Example usage for com.google.common.collect Iterables toString

List of usage examples for com.google.common.collect Iterables toString

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Introduction

In this page you can find the example usage for com.google.common.collect Iterables toString.

Prototype

public static String toString(Iterable<?> iterable)

Source Link

Document

Returns a string representation of iterable , with the format [e1, e2, ..., en] (that is, identical to java.util.Arrays Arrays .toString(Iterables.toArray(iterable)) ).

Usage

From source file:edu.umn.msi.tropix.proteomics.itraqquantitation.impl.WeightedRatiosCalculatorImpl.java

public Ratios computeRatios(final ITraqLabel numLabel, final ITraqLabel denLabel,
        final ReportSummary reportSummary, final Function<Double, Double> weightFunction,
        final boolean normalized) {
    final double[] ratios = new double[reportSummary.getNumGroups()],
            pValues = new double[reportSummary.getNumGroups()];
    int groupNum = 0;
    for (final String groupLabel : reportSummary.getGroups()) {
        final GroupSummary proteinSummary = reportSummary.getGroupSummary(groupLabel);
        final double[] iRatio = new double[proteinSummary.getNumEntries()];
        final double[] num = proteinSummary.getIntensities(numLabel);
        final double[] den = proteinSummary.getIntensities(denLabel);

        double[] weights = proteinSummary.getLogIntensitiesProducts();
        if (weightFunction != null) {
            final double[] modifiedWeights = new double[weights.length];
            for (int i = 0; i < weights.length; i++) {
                modifiedWeights[i] = weightFunction.apply(weights[i]);
            }//from   w ww .j a  v  a2 s .  c om
            weights = modifiedWeights;
        }

        for (int i = 0; i < iRatio.length; i++) {
            iRatio[i] = Math.log(num[i] / den[i]);
        }

        // final String logRatioStr = Iterables.toString(Doubles.asList(iRatio));
        // System.out.println(logRatioStr);

        if (normalized) {
            final double median = RUtils.median(iRatio);
            for (int i = 0; i < iRatio.length; i++) {
                iRatio[i] = iRatio[i] / median;
            }
        }

        final double iRatioW1 = RUtils.weightedMean(iRatio, weights);
        final double iRatioW = Math.exp(iRatioW1);
        double pValue = 2.0;
        if (iRatio.length > 2) {
            pValue = RMethods.getWeightedPValue(iRatio, weights);
        }

        if (pValue < 0) {
            // This hasn't been a problem since upgrading commons-math
            final String ratioStr = Iterables.toString(Doubles.asList(iRatio));
            final String weightsStr = Iterables.toString(Doubles.asList(weights));
            System.out.println(String.format("Negative p-value found for ratios %s and weights %s.", ratioStr,
                    weightsStr));
        }

        ratios[groupNum] = iRatioW;
        pValues[groupNum] = pValue;

        groupNum++;
    }

    return new Ratios(ratios, pValues);
}

From source file:brooklyn.location.docker.strategy.affinity.DockerAffinityRuleStrategy.java

@Override
public List<DockerHostLocation> filterLocations(List<DockerHostLocation> locations, Entity entity) {
    List<DockerHostLocation> available = Lists.newArrayList();

    // Select hosts that satisfy the affinity rules
    for (DockerHostLocation machine : locations) {
        Optional<List<String>> entityRules = Optional
                .fromNullable(entity.config().get(DockerHost.DOCKER_HOST_AFFINITY_RULES));
        Optional<List<String>> hostRules = Optional
                .fromNullable(machine.getOwner().config().get(DockerHost.DOCKER_HOST_AFFINITY_RULES));
        Optional<List<String>> infrastructureRules = Optional.fromNullable(
                machine.getOwner().getInfrastructure().config().get(DockerHost.DOCKER_HOST_AFFINITY_RULES));
        Iterable<String> combined = Iterables.concat(
                Optional.presentInstances(ImmutableList.of(entityRules, hostRules, infrastructureRules)));
        AffinityRules rules = AffinityRules.rulesFor(entity).parse(combined);

        Iterable<Entity> entities = getBrooklynManagementContext().getEntityManager()
                .findEntities(EntityPredicates.locationsIncludes(machine));
        if (Iterables.isEmpty(entities)) {
            if (rules.allowEmptyLocations()) {
                available.add(machine);/*from w w w  .j ava  2 s . c  om*/
            }
        } else {
            Iterable<Entity> filtered = Iterables.filter(entities, rules);
            if (Iterables.size(filtered) == Iterables.size(entities)) {
                available.add(machine);
            }
        }
    }

    if (LOG.isDebugEnabled()) {
        LOG.debug("Available Docker hosts: {}", Iterables.toString(available));
    }
    return available;
}

From source file:us.eharning.atomun.mnemonic.spi.electrum.v2.MnemonicBuilderSpiImpl.java

/**
 * Checks that the given extension parameter is valid.
 *
 * @param parameter//from w ww .  j a va  2s .c om
 *         instance containing extension parameters.
 *
 * @throws IllegalArgumentException
 *         if the parameter contains unknown parameters.
 */
private static void checkExtensionNames(ExtensionBuilderParameter parameter) {
    Map<String, Object> extensions = parameter.getExtensions();
    if (!KNOWN_EXTENSION_NAMES.containsAll(extensions.keySet())) {
        Iterable<String> unknownNames = Iterables.filter(extensions.keySet(),
                Predicates.not(Predicates.in(KNOWN_EXTENSION_NAMES)));
        throw new IllegalArgumentException(
                "Found unhandled extension names: " + Iterables.toString(unknownNames));
    }
}

From source file:org.impressivecode.depress.scm.common.SCMInputTransformer.java

@Override
public InputTransformer<SCMDataType> validate() throws InvalidSettingsException {
    checkNotNull(this.minimalTableSpec, "Minimal DataTableSpec hat to be set");
    checkNotNull(this.inputTableSpec, "Input DataTableSpec hat to be set");

    Set<String> missing = DataTableSpecUtils.findMissingColumnSubset(this.inputTableSpec,
            this.minimalTableSpec);
    if (!missing.isEmpty()) {
        throw new InvalidSettingsException("History data table does not contain required columns. Missing: "
                + Iterables.toString(missing));
    }//from   w w w  . j a v  a 2s .c om
    return this;
}

From source file:mvm.rya.api.persist.query.BatchRyaQuery.java

@Override
public String toString() {
    return "BatchRyaQuery{" + "queries=" + Iterables.toString(queries) + "options={" + super.toString() + '}'
            + '}';
}

From source file:org.jclouds.vcloud.director.v1_5.predicates.EntityPredicates.java

/**
 * Matches {@link EntityType entities} with names in the given collection.
 *
 * @param T type of the entity, for example {@link Vm}
 * @param names collection of values for the name attribute of the entity
 * @return predicate that will match entities with names starting with the given prefix
 *///from   w w w  . ja va2s .  c  o m
public static <T extends Entity> Predicate<T> nameIn(final Iterable<String> names) {
    checkNotNull(names, "names must be defined");

    return new Predicate<T>() {
        @Override
        public boolean apply(T entity) {
            String name = entity.getName();
            return Iterables.contains(names, name);
        }

        @Override
        public String toString() {
            return "nameIn(" + Iterables.toString(names) + ")";
        }
    };
}

From source file:eu.interedition.collatex.jung.JungVariantGraphVertex.java

@Override
public String toString() {
    return Iterables.toString(tokens);
}

From source file:org.eclipse.xtend.maven.AbstractXtend2CompilerMojo.java

protected void compile(XtendBatchCompiler xtend2BatchCompiler, String classPath, List<String> sourceDirectories,
        String outputPath) throws MojoExecutionException {
    Iterable<String> filtered = filter(sourceDirectories, FILE_EXISTS);
    if (Iterables.isEmpty(filtered)) {
        getLog().info("skip compiling sources because the configured directory '"
                + Iterables.toString(sourceDirectories) + "' does not exists.");
        return;//from  www.jav a 2 s . c  o m
    }
    getLog().debug("Set temp directory: " + getTempDirectory());
    xtend2BatchCompiler.setTempDirectory(getTempDirectory());
    getLog().debug("Set DeleteTempDirectory: " + false);
    xtend2BatchCompiler.setDeleteTempDirectory(false);
    getLog().debug("Set classpath: " + classPath);
    xtend2BatchCompiler.setClassPath(classPath);
    getLog().debug("Set source path: " + concat(File.pathSeparator, newArrayList(filtered)));
    xtend2BatchCompiler.setSourcePath(concat(File.pathSeparator, newArrayList(filtered)));
    getLog().debug("Set output path: " + outputPath);
    xtend2BatchCompiler.setOutputPath(outputPath);
    getLog().debug("Set encoding: " + encoding);
    xtend2BatchCompiler.setFileEncoding(encoding);
    if (!xtend2BatchCompiler.compile()) {
        throw new MojoExecutionException("Error compiling xtend sources in '"
                + concat(File.pathSeparator, newArrayList(filtered)) + "'.");
    }
}

From source file:com.google.devtools.build.lib.events.EventCollector.java

@Override
public synchronized String toString() {
    return "EventCollector: " + Iterables.toString(collected);
}

From source file:org.eclipse.jdt.ls.core.internal.highlighting.SemanticHighlightingService.java

/**
 * Returns with the scope for the index. If not found, throws an exception.
 *//*from   ww  w  .j a v  a2 s  .co  m*/
public static int getIndex(List<String> scopes) {
    Integer index = LOOKUP_TABLE.inverse().get(scopes);
    Assert.isNotNull(index, "Cannot get index for scopes: " + Iterables.toString(scopes));
    return index;
}