Example usage for java.util Collection addAll

List of usage examples for java.util Collection addAll

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Introduction

In this page you can find the example usage for java.util Collection addAll.

Prototype

boolean addAll(Collection<? extends E> c);

Source Link

Document

Adds all of the elements in the specified collection to this collection (optional operation).

Usage

From source file:chibi.gemmaanalysis.GeneExpressionWriterCLI.java

@Override
protected Exception doWork(String[] args) {

    StopWatch timer = new StopWatch();
    timer.start();//from   w  ww .  j  a va 2  s . co m

    String HEADER = "HEADER";

    processCommandLine(args);

    Collection<Gene> genes;
    try {
        genes = getQueryGenes();
    } catch (IOException e) {
        return e;
    }

    StringBuffer sb = new StringBuffer();
    for (Gene gene : genes) {
        sb.append(gene.toString());
        sb.append(", ");
    }
    log.info(genes.size() + " genes: " + sb.toString());

    sb = new StringBuffer();
    for (BioAssaySet bas : this.expressionExperiments) {
        sb.append(bas.toString());
        sb.append(", ");
    }
    log.info(this.expressionExperiments.size() + " experiments: " + sb.toString());

    Map<Object, StringBuffer> outBuffs = new HashMap<>();

    String fileName = outFilePrefix + ".txt";

    log.info("Output filename " + fileName);

    for (BioAssaySet bas : this.expressionExperiments) {
        ExpressionExperiment ee = (ExpressionExperiment) bas;
        Collection<ArrayDesign> ads = eeService.getArrayDesignsUsed(ee);
        Collection<CompositeSequence> css = new HashSet<CompositeSequence>();
        for (ArrayDesign ad : ads) {
            css.addAll(adService.getCompositeSequences(ad));
        }

        log.info("====================================");
        log.info("Experiment " + ee + "; Array Design " + ads + "; Composite sequences " + css.size());

        Map<Gene, Collection<CompositeSequence>> gene2css = getGene2CsMap(css);
        // ExpressionDataDoubleMatrix dataMatrix = expressionDataMatrixService.getFilteredMatrix( ee, filterConfig
        // );
        ExpressionDataDoubleMatrix dataMatrix = expressionDataMatrixService
                .getProcessedExpressionDataMatrix(ee);

        // store values inside a buffer
        if (!outBuffs.containsKey(HEADER)) {
            StringBuffer hb = new StringBuffer();
            hb.append("Gene\tProbe\tID");
            outBuffs.put(HEADER, hb);
        }
        for (BioMaterial bm : dataMatrix.getMatrix().getColNames()) {
            // bm.getFactorValues()
            // bm.getCharacteristics()
            // outBuffs.get( HEADER )
            // .append(
            // "\t" + bm.getName() + "."
            // + StringUtils.collectionToDelimitedString( bm.getFactorValues(), "," ) );
            outBuffs.get(HEADER)
                    .append("\t" + ee.getShortName() + "." + bm.getName() + "."
                            + StringUtils.collectionToDelimitedString(bm.getCharacteristics(), ",") + "."
                            + StringUtils.collectionToDelimitedString(bm.getFactorValues(), ","));
        }

        for (Gene gene : genes) {
            log.debug(" Getting component sequence for gene " + gene);
            Collection<CompositeSequence> c = gene2css.get(gene);

            if (c == null) {
                log.error("No composite sequences found for gene " + gene);
                continue;
            }

            for (CompositeSequence cs : c) {

                Double[] row = dataMatrix.getRow(cs);
                if (row == null) {
                    log.error("Cannot get data from data matrix for " + gene.getOfficialSymbol() + " ("
                            + cs.getName() + ")");
                    // continue;
                    row = new Double[dataMatrix.getMatrix().columns()];
                }

                if (!outBuffs.containsKey(cs)) {
                    StringBuffer gb = new StringBuffer();
                    gb.append(gene.getOfficialSymbol() + "\t" + cs.getName() + "\t" + cs.getId());
                    outBuffs.put(cs, gb);
                }

                StringBuffer buf = new StringBuffer();
                for (Double d : row) {
                    if (d == null)
                        buf.append("NA");
                    else
                        buf.append(d);
                    buf.append("\t");
                }
                buf.deleteCharAt(buf.length() - 1);
                outBuffs.get(cs).append("\t" + buf.toString());
            }
        }

    }

    // Output to file
    try (PrintWriter out = new PrintWriter(new FileWriter(fileName));) {
        out.println(outBuffs.get(HEADER));
        for (Object key : outBuffs.keySet()) {
            if (key.equals(HEADER)) {
                continue;
            }
            out.println(outBuffs.get(key));
        }
    } catch (IOException e) {
        return e;
    }

    log.info("Done. Wrote " + genes.size() + " genes and " + (outBuffs.keySet().size() - 1)
            + " composite sequences in " + this.expressionExperiments.size() + " experiments which took "
            + timer.getTime() + " ms. Output file " + fileName);

    return null;
}

From source file:org.reusables.dbunit.DbUnitDatasetExecutionListener.java

/**
 * Load the dataset using the given annotation information.
 * /*ww  w  . j a v a  2  s.  co m*/
 * @param operation The operation to perform.
 * @param testContext The context for the current test.
 * @param classAnnotation Dataset resource information of the test class.
 * @param methodAnnotation Dataset resource information of the test method.
 * @throws Exception Any error.
 * @since 1.3.0
 */
protected void handleDataset(final DatabaseOperation operation, final TestContext testContext,
        final DbUnitDataset classAnnotation, final DbUnitDataset methodAnnotation) throws Exception {
    LOG.debug("Getting datasets for operation: {}", operation.getClass().getSimpleName());

    final Collection<IDataSet> datasets = new ArrayList<IDataSet>();
    datasets.addAll(createDataSets(testContext, classAnnotation, false));
    datasets.addAll(createDataSets(testContext, methodAnnotation, true));

    if (datasets.isEmpty()) {
        LOG.debug("No datasets found.");
        return;
    }

    final IDataSet dataset = createAutoCompletionDataSet(
            new CompositeDataSet(datasets.toArray(new IDataSet[0])), testContext);
    final ConnectionType connectionType = getConnectionType(testContext, classAnnotation);
    handleOperation(new DatasetTask(operation, dataset), testContext, connectionType);
}

From source file:com.google.api.server.spi.request.ServletRequestParamReader.java

private <T> Collection<T> deserializeCollection(Class<?> clazz, ParameterizedType collectionType,
        JsonNode nodeValue) throws IOException {
    @SuppressWarnings("unchecked")
    Class<? extends Collection<T>> collectionClass = (Class<? extends Collection<T>>) clazz;
    @SuppressWarnings("unchecked")
    Class<T> paramClass = (Class<T>) EndpointMethod
            .getClassFromType(collectionType.getActualTypeArguments()[0]);
    @SuppressWarnings("unchecked")
    Class<T[]> arrayClazz = (Class<T[]>) Array.newInstance(paramClass, 0).getClass();
    Collection<T> collection = objectReader.forType(collectionClass).readValue(objectReader.createArrayNode());
    if (nodeValue != null) {
        T[] array = objectReader.forType(arrayClazz).readValue(nodeValue);
        collection.addAll(Arrays.asList(array));
    }/*w  ww.  ja v a2  s. c om*/
    return collection;
}

From source file:com.reprezen.swagedit.assist.SwaggerProposalProvider.java

protected Collection<Proposal> getProposals(TypeDefinition type, AbstractNode node, String prefix) {
    if (type instanceof ReferenceTypeDefinition) {
        type = ((ReferenceTypeDefinition) type).resolve();
    }/*from w w w  .j a  va2  s. c om*/

    ContentAssistExt ext = findExtension(type);
    if (ext != null) {
        return ext.getProposals(type, node, prefix);
    }

    switch (type.getType()) {
    case STRING:
    case INTEGER:
    case NUMBER:
        return createPrimitiveProposals(type);
    case BOOLEAN:
        return createBooleanProposals(type);
    case ENUM:
        return createEnumProposals(type, node);
    case ARRAY:
        return createArrayProposals((ArrayTypeDefinition) type, node);
    case OBJECT:
        return createObjectProposals((ObjectTypeDefinition) type, node, prefix);
    case ALL_OF:
    case ANY_OF:
    case ONE_OF:
        return createComplextTypeProposals((ComplexTypeDefinition) type, node, prefix);
    case UNDEFINED:
        Collection<Proposal> proposals = new LinkedHashSet<>();
        if (type instanceof MultipleTypeDefinition) {
            for (TypeDefinition currentType : ((MultipleTypeDefinition) type).getMultipleTypes()) {
                proposals.addAll(getProposals(currentType, node, prefix));
            }
        }
        return proposals;
    }
    return Collections.emptyList();
}

From source file:chibi.gemmaanalysis.cli.deprecated.BioSequenceCleanupCli.java

@Override
protected Exception doWork(String[] args) {

    Exception err = processCommandLine(args);
    if (err != null)
        return err;

    Collection<ArrayDesign> ads = new HashSet<ArrayDesign>();
    if (!this.arrayDesignsToProcess.isEmpty()) {
        ads.addAll(this.arrayDesignsToProcess);
    } else if (file != null) {
        try (InputStream is = new FileInputStream(file);
                BufferedReader br = new BufferedReader(new InputStreamReader(is));) {

            String id = null;//from  w  w  w .  j a  v  a  2s .c o m
            Collection<Long> ids = new HashSet<Long>();
            while ((id = br.readLine()) != null) {
                if (StringUtils.isBlank(id)) {
                    continue;
                }
                ids.add(Long.parseLong(id));
            }

            Collection<BioSequence> bioSequences = bss.loadMultiple(ids);
            bioSequences = bss.thaw(bioSequences);
            processSequences(bioSequences);
            return null;
        } catch (Exception e) {
            return e;
        }
    } else {
        ads = this.arrayDesignService.loadAll();
    }

    for (ArrayDesign design : ads) {
        log.info(design);
        design = unlazifyArrayDesign(design);

        Collection<BioSequence> bioSequences = new HashSet<BioSequence>();

        for (CompositeSequence cs : design.getCompositeSequences()) {
            if (cs == null)
                continue;
            if (cs.getBiologicalCharacteristic() == null)
                continue;
            bioSequences.add(cs.getBiologicalCharacteristic());
        }

        processSequences(bioSequences); // fast.

        log.info("Phase II starting");

        // ///////////////////////////////
        // Second phase: make sure composite sequences don't refer to sequences that have duplicates based on name,
        // using stricter equality criteria.
        int i = 0;
        for (CompositeSequence cs : design.getCompositeSequences()) {

            if (++i % 500 == 0) {
                log.info("Processing: " + i + "/" + bioSequences.size() + " sequences");
            }

            BioSequence anchorSeq = cs.getBiologicalCharacteristic();
            if (anchorSeq == null) {
                continue;
            }
            Collection<BioSequence> seqs = bss.findByName(anchorSeq.getName());

            // no evidence of duplicates?
            if (seqs.size() == 1) {
                continue;
            }

            seqs.remove(anchorSeq);

            seqs = this.bss.thaw(seqs);

            // ensure this group really does contain all duplicates.
            if (log.isDebugEnabled())
                log.debug("Examining set of " + seqs.size() + " possible duplicates of " + anchorSeq);

            Collection<BioSequence> notDuplicate = new HashSet<BioSequence>();
            for (BioSequence candidateForRemoval : seqs) {
                if (log.isDebugEnabled())
                    log.debug("   Examining: " + candidateForRemoval);
                assert !candidateForRemoval.equals(anchorSeq) : candidateForRemoval + " equals " + anchorSeq;
                if (!this.equals(anchorSeq, candidateForRemoval)) {
                    notDuplicate.add(candidateForRemoval);
                } else {
                    if (log.isDebugEnabled())
                        log.debug("    Duplicate: " + anchorSeq + " " + candidateForRemoval);
                }
            }

            seqs.removeAll(notDuplicate);

            for (BioSequence toChange : seqs) {
                if (log.isDebugEnabled())
                    log.debug("Processing " + toChange);
                if (!this.equals(anchorSeq, toChange)) {
                    throw new IllegalStateException(
                            "Sequences weren't equal " + anchorSeq + " and " + toChange);
                }
                switchAndDeleteExtra(anchorSeq, toChange);

            }
        }
    }

    return null;

}

From source file:net.sf.jasperreports.engine.JRPropertiesMap.java

protected void collectPropertyNames(Collection<String> names) {
    if (base != null) {
        base.collectPropertyNames(names);
    }//from  www. j a  va  2  s  .  c  o  m

    if (propertiesList != null) {
        names.addAll(propertiesList);
    }
}

From source file:net.sourceforge.metware.binche.graph.ChebiGraph.java

/**
 * Removes a vertex and its connected edges.
 * @param chebiVertex/*from  ww  w  .java  2 s.co  m*/
 */
public void removeVertex(ChebiVertex chebiVertex) {
    Collection<ChebiEdge> toRemove = new LinkedList<ChebiEdge>(getInEdges(chebiVertex));
    toRemove.addAll(getOutEdges(chebiVertex));

    for (ChebiEdge chebiEdge : toRemove) {
        graph.removeEdge(chebiEdge);
    }

    graph.removeVertex(chebiVertex);
}

From source file:eu.europa.ec.markt.dss.signature.pades.PAdESProfileEPES.java

CMSSignedDataGenerator createCMSSignedDataGenerator(ContentSigner contentSigner,
        DigestCalculatorProvider digestCalculatorProvider, final SignatureParameters parameters,
        final byte[] messageDigest) throws IOException {
    try {/*from w w  w  . jav  a 2 s  . com*/

        CMSSignedDataGenerator generator = new CMSSignedDataGenerator();

        X509Certificate signerCertificate = parameters.getSigningCertificate();

        X509CertificateHolder certHolder = new X509CertificateHolder(signerCertificate.getEncoded());

        SignerInfoGeneratorBuilder sigenb = new SignerInfoGeneratorBuilder(digestCalculatorProvider);

        final CAdESProfileEPES profile = new CAdESProfileEPES(true);

        sigenb = sigenb.setSignedAttributeGenerator(new CMSAttributeTableGenerator() {
            @Override
            public AttributeTable getAttributes(Map params) throws CMSAttributeTableGenerationException {
                Hashtable clone = (Hashtable) profile.getSignedAttributes(parameters).clone();

                if (!clone.containsKey(CMSAttributes.contentType)) {
                    DERObjectIdentifier contentType = (DERObjectIdentifier) params
                            .get(CMSAttributeTableGenerator.CONTENT_TYPE);

                    // contentType will be null if we're trying to generate a counter signature.
                    if (contentType != null) {
                        Attribute attr = new Attribute(CMSAttributes.contentType, new DERSet(contentType));
                        clone.put(attr.getAttrType(), attr);
                    }
                }

                if (!clone.containsKey(CMSAttributes.messageDigest)) {
                    System.out.println("Digest propos : "
                            + org.apache.commons.codec.binary.Hex.encodeHexString(messageDigest));
                    // byte[] messageDigest = (byte[]) params.get(CMSAttributeTableGenerator.DIGEST);
                    Attribute attr = new Attribute(CMSAttributes.messageDigest,
                            new DERSet(new DEROctetString(messageDigest)));
                    clone.put(attr.getAttrType(), attr);
                }

                if (parameters.getCommitmentTypeIndication() != null
                        && !parameters.getCommitmentTypeIndication().isEmpty()) {
                    ASN1EncodableVector vector = new ASN1EncodableVector();
                    for (String id : parameters.getCommitmentTypeIndication()) {
                        vector.add(new DERObjectIdentifier(id));
                    }
                    DERSet set = new DERSet(new DERSequence(vector));
                    Attribute attr = new Attribute(new DERObjectIdentifier("1.2.840.113549.1.9.16.2.16"), set);
                    clone.put(attr.getAttrType(), attr);
                }

                return new AttributeTable(clone);
            }
        });

        // sigenb.setUnsignedAttributeGenerator(new SimpleAttributeTableGenerator(new AttributeTable(
        // new Hashtable<ASN1ObjectIdentifier, ASN1Encodable>())));

        /*
         * We don't include a unsigned attribute table if not needed : a unsignedAttrs of signerInfo includes no
         * Attribute, UnsignedAttributes ::= SET SIZE (1..MAX) OF Attribute(defined in RFC3852).
         */
        SignerInfoGenerator sigen = sigenb.build(contentSigner, certHolder);

        generator.addSignerInfoGenerator(sigen);

        Collection<X509Certificate> certs = new ArrayList<X509Certificate>();
        if (parameters.getCertificateChain() == null
                || !parameters.getCertificateChain().contains(parameters.getSigningCertificate())) {
            certs.add(parameters.getSigningCertificate());
        }
        certs.addAll(parameters.getCertificateChain());
        JcaCertStore certStore = new JcaCertStore(certs);
        generator.addCertificates(certStore);

        System.out.println("Gnrator cr");
        return generator;

    } catch (CertificateException e) {
        throw new IOException(e);
    } catch (OperatorCreationException e) {
        throw new IOException(e);
    } catch (CMSException e) {
        throw new IOException(e);
    }

}

From source file:com.xchanging.support.batch.admin.service.SimpleJobService.java

public int countJobs() {
    Collection<String> names = new HashSet<String>(jobLocator.getJobNames());
    names.addAll(jobInstanceDao.getJobNames());
    return names.size();
}

From source file:edu.northwestern.bioinformatics.studycalendar.service.presenter.StudyWorkflowStatus.java

public Collection<WorkflowMessage> getStructureRelatedMessages() {
    Collection<WorkflowMessage> messages = new ArrayList<WorkflowMessage>();
    if (study.getHasTemporaryAssignedIdentifier()) {
        messages.add(workflowMessageFactory.createMessage(WorkflowStep.SET_ASSIGNED_IDENTIFIER, utr));
    } else if (getRevisionWorkflowStatus() != null && isNotEmpty(revisionWorkflowStatus.getMessages())) {
        messages.addAll(revisionWorkflowStatus.getStructureMessages());
    }//from   w  ww  .  j  a  va2 s  .  co m
    return messages;
}