Example usage for java.util LinkedHashSet size

List of usage examples for java.util LinkedHashSet size

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Introduction

In this page you can find the example usage for java.util LinkedHashSet size.

Prototype

int size();

Source Link

Document

Returns the number of elements in this set (its cardinality).

Usage

From source file:org.apache.druid.initialization.Initialization.java

/**
 * Find all the extension files that should be loaded by druid.
 * <p/>//  www  .j a  va 2  s  .  co m
 * If user explicitly specifies druid.extensions.loadList, then it will look for those extensions under root
 * extensions directory. If one of them is not found, druid will fail loudly.
 * <p/>
 * If user doesn't specify druid.extension.toLoad (or its value is empty), druid will load all the extensions
 * under the root extensions directory.
 *
 * @param config ExtensionsConfig configured by druid.extensions.xxx
 *
 * @return an array of druid extension files that will be loaded by druid process
 */
public static File[] getExtensionFilesToLoad(ExtensionsConfig config) {
    final File rootExtensionsDir = new File(config.getDirectory());
    if (rootExtensionsDir.exists() && !rootExtensionsDir.isDirectory()) {
        throw new ISE("Root extensions directory [%s] is not a directory!?", rootExtensionsDir);
    }
    File[] extensionsToLoad;
    final LinkedHashSet<String> toLoad = config.getLoadList();
    if (toLoad == null) {
        extensionsToLoad = rootExtensionsDir.listFiles();
    } else {
        int i = 0;
        extensionsToLoad = new File[toLoad.size()];
        for (final String extensionName : toLoad) {
            File extensionDir = new File(extensionName);
            if (!extensionDir.isAbsolute()) {
                extensionDir = new File(rootExtensionsDir, extensionName);
            }

            if (!extensionDir.isDirectory()) {
                throw new ISE("Extension [%s] specified in \"druid.extensions.loadList\" didn't exist!?",
                        extensionDir.getAbsolutePath());
            }
            extensionsToLoad[i++] = extensionDir;
        }
    }
    return extensionsToLoad == null ? new File[] {} : extensionsToLoad;
}

From source file:org.opencb.opencga.storage.core.metadata.StudyConfiguration.java

public static LinkedHashMap<String, Integer> getReturnedSamplesPosition(StudyConfiguration studyConfiguration,
        LinkedHashSet<String> returnedSamples,
        Function<StudyConfiguration, BiMap<String, Integer>> getIndexedSamplesPosition) {
    LinkedHashMap<String, Integer> samplesPosition;
    if (returnedSamples == null || returnedSamples.isEmpty()) {
        BiMap<Integer, String> unorderedSamplesPosition = getIndexedSamplesPosition(studyConfiguration)
                .inverse();//w w  w . jav  a 2 s.  c o m
        samplesPosition = new LinkedHashMap<>(unorderedSamplesPosition.size());
        for (int i = 0; i < unorderedSamplesPosition.size(); i++) {
            samplesPosition.put(unorderedSamplesPosition.get(i), i);
        }
    } else {
        samplesPosition = new LinkedHashMap<>(returnedSamples.size());
        int index = 0;
        BiMap<String, Integer> indexedSamplesId = getIndexedSamplesPosition.apply(studyConfiguration);
        for (String returnedSample : returnedSamples) {
            if (!returnedSample.isEmpty() && StringUtils.isNumeric(returnedSample)) {
                returnedSample = studyConfiguration.getSampleIds().inverse()
                        .get(Integer.parseInt(returnedSample));
            }
            if (!samplesPosition.containsKey(returnedSample)) {
                if (indexedSamplesId.containsKey(returnedSample)) {
                    samplesPosition.put(returnedSample, index++);
                }
            }
        }
        //                for (String sample : indexedSamplesId.keySet()) {
        //                    samplesPosition.put(sample, index++);
        //                }
    }
    return samplesPosition;
}

From source file:com.google.gwt.emultest.java.util.LinkedHashSetTest.java

@SuppressWarnings("unchecked")
public void testClone() {
    LinkedHashSet<String> srcSet = new LinkedHashSet<String>();
    checkEmptyLinkedHashSetAssumptions(srcSet);

    // Check empty clone behavior
    LinkedHashSet<String> dstSet = (LinkedHashSet<String>) srcSet.clone();
    assertNotNull(dstSet);// w ww. ja va2 s. c om
    assertEquals(dstSet.size(), srcSet.size());
    assertEquals(dstSet.toArray(), srcSet.toArray());

    // Check non-empty clone behavior
    srcSet.add(VALUE_1);
    srcSet.add(VALUE_2);
    srcSet.add(VALUE_3);
    srcSet.add(VALUE_4);
    dstSet = (LinkedHashSet<String>) srcSet.clone();
    assertNotNull(dstSet);
    assertEquals(dstSet.size(), srcSet.size());
    assertEquals(dstSet.toArray(), srcSet.toArray());
}

From source file:com.aurel.track.teamgeist.TeamgeistServicesTest.java

/**
 * This method iterate through the Set which contains all action names used by Teamgeist.
 * If an action missing the test fails.//w  w  w. ja  v a 2s  .co m
 */
@Test
public void testServices() {
    LinkedHashSet<String> actionNamesSet = getActinNames();
    if (actionNamesSet != null && actionNamesSet.size() > 0) {
        for (String actionName : actionNamesSet) {
            try {
                ActionProxy actionProxy = getActionProxy("/" + actionName);
                assertNotNull(actionProxy);
                Class<?> actionClass = Class.forName(actionProxy.getAction().getClass().getName());
                actionClass.getMethod(actionProxy.getMethod());
            } catch (NoSuchMethodException noMethodEX) {
                fail("No such method exception at: " + actionName);
                System.out.println("No such method: " + actionName);
            } catch (ClassNotFoundException noClassEx) {
                fail("Class not found exception at: " + actionName);
                System.out.println("No such class: " + actionName);
            } catch (NullPointerException nullEx) {
                fail("Null pointer exception at: " + actionName);
                System.out.println("Null pointer at: " + actionName);
            }
        }
        System.out.println(
                "Number of actions: " + actionNamesSet.size() + ". " + "The test was executed successfully!");
    } else {
        fail("Error while parsing Services file!");
    }
}

From source file:org.mskcc.cbio.oncokb.quest.VariantAnnotationXML.java

public static String annotate(Alteration alt, String tumorType) {
        //        GeneBo geneBo = ApplicationContextSingleton.getGeneBo();

        StringBuilder sb = new StringBuilder();

        Gene gene = alt.getGene();//from   w w w  . j a  v  a2 s  .c  o m

        //        Set<Gene> genes = new HashSet<Gene>();
        //        if (gene.getEntrezGeneId() > 0) {
        //            genes.add(gene);
        //        } else {
        // fake gene... could be a fusion gene
        //            Set<String> aliases = gene.getGeneAliases();
        //            for (String alias : aliases) {
        //                Gene g = geneBo.findGeneByHugoSymbol(alias);
        //                if (g != null) {
        //                    genes.add(g);
        //                }
        //            }
        //        }

        List<TumorType> relevantTumorTypes = TumorTypeUtils.getMappedOncoTreeTypesBySource(tumorType, "quest");

        AlterationUtils.annotateAlteration(alt, alt.getAlteration());

        AlterationBo alterationBo = ApplicationContextSingleton.getAlterationBo();
        LinkedHashSet<Alteration> alterations = alterationBo.findRelevantAlterations(alt, true);

        // In previous logic, we do not include alternative alleles
        List<Alteration> alternativeAlleles = AlterationUtils.getAlleleAlterations(alt);
        alterations.removeAll(alternativeAlleles);

        EvidenceBo evidenceBo = ApplicationContextSingleton.getEvidenceBo();

        // find all drugs
        //List<Drug> drugs = evidenceBo.findDrugsByAlterations(alterations);

        // find tumor types
        Set<String> tumorTypes = new HashSet<>();

        if (alterations != null && alterations.size() > 0) {
            List<Object> tumorTypesEvidence = evidenceBo
                    .findTumorTypesWithEvidencesForAlterations(new ArrayList<>(alterations));
            for (Object evidence : tumorTypesEvidence) {
                if (evidence != null) {
                    Object[] evidences = (Object[]) evidence;
                    if (evidences.length > 0 && evidences[0] != null) {
                        tumorTypes.add((String) evidences[0]);
                    }
                }
            }
        }

        //        sortTumorType(tumorTypes, tumorType);
        Query query = new Query(alt);
        query.setTumorType(tumorType);
        // summary
        sb.append("<annotation_summary>");
        sb.append(SummaryUtils.fullSummary(gene, alt,
                alterations.isEmpty() ? Collections.singletonList(alt) : new ArrayList<>(alterations), query,
                relevantTumorTypes));
        sb.append("</annotation_summary>\n");

        // gene background
        List<Evidence> geneBgEvs = evidenceBo.findEvidencesByGene(Collections.singleton(gene),
                Collections.singleton(EvidenceType.GENE_BACKGROUND));
        if (!geneBgEvs.isEmpty()) {
            Evidence ev = geneBgEvs.get(0);
            sb.append("<gene_annotation>\n");
            sb.append("    <description>");
            sb.append(StringEscapeUtils.escapeXml10(ev.getDescription()).trim());
            sb.append("</description>\n");
            exportRefereces(ev, sb, "    ");
            sb.append("</gene_annotation>\n");
        }

        if (alterations.isEmpty()) {
            sb.append("<!-- There is no information about the function of this variant in the MSKCC OncoKB. -->");
            return sb.toString();
        }

        List<Evidence> mutationEffectEbs = evidenceBo.findEvidencesByAlteration(alterations,
                Collections.singleton(EvidenceType.MUTATION_EFFECT));
        for (Evidence ev : mutationEffectEbs) {
            sb.append("<variant_effect>\n");
            sb.append("    <effect>");
            if (ev != null) {
                sb.append(ev.getKnownEffect());
            }
            sb.append("</effect>\n");
            if (ev.getDescription() != null) {
                sb.append("    <description>");
                sb.append(StringEscapeUtils.escapeXml10(ev.getDescription()).trim());
                sb.append("</description>\n");
            }
            if (ev != null) {
                exportRefereces(ev, sb, "    ");
            }

            sb.append("</variant_effect>\n");
        }

        for (String tt : tumorTypes) {
            TumorType oncoTreeType = TumorTypeUtils.getMappedOncoTreeTypesBySource(tt, "quest").get(0);
            boolean isRelevant = relevantTumorTypes.contains(oncoTreeType);

            StringBuilder sbTumorType = new StringBuilder();
            sbTumorType.append("<cancer_type type=\"").append(tt).append("\" relevant_to_patient_disease=\"")
                    .append(isRelevant ? "Yes" : "No").append("\">\n");
            int nEmp = sbTumorType.length();

            // find prognostic implication evidence blob
            Set<Evidence> prognosticEbs = new HashSet<Evidence>(evidenceBo.findEvidencesByAlteration(alterations,
                    Collections.singleton(EvidenceType.PROGNOSTIC_IMPLICATION),
                    Collections.singleton(oncoTreeType)));
            if (!prognosticEbs.isEmpty()) {
                sbTumorType.append("    <prognostic_implications>\n");
                sbTumorType.append("        <description>\n");
                for (Evidence ev : prognosticEbs) {
                    String description = ev.getDescription();
                    if (description != null) {
                        sbTumorType.append("        ").append(StringEscapeUtils.escapeXml10(description).trim())
                                .append("\n");
                    }
                }
                sbTumorType.append("</description>\n");

                for (Evidence ev : prognosticEbs) {
                    exportRefereces(ev, sbTumorType, "        ");
                }
                sbTumorType.append("    </prognostic_implications>\n");
            }

            // STANDARD_THERAPEUTIC_IMPLICATIONS
            List<Evidence> stdImpEbsSensitivity = evidenceBo.findEvidencesByAlteration(alterations,
                    Collections.singleton(EvidenceType.STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY),
                    Collections.singleton(oncoTreeType));
            List<Evidence> stdImpEbsResisitance = evidenceBo.findEvidencesByAlteration(alterations,
                    Collections.singleton(EvidenceType.STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE),
                    Collections.singleton(oncoTreeType));

            //Remove level_0
            stdImpEbsSensitivity = filterLevelZeroEvidence(stdImpEbsSensitivity);

            //Remove level_R3
            stdImpEbsResisitance = filterResistanceEvidence(stdImpEbsResisitance);

            exportTherapeuticImplications(relevantTumorTypes, stdImpEbsSensitivity, stdImpEbsResisitance,
                    "standard_therapeutic_implications", sbTumorType, "    ", isRelevant);

            // INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS
            List<Evidence> invImpEbsSensitivity = evidenceBo.findEvidencesByAlteration(alterations,
                    Collections.singleton(EvidenceType.INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY),
                    Collections.singleton(oncoTreeType));
            List<Evidence> invImpEbsResisitance = evidenceBo.findEvidencesByAlteration(alterations,
                    Collections.singleton(EvidenceType.INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE),
                    Collections.singleton(oncoTreeType));

            //Remove level_R3
            invImpEbsResisitance = filterResistanceEvidence(invImpEbsResisitance);

            exportTherapeuticImplications(relevantTumorTypes, invImpEbsSensitivity, invImpEbsResisitance,
                    "investigational_therapeutic_implications", sbTumorType, "    ", isRelevant);

            if (sbTumorType.length() > nEmp) {
                sbTumorType.append("</cancer_type>\n");
                sb.append(sbTumorType);
            }
        }

        return sb.toString();
    }

From source file:com.amashchenko.struts2.pdfstream.PdfStreamResultTest.java

@Test
public void testStringToSet2() throws Exception {
    Assert.assertNotNull(pdfStreamResult);

    final String paths = "somepath/style.css,    /another/style2.css, ";
    LinkedHashSet<String> set = pdfStreamResult.stringToSet(paths);
    Assert.assertNotNull(set);// w  w  w .  j  a  va  2  s .c  o  m
    Assert.assertEquals(2, set.size());
    Assert.assertEquals("somepath/style.css", set.toArray()[0]);
    Assert.assertEquals("/another/style2.css", set.toArray()[1]);
}

From source file:com.amashchenko.struts2.pdfstream.PdfStreamResultTest.java

@Test
public void testStringToSet() throws Exception {
    Assert.assertNotNull(pdfStreamResult);

    final String paths = "/somepath/style.css";
    final LinkedHashSet<String> set = pdfStreamResult.stringToSet(paths);
    Assert.assertNotNull(set);//from  www . j av a  2  s . c o m
    Assert.assertEquals(1, set.size());
    Assert.assertEquals("/somepath/style.css", set.toArray()[0]);
}

From source file:com.geewhiz.pacify.managers.FilterManager.java

private LinkedHashSet<Defect> filterPArchive(PArchive pArchive) {
    logger.info("      Customize Archive [{}]", pArchive.getRelativePath());

    LinkedHashSet<Defect> defects = new LinkedHashSet<Defect>();

    Map<PFile, File> replaceFiles = new HashMap<PFile, File>();

    for (PFile pFile : pArchive.getPFiles()) {
        logger.info("         Customize File [{}]", pFile.getRelativePath());
        logger.debug("             Filtering [{}] in archive [{}] using encoding [{}] and filter [{}]",
                pFile.getRelativePath(), pMarker.getAbsoluteFileFor(pArchive).getAbsolutePath(),
                pFile.getEncoding(), pFile.getFilterClass());

        File fileToFilter = extractFile(pArchive, pFile);
        PacifyFilter pacifyFilter = getFilterForPFile(pArchive, pFile);

        Map<String, String> propertyValues = new HashMap<String, String>();
        LinkedHashSet<Defect> propertyValueDefects = fillPropertyValuesFor(propertyValues, pFile);
        if (propertyValueDefects.size() > 0) {
            return propertyValueDefects;
        }/* w  w  w  . j a v a2  s.  c o  m*/

        String beginToken = pMarker.getBeginTokenFor(pArchive, pFile);
        String endToken = pMarker.getEndTokenFor(pArchive, pFile);
        String encoding = pFile.getEncoding();

        defects.addAll(pacifyFilter.filter(propertyValues, beginToken, endToken, fileToFilter, encoding));

        replaceFiles.put(pFile, fileToFilter);
        logger.info("             [{}] placeholders replaced.", pFile.getPProperties().size());
    }

    try {
        FileUtils.replaceFilesInArchive(pMarker, pArchive, replaceFiles);
    } catch (ArchiveDefect e) {
        defects.add(e);
    }

    for (Entry<PFile, File> entry : replaceFiles.entrySet()) {
        entry.getValue().delete();
    }

    return defects;
}

From source file:ch.unibas.fittingwizard.application.tools.charges.ChargesFileGenerator.java

public File generate(File destination, String chargesFileName, LinkedHashSet<ChargeValue> chargeValues) {
    destination.mkdir();//from w w  w. j a  va2 s.  c o  m
    if (destination == null || !destination.isDirectory()) {
        throw new IllegalArgumentException("Invalid destination directory.");
    }
    if (chargeValues == null || chargeValues.size() == 0) {
        throw new IllegalArgumentException("chargeValues are empty.");
    }

    File output = new File(destination, chargesFileName);
    output.delete();

    List<String> content = new ArrayList<>();
    for (ChargeValue chargeLine : chargeValues) {
        String line = String.format("%s_%s %s", chargeLine.getAtomTypeId().getName(), chargeLine.getType(),
                String.valueOf(chargeLine.getValue()));
        content.add(line);
    }

    try {
        FileUtils.writeLines(output, content);
    } catch (IOException e) {
        throw new RuntimeException("Could not write charges file.");
    }

    return output;
}

From source file:org.apache.cassandra.db.SystemKeyspaceTest.java

private int getDeferredDeletionCount() {
    try {/*  ww w.  j a v  a  2 s .co  m*/
        Class c = Class.forName("java.io.DeleteOnExitHook");
        LinkedHashSet<String> files = (LinkedHashSet<String>) FBUtilities.getProtectedField(c, "files").get(c);
        return files.size();
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
}