Example usage for java.util Collection clear

List of usage examples for java.util Collection clear

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Introduction

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

Prototype

void clear();

Source Link

Document

Removes all of the elements from this collection (optional operation).

Usage

From source file:ubic.gemma.core.loader.expression.arrayDesign.ArrayDesignSequenceProcessingServiceImpl.java

@Override
public Collection<BioSequence> processArrayDesign(ArrayDesign arrayDesign, InputStream sequenceIdentifierFile,
        String[] databaseNames, String blastDbHome, Taxon taxon, boolean force, FastaCmd fc)
        throws IOException {
    this.checkForCompositeSequences(arrayDesign);

    Map<String, String> probe2acc = this.parseAccessionFile(sequenceIdentifierFile);

    // values that were not found
    Collection<String> notFound = new HashSet<>(probe2acc.values());

    // the actual thing values to search for (with version numbers)
    Collection<String> accessionsToFetch = new HashSet<>(probe2acc.values());

    // only 1 taxon should be on array design if taxon not supplied on command line
    taxon = this.validateTaxon(taxon, arrayDesign);

    /*/*from   w  w w.  j a  v  a  2s. c  om*/
     * Fill in sequences from BLAST databases.
     */
    int numSwitched = 0;
    if (fc == null)
        fc = new SimpleFastaCmd();

    Collection<BioSequence> retrievedSequences = this.searchBlastDbs(databaseNames, blastDbHome, notFound, fc);

    // map of accessions to sequence.
    Map<String, BioSequence> found = this.findOrUpdateSequences(accessionsToFetch, retrievedSequences, taxon,
            force);

    Collection<BioSequence> finalResult = new HashSet<>(retrievedSequences);

    // replace the sequences.
    numSwitched = this.replaceSequences(arrayDesign, probe2acc, numSwitched, found);

    notFound = this.getUnFound(notFound, found);

    if (!notFound.isEmpty() && taxon != null) {

        Collection<String> stillLooking = new HashSet<>(notFound);
        notFound.clear();

        /*
         * clear the version number.
         */
        for (String accession : stillLooking) {
            notFound.remove(accession);
            accession = accession.replaceFirst("\\.\\d+$", "");
            notFound.add(accession);
        }
        assert notFound.size() > 0;
        /*
         * See if they're already in Gemma. This is good for sequences that are not in genbank but have been loaded
         * previously.
         */
        found = this.findLocalSequences(notFound, taxon);
        finalResult.addAll(found.values());

        numSwitched = this.replaceSequences(arrayDesign, probe2acc, numSwitched, found);
        notFound = this.getUnFound(notFound, found);
    }

    if (!notFound.isEmpty()) {
        this.logMissingSequences(arrayDesign, notFound);
    }

    ArrayDesignSequenceProcessingServiceImpl.log
            .info(numSwitched + " composite sequences had their biologicalCharacteristics changed");

    arrayDesignService.update(arrayDesign);

    arrayDesignReportService.generateArrayDesignReport(arrayDesign.getId());
    return finalResult;

}

From source file:org.apache.openjpa.jdbc.meta.ReverseMappingTool.java

/**
 * Generate mappings and class code for the current schema group.
 *//*from w  ww .j a v  a 2 s . c  o m*/
public void run() {
    // map base classes first
    Schema[] schemas = getSchemaGroup().getSchemas();
    Table[] tables;
    for (int i = 0; i < schemas.length; i++) {
        tables = schemas[i].getTables();
        for (int j = 0; j < tables.length; j++)
            if (isBaseTable(tables[j]))
                mapBaseClass(tables[j]);
    }

    // map vertical subclasses
    Set subs = null;
    for (int i = 0; i < schemas.length; i++) {
        tables = schemas[i].getTables();
        for (int j = 0; j < tables.length; j++) {
            if (!_tables.containsKey(tables[j]) && getSecondaryType(tables[j], false) == TABLE_SUBCLASS) {
                if (subs == null)
                    subs = new HashSet();
                subs.add(tables[j]);
            }
        }
    }
    if (subs != null)
        mapSubclasses(subs);

    // map fields in the primary tables of the classes
    ClassMapping cls;
    for (Iterator itr = _tables.values().iterator(); itr.hasNext();) {
        cls = (ClassMapping) itr.next();
        mapColumns(cls, cls.getTable(), null, false);
    }

    // map association tables, join tables, and secondary tables
    for (int i = 0; i < schemas.length; i++) {
        tables = schemas[i].getTables();
        for (int j = 0; j < tables.length; j++)
            if (!_tables.containsKey(tables[j]))
                mapTable(tables[j], getSecondaryType(tables[j], false));
    }

    // map discriminators and versions, make sure identity type is correct,
    // set simple field column java types, and ref schema components so
    // we can tell what is unmapped
    FieldMapping[] fields;
    for (Iterator itr = _tables.values().iterator(); itr.hasNext();) {
        cls = (ClassMapping) itr.next();
        cls.refSchemaComponents();
        if (cls.getDiscriminator().getStrategy() == null)
            getStrategyInstaller().installStrategy(cls.getDiscriminator());
        cls.getDiscriminator().refSchemaComponents();
        if (cls.getVersion().getStrategy() == null)
            getStrategyInstaller().installStrategy(cls.getVersion());
        cls.getVersion().refSchemaComponents();

        // double-check identity type; if it was set for builtin identity
        // it might have to switch to std application identity if pk field
        // not compatible
        if (cls.getPCSuperclass() == null && cls.getIdentityType() == ClassMapping.ID_APPLICATION) {
            if (cls.getPrimaryKeyFields().length == 0)
                throw new MetaDataException(_loc.get("no-pk-fields", cls));
            if (cls.getObjectIdType() == null || (cls.isOpenJPAIdentity() && !isBuiltinIdentity(cls)))
                setObjectIdType(cls);
        } else if (cls.getIdentityType() == ClassMapping.ID_DATASTORE)
            cls.getPrimaryKeyColumns()[0].setJavaType(JavaTypes.LONG);

        // set java types for simple fields;
        fields = cls.getDeclaredFieldMappings();
        for (int i = 0; i < fields.length; i++) {
            fields[i].refSchemaComponents();
            setColumnJavaType(fields[i]);
            setColumnJavaType(fields[i].getElementMapping());
        }
    }

    // set the java types of foreign key columns; we couldn't do this
    // earlier because we rely on the linked-to columns to do it
    for (Iterator itr = _tables.values().iterator(); itr.hasNext();) {
        cls = (ClassMapping) itr.next();
        setForeignKeyJavaType(cls.getJoinForeignKey());

        fields = cls.getDeclaredFieldMappings();
        for (int i = 0; i < fields.length; i++) {
            setForeignKeyJavaType(fields[i].getJoinForeignKey());
            setForeignKeyJavaType(fields[i].getForeignKey());
            setForeignKeyJavaType(fields[i].getElementMapping().getForeignKey());
        }
    }

    // allow customizer to map unmapped tables, and warn about anything
    // that ends up unmapped
    Column[] cols;
    Collection unmappedCols = new ArrayList(5);
    for (int i = 0; i < schemas.length; i++) {
        tables = schemas[i].getTables();
        for (int j = 0; j < tables.length; j++) {
            unmappedCols.clear();
            cols = tables[j].getColumns();
            for (int k = 0; k < cols.length; k++)
                if (cols[k].getRefCount() == 0)
                    unmappedCols.add(cols[k]);

            if (unmappedCols.size() == cols.length) {
                if (_custom == null || !_custom.unmappedTable(tables[j]))
                    _log.info(_loc.get("unmap-table", tables[j]));
            } else if (unmappedCols.size() > 0)
                _log.info(_loc.get("unmap-cols", tables[j], unmappedCols));
        }
    }
    if (_custom != null)
        _custom.close();

    // resolve mappings
    for (Iterator itr = _tables.values().iterator(); itr.hasNext();)
        ((ClassMapping) itr.next()).resolve(MODE_META | MODE_MAPPING);
}

From source file:eu.stratosphere.nephele.services.memorymanager.spi.DefaultMemoryManager.java

@Override
public <T extends MemorySegment> void release(Collection<T> segments) {

    // sanity checks
    if (segments == null) {
        return;//from   w ww.  j a  va2s  . c  om
    }

    // -------------------- BEGIN CRITICAL SECTION -------------------
    synchronized (this.lock) {
        if (this.isShutDown) {
            throw new IllegalStateException("Memory manager has been shut down.");
        }

        final Iterator<T> segmentsIterator = segments.iterator();

        AbstractInvokable lastOwner = null;
        Set<DefaultMemorySegment> segsForOwner = null;

        // go over all segments
        while (segmentsIterator.hasNext()) {

            final MemorySegment seg = segmentsIterator.next();
            if (seg.isFreed()) {
                continue;
            }

            final DefaultMemorySegment defSeg = (DefaultMemorySegment) seg;
            final AbstractInvokable owner = defSeg.owner;

            try {
                // get the list of segments by this owner only if it is a different owner than for
                // the previous one (or it is the first segment)
                if (lastOwner != owner) {
                    lastOwner = owner;
                    segsForOwner = this.allocatedSegments.get(owner);
                }

                // remove the segment from the list
                if (segsForOwner != null) {
                    segsForOwner.remove(defSeg);
                    if (segsForOwner.isEmpty()) {
                        this.allocatedSegments.remove(owner);
                    }
                }
            } catch (Throwable t) {
                LOG.error("Error removing book-keeping reference to allocated memory segment.", t);
            } finally {
                // release the memory in any case
                byte[] buffer = defSeg.destroy();
                this.freeSegments.add(buffer);
            }
        }

        segments.clear();
    }
    // -------------------- END CRITICAL SECTION -------------------
}

From source file:ubic.gemma.analysis.service.ArrayDesignAnnotationServiceImpl.java

@Override
public int generateAnnotationFile(Writer writer,
        Map<CompositeSequence, Collection<BioSequence2GeneProduct>> genesWithSpecificity, OutputType ty)
        throws IOException {

    int compositeSequencesProcessed = 0;
    int simple = 0;
    int empty = 0;
    int complex = 0;
    Collection<OntologyTerm> goTerms = new LinkedHashSet<OntologyTerm>();
    Set<String> genes = new LinkedHashSet<String>();
    Set<String> geneDescriptions = new LinkedHashSet<String>();
    Set<String> geneIds = new LinkedHashSet<String>();
    Set<String> ncbiIds = new LinkedHashSet<String>();

    Map<Gene, Collection<VocabCharacteristic>> goMappings = getGOMappings(genesWithSpecificity);

    for (CompositeSequence cs : genesWithSpecificity.keySet()) {

        Collection<BioSequence2GeneProduct> geneclusters = genesWithSpecificity.get(cs);

        if (++compositeSequencesProcessed % 2000 == 0 && log.isInfoEnabled()) {
            log.info("Processed " + compositeSequencesProcessed + "/" + genesWithSpecificity.size()
                    + " compositeSequences " + empty + " empty; " + simple + " simple; " + complex
                    + " complex;");
        }/* w  w w . j ava2s  .  c o  m*/

        if (geneclusters.isEmpty()) {
            writeAnnotationLine(writer, cs.getName(), "", "", null, "", "");
            empty++;
            continue;
        }

        if (geneclusters.size() == 1) {
            // common case, do it quickly.
            BioSequence2GeneProduct b2g = geneclusters.iterator().next();
            Gene g = b2g.getGeneProduct().getGene();
            goTerms = getGoTerms(g, goMappings.get(g), ty);
            String gemmaId = g.getId() == null ? "" : g.getId().toString();
            String ncbiId = g.getNcbiGeneId() == null ? "" : g.getNcbiGeneId().toString();
            writeAnnotationLine(writer, cs.getName(), g.getOfficialSymbol(), g.getOfficialName(), goTerms,
                    gemmaId, ncbiId);
            simple++;
            continue;
        }

        goTerms.clear();
        genes.clear();
        geneDescriptions.clear();
        geneIds.clear();
        ncbiIds.clear();

        for (BioSequence2GeneProduct bioSequence2GeneProduct : geneclusters) {

            Gene g = bioSequence2GeneProduct.getGeneProduct().getGene();

            genes.add(g.getOfficialSymbol());
            geneDescriptions.add(g.getOfficialName());
            geneIds.add(g.getId().toString());
            Integer ncbiGeneId = g.getNcbiGeneId();
            if (ncbiGeneId != null) {
                ncbiIds.add(ncbiGeneId.toString());
            }
            goTerms.addAll(getGoTerms(g, goMappings.get(g), ty));

        }

        String geneString = StringUtils.join(genes, "|");
        String geneDescriptionString = StringUtils.join(geneDescriptions, "|");
        String geneIdsString = StringUtils.join(geneIds, "|");
        String ncbiIdsString = StringUtils.join(ncbiIds, "|");
        writeAnnotationLine(writer, cs.getName(), geneString, geneDescriptionString, goTerms, geneIdsString,
                ncbiIdsString);
        complex++;

    }
    writer.close();
    return compositeSequencesProcessed;
}

From source file:ubic.gemma.persistence.service.expression.experiment.ExpressionExperimentDaoImpl.java

@Override
public Map<ExpressionExperiment, FactorValue> findByFactorValues(Collection<FactorValue> fvs) {

    if (fvs.isEmpty())
        return new HashMap<>();

    //language=HQL
    final String queryString = "select distinct ee, f from ExpressionExperiment ee "
            + " join ee.experimentalDesign ed join ed.experimentalFactors ef join ef.factorValues f"
            + " where f in (:fvs) group by ee";
    Map<ExpressionExperiment, FactorValue> results = new HashMap<>();
    Collection<FactorValue> batch = new HashSet<>();
    for (FactorValue o : fvs) {
        batch.add(o);//from   w ww. j av  a 2 s  . c om
        if (batch.size() == ExpressionExperimentDaoImpl.BATCH_SIZE) {

            //noinspection unchecked
            List<Object> r2 = this.getSessionFactory().getCurrentSession().createQuery(queryString)
                    .setParameterList("fvs", batch).list();
            for (Object o1 : r2) {
                Object[] a = (Object[]) o1;
                results.put((ExpressionExperiment) a[0], (FactorValue) a[1]);
            }

            batch.clear();
        }
    }

    if (batch.size() > 0) {

        //noinspection unchecked
        List<Object> r2 = this.getSessionFactory().getCurrentSession().createQuery(queryString)
                .setParameterList("fvs", batch).list();
        for (Object o1 : r2) {
            Object[] a = (Object[]) o1;
            results.put((ExpressionExperiment) a[0], (FactorValue) a[1]);
        }

    }

    return results;

}

From source file:eu.dime.ps.semantic.service.impl.PimoService.java

public URI getPIMOTypeForOccurrenceNIEType(org.ontoware.rdf2go.model.node.Resource resource) {
    URI pimoType = null;/*  w  ww.ja va2  s. c o m*/
    URI possibleClass = null;

    Set<URI> occTypes = new HashSet<URI>();
    ClosableIterator<? extends Statement> it = tripleStore.findStatements(Variable.ANY, resource, RDF.type,
            Variable.ANY);
    while (it.hasNext()) {
        occTypes.add(it.next().getObject().asURI());
    }
    it.close();

    // there is none type
    if (occTypes.isEmpty()) {
        pimoType = PIMO.Thing;
    }

    if (pimoType == null) {
        for (URI occType : occTypes) {
            if (occType.equals(NCAL.Event)) {
                pimoType = PIMO.SocialEvent;
                break;
            } else if (occType.equals(NCO.PersonContact)) {
                pimoType = PIMO.Person;
                break;
            }
        }
    }

    if (pimoType == null) {
        for (URI occType : occTypes) {
            // we can use the mapping of classes
            Collection<URI> types = getPossiblePIMOTypeForNIEType(occType);
            if (possibleClass == null && !types.isEmpty())
                possibleClass = types.iterator().next();
            if (types.size() == 1) {
                // the best case is, if there is only one possible
                // PIMO type for this thing.
                pimoType = types.iterator().next();
                break;
            }
            types.clear();
        }
    }

    if (pimoType == null) {
        for (URI occType : occTypes) {
            // if the type of the information element is a subclass of a type of the pimo,
            // we can use this type from the information element
            ClosableIterator<? extends Statement> isupertypes = tripleStore.findStatements(Variable.ANY,
                    occType, RDFS.subClassOf, Variable.ANY);
            while (isupertypes.hasNext()) {
                URI supertype = (URI) isupertypes.next().getObject();
                if (supertype.toString().startsWith(PIMO.NS_PIMO.toString())) {
                    pimoType = occType;
                    break;
                }
            }
        }
    }

    if (pimoType == null) {
        // assign the first class which we found
        pimoType = possibleClass;
    }

    return pimoType;
}

From source file:eu.dime.ps.semantic.service.impl.PimoService.java

/**
 * Creates a Thing from a given occurrence. 
 * The URI of the occurrence will be added as groundingOccurrence.
 * All identifiers from the occurrence, which can be found in the pimo will be added
 * as statements in the model.//from   w  w w  .j  a  v a2 s . com
 * 
 * @param occurrence the occurrence from which to create a resoucre
 * @param label the name of the resource, used as label and part of the uri
 * @param ofClass the URI of the class of the created resource
 * @return the URI of the created resource
 * @throws OntologyInvalidException if the passed URI is not defined as
 *       class in the pimo.
 */
public URI createResourceFromGroundingOccurrence(URI occurrence, String label, URI ofClass)
        throws OntologyInvalidException {
    // detect label and class
    URI clazz = ofClass;
    Set<URI> occTypes = new HashSet<URI>();

    if (clazz == null) {
        ClosableIterator<? extends Statement> it = tripleStore.findStatements(Variable.ANY, occurrence,
                RDF.type, Variable.ANY);
        while (it.hasNext()) {
            occTypes.add(it.next().getObject().asURI());
        }
        it.close();
        // no type was found
        if (occTypes.isEmpty()) {
            clazz = PIMO.Thing;
        }
    }

    URI candidateClass = null;
    if (clazz == null) {
        for (URI occType : occTypes) {
            // can use the mapping of classes
            Collection<URI> types = getPossiblePIMOTypeForNIEType(occType);
            if (candidateClass == null && !types.isEmpty())
                candidateClass = types.iterator().next();
            if (types.size() == 1) {
                // the best case is, if there is only one possible
                // PIMO type for this thing.
                clazz = types.iterator().next();
                break;
            }
            types.clear();
        }
    }
    if (clazz == null) {
        for (URI occType : occTypes) {
            // first check whether there is a type which has the same name
            // if the labels are the same, the possibility is high, that 
            // these are equal types.
            String occTypeLabel = ResourceUtils.guessPreferredLabel(tripleStore, occType);
            List<URI> candidates = new LinkedList<URI>();
            ClosableIterator<? extends Statement> statements = null;
            try {
                Literal rdfsLabel = new PlainLiteralImpl(occTypeLabel);
                for (statements = tripleStore.findStatements(PIMO.NS_PIMO, Variable.ANY, RDFS.label,
                        rdfsLabel); statements.hasNext();) {
                    candidates.add(statements.next().getSubject().asURI());
                }
            } finally {
                statements.close();
            }
            if (candidateClass == null && !candidates.isEmpty())
                candidateClass = candidates.iterator().next();
            // check whether the result contains more than one type.
            // if this is the case, we can't say anything about which
            // type is the better one.
            if (candidates.size() == 1) {
                clazz = candidates.iterator().next();
                break;
            }
        }
    }
    if (clazz == null) {
        for (URI occType : occTypes) {
            // if the type of the information element is a subclass of a type of the pimo,
            // we can use this type from the information element
            ClosableIterator<? extends Statement> isupertypes = tripleStore.findStatements(Variable.ANY,
                    occType, RDFS.subClassOf, Variable.ANY);
            while (isupertypes.hasNext()) {
                URI supertype = (URI) isupertypes.next().getObject();
                if (supertype.toString().startsWith(PIMO.NS_PIMO.toString())) {
                    clazz = occType;
                    break;
                }
            }
            isupertypes.close();
        }
    }

    if (clazz == null)
        clazz = candidateClass; // assign the first class which we found
    if (clazz == null)
        clazz = PIMO.Topic;

    /**
     * find a proper label for the new thing based on the resource
     */
    if (label == null || label.equals("")) {
        label = ResourceUtils.guessPreferredLabel(tripleStore, occurrence);
    }

    // create thing
    return createResourceFromGroundingOccurrence(occurrence, tripleStore, label, clazz);
}

From source file:org.apache.ojb.broker.QueryTest.java

/**
 * Simple ReportQuery returning rows with 3 columns of Person
 * needs SQL paging/* www .  j ava  2 s. c  om*/
 */
public void testReportQueryWithStartAndEnd() {
    Criteria crit = new Criteria();
    Collection results = new Vector();
    crit.addLike("firstname", "%o%");
    ReportQueryByCriteria q = QueryFactory.newReportQuery(Person.class, crit);
    q.setAttributes(new String[] { "id", "firstname", "count(*)" });
    q.addGroupBy(new String[] { "id", "firstname" });

    q.setStartAtIndex(3);
    q.setEndAtIndex(5);
    Iterator iter = broker.getReportQueryIteratorByQuery(q);
    assertNotNull(iter);
    while (iter.hasNext()) {
        results.add(iter.next());
    }
    assertTrue(results.size() == 3);

    results.clear();
    q.setStartAtIndex(1);
    q.setEndAtIndex(5);
    iter = broker.getReportQueryIteratorByQuery(q);
    assertNotNull(iter);
    while (iter.hasNext()) {
        results.add(iter.next());
    }
    assertTrue(results.size() == 5);
}

From source file:org.apache.openjpa.persistence.XMLPersistenceMetaDataSerializer.java

/**
 * Serialize cascades.//  w  ww.  j  a va 2 s.co  m
 */
private void serializeCascades(ValueMetaData vmd) throws SAXException {
    Collection<String> cascades = null;
    if (vmd.getCascadePersist() == ValueMetaData.CASCADE_IMMEDIATE) {
        if (cascades == null)
            cascades = new ArrayList<String>();
        cascades.add("cascade-persist");
    }
    if (vmd.getCascadeAttach() == ValueMetaData.CASCADE_IMMEDIATE) {
        if (cascades == null)
            cascades = new ArrayList<String>();
        cascades.add("cascade-merge");
    }
    if (vmd.getCascadeDelete() == ValueMetaData.CASCADE_IMMEDIATE) {
        if (cascades == null)
            cascades = new ArrayList<String>();
        cascades.add("cascade-remove");
    }
    if (vmd.getCascadeRefresh() == ValueMetaData.CASCADE_IMMEDIATE) {
        if (cascades == null)
            cascades = new ArrayList<String>();
        cascades.add("cascade-refresh");
    }
    if (vmd.getCascadeDetach() == ValueMetaData.CASCADE_IMMEDIATE) {
        if (cascades == null)
            cascades = new ArrayList<String>();
        cascades.add("cascade-detach");
    }
    if (cascades != null && cascades.size() == 5) // ALL
    {
        cascades.clear();
        cascades.add("cascade-all");
    }
    if (cascades != null) {
        startElement("cascade");
        for (String cascade : cascades) {
            startElement(cascade);
            endElement(cascade);
        }
        endElement("cascade");
    }
}