 1 with Parameter

use of com.beust.jcommander.Parameter in project copybara by google.

the class MarkdownGenerator method generateFlagsInfo.

private CharSequence generateFlagsInfo(Element classElement) throws ElementException {
    StringBuilder sb = new StringBuilder();
    AnnotationHelper<UsesFlags> annotation = annotationHelper(classElement, UsesFlags.class);
    if (annotation == null) {
        return sb;
    }
    StringBuilder flagsString = new StringBuilder();
    for (DeclaredType flag : annotation.getClassListValue("value")) {
        Element flagClass = flag.asElement();
        for (Element member : flagClass.getEnclosedElements()) {
            Parameter flagAnnotation = member.getAnnotation(Parameter.class);
            if (flagAnnotation == null || !(member instanceof VariableElement) || flagAnnotation.hidden()) {
                continue;
            }
            VariableElement field = (VariableElement) member;
            flagsString.append(Joiner.on(", ").join(flagAnnotation.names()));
            flagsString.append(" | *");
            flagsString.append(simplerJavaTypes(field));
            flagsString.append("* | ");
            flagsString.append(flagAnnotation.description());
            flagsString.append("\n");
        }
    }
    if (flagsString.length() > 0) {
        sb.append("\n\n**Command line flags:**\n\n");
        sb.append("Name | Type | Description\n");
        sb.append("---- | ----------- | -----------\n");
        sb.append(flagsString);
        sb.append("\n");
    }
    return sb;
}

Example 2 with Parameter

use of com.beust.jcommander.Parameter in project mixcr by milaboratory.

the class ActionAssembleContigs method go.

@Override
public void go(ActionHelper helper) throws Exception {
    // TODO FIX!!!!!!!!!!!!!
    if (parameters.threads > 1)
        throw new ParameterException("Multithreaded processing is not supported yet.");
    long beginTimestamp = System.currentTimeMillis();
    FullSeqAssemblerParameters p = FullSeqAssemblerParameters.getByName("default");
    if (!parameters.overrides.isEmpty()) {
        // Perform parameters overriding
        p = JsonOverrider.override(p, FullSeqAssemblerParameters.class, parameters.overrides);
        if (p == null)
            throw new ProcessException("Failed to override some parameter.");
    }
    final FullSeqAssemblerReport report = new FullSeqAssemblerReport();
    FullSeqAssemblerParameters assemblerParameters = p;
    int totalClonesCount = 0;
    List<VDJCGene> genes;
    VDJCAlignerParameters alignerParameters;
    CloneAssemblerParameters cloneAssemblerParameters;
    try (ClnAReader reader = new ClnAReader(parameters.getInputFileName(), VDJCLibraryRegistry.getDefault());
        PrimitivO tmpOut = new PrimitivO(new BufferedOutputStream(new FileOutputStream(parameters.getOutputFileName())))) {
        final CloneFactory cloneFactory = new CloneFactory(reader.getAssemblerParameters().getCloneFactoryParameters(), reader.getAssemblingFeatures(), reader.getGenes(), reader.getAlignerParameters().getFeaturesToAlignMap());
        alignerParameters = reader.getAlignerParameters();
        cloneAssemblerParameters = reader.getAssemblerParameters();
        genes = reader.getGenes();
        IOUtil.registerGeneReferences(tmpOut, genes, alignerParameters);
        ClnAReader.CloneAlignmentsPort cloneAlignmentsPort = reader.clonesAndAlignments();
        SmartProgressReporter.startProgressReport("Assembling", cloneAlignmentsPort);
        OutputPort<Clone[]> parallelProcessor = new ParallelProcessor<>(cloneAlignmentsPort, cloneAlignments -> {
            FullSeqAssembler fullSeqAssembler = new FullSeqAssembler(cloneFactory, assemblerParameters, cloneAlignments.clone, alignerParameters);
            fullSeqAssembler.setReport(report);
            FullSeqAssembler.RawVariantsData rawVariantsData = fullSeqAssembler.calculateRawData(() -> {
                try {
                    return cloneAlignments.alignments();
                } catch (IOException e) {
                    throw new RuntimeException(e);
                }
            });
            return fullSeqAssembler.callVariants(rawVariantsData);
        }, parameters.threads);
        for (Clone[] clones : CUtils.it(parallelProcessor)) {
            totalClonesCount += clones.length;
            for (Clone cl : clones) tmpOut.writeObject(cl);
        }
        assert report.getInitialCloneCount() == reader.numberOfClones();
    }
    assert report.getFinalCloneCount() == totalClonesCount;
    assert report.getFinalCloneCount() >= report.getInitialCloneCount();
    Clone[] clones = new Clone[totalClonesCount];
    try (PrimitivI tmpIn = new PrimitivI(new BufferedInputStream(new FileInputStream(parameters.getOutputFileName())))) {
        IOUtil.registerGeneReferences(tmpIn, genes, alignerParameters);
        int i = 0;
        for (Clone clone : CUtils.it(new PipeDataInputReader<>(Clone.class, tmpIn, totalClonesCount))) clones[i++] = clone;
    }
    Arrays.sort(clones, Comparator.comparingDouble(c -> -c.getCount()));
    for (int i = 0; i < clones.length; i++) clones[i] = clones[i].setId(i);
    CloneSet cloneSet = new CloneSet(Arrays.asList(clones), genes, alignerParameters.getFeaturesToAlignMap(), alignerParameters, cloneAssemblerParameters);
    try (CloneSetIO.CloneSetWriter writer = new CloneSetIO.CloneSetWriter(cloneSet, parameters.getOutputFileName())) {
        SmartProgressReporter.startProgressReport(writer);
        writer.write();
    }
    ReportWrapper reportWrapper = new ReportWrapper(command(), report);
    reportWrapper.setStartMillis(beginTimestamp);
    reportWrapper.setInputFiles(parameters.getInputFileName());
    reportWrapper.setOutputFiles(parameters.getOutputFileName());
    reportWrapper.setCommandLine(helper.getCommandLineArguments());
    reportWrapper.setFinishMillis(System.currentTimeMillis());
    // Writing report to stout
    System.out.println("============= Report ==============");
    Util.writeReportToStdout(report);
    if (parameters.report != null)
        Util.writeReport(parameters.report, reportWrapper);
    if (parameters.jsonReport != null)
        Util.writeJsonReport(parameters.jsonReport, reportWrapper);
}

Example 3 with Parameter

use of com.beust.jcommander.Parameter in project halyard by spinnaker.

the class NestableCommand method commandDocs.

private void commandDocs(StringBuilder result) {
    List<ParameterDescription> parameters = commander.getParameters().stream().filter(p -> !p.getParameter().hidden()).collect(Collectors.toList());
    parameters.sort(Comparator.comparing(ParameterDescription::getNames));
    int parameterCount = 0;
    for (ParameterDescription parameter : parameters) {
        if (GlobalOptions.isGlobalOption(parameter.getLongestName())) {
            parameterCount++;
        }
    }
    String longDescription = getLongDescription() != null ? getLongDescription() : getDescription();
    result.append("## ").append(fullCommandName).append("\n\n").append(longDescription).append("\n\n").append("#### Usage").append("\n```\n").append(fullCommandName);
    ParameterDescription mainParameter = commander.getMainParameter();
    if (mainParameter != null) {
        result.append(" ").append(getMainParameter().toUpperCase());
    }
    if (parameters.size() > parameterCount) {
        result.append(" [parameters]");
    }
    if (!subcommands.isEmpty()) {
        result.append(" [subcommands]");
    }
    result.append("\n```\n");
    if (!parameters.isEmpty()) {
        if (getCommandName() == "hal") {
            result.append("#### Global Parameters\n");
        }
        for (ParameterDescription parameter : parameters) {
            if (GlobalOptions.isGlobalOption(parameter.getLongestName())) {
                // Omit printing global parameters for everything but the top-level command
                if (getCommandName() == "hal") {
                    parameterDoc(result, parameter);
                }
            }
        }
        result.append("\n");
    }
    if (parameters.size() > parameterCount) {
        result.append("#### Parameters\n");
        if (mainParameter != null) {
            result.append('`').append(getMainParameter().toUpperCase()).append('`').append(": ").append(mainParameter.getDescription()).append("\n");
        }
        for (ParameterDescription parameter : parameters) {
            if (!GlobalOptions.isGlobalOption(parameter.getLongestName())) {
                parameterDoc(result, parameter);
            }
        }
        result.append("\n");
    }
    if (!subcommands.isEmpty()) {
        result.append("#### Subcommands\n");
        List<String> keys = new ArrayList<>(subcommands.keySet());
        keys.sort(String::compareTo);
        for (String key : keys) {
            NestableCommand subcommand = subcommands.get(key);
            String modifiers = "";
            if (subcommand instanceof DeprecatedCommand) {
                modifiers += " _(Deprecated)_ ";
            }
            String shortDescription = subcommand.getShortDescription() != null ? subcommand.getShortDescription() : subcommand.getDescription();
            result.append(" * ").append("`").append(key).append("`").append(modifiers).append(": ").append(shortDescription).append("\n");
        }
    }
    result.append("\n---\n");
}