Example usage for org.apache.commons.collections IteratorUtils toList

Introduction

In this page you can find the example usage for org.apache.commons.collections IteratorUtils toList.

Prototype

public static List toList(Iterator iterator) 

Source Link

Document

Gets a list based on an iterator.

Usage

From source file:org.intermine.bio.postprocess.CreateIntergenicRegionFeaturesProcessTest.java

public void testCreateIntergenicRegionFeatures() throws Exception {
    CreateIntergenicRegionFeaturesProcess iru = new CreateIntergenicRegionFeaturesProcess(osw);

    List chrXgeneLocList = new ArrayList();
    Map chrXlocMap = new HashMap();
    Integer chrXId = createChrX(chrXgeneLocList, chrXlocMap, 1000);
    Iterator irIter = iru.createFeatures(new HashSet(chrXgeneLocList), chrXlocMap, chrXId);

    {//  w  ww. j av  a 2  s  .co  m
        Set intergenicRegions = new HashSet(IteratorUtils.toList(irIter));

        assertEquals(5, intergenicRegions.size());
    }

    List chr1geneLocList = new ArrayList();
    Map chr1locMap = new HashMap();
    Integer chr1Id = createChr1(chr1geneLocList, chr1locMap, 2000);
    irIter = iru.createFeatures(new HashSet(chr1geneLocList), chr1locMap, chr1Id);

    {
        Set intergenicRegions = new HashSet(IteratorUtils.toList(irIter));

        assertEquals(3, intergenicRegions.size());
    }
}

---

From source file:org.intermine.bio.postprocess.CreateIntergenicRegionFeaturesProcessTest.java

public void testCreateIntergenicRegionFeaturesRefs() throws Exception {
    CreateIntergenicRegionFeaturesProcess iru = new CreateIntergenicRegionFeaturesProcess(osw);

    List chrXgeneLocList = new ArrayList();
    Map chrXlocMap = new HashMap();
    createChrX(chrXgeneLocList, chrXlocMap, 3000);
    List chr1geneLocList = new ArrayList();
    Map chr1locMap = new HashMap();
    Integer chr1Id = createChr1(chr1geneLocList, chr1locMap, 4000);

    iru.postProcess();// w w w  .j av a  2s.c  o  m

    ObjectStore os = osw.getObjectStore();
    os.flushObjectById();

    Query q = new Query();

    QueryClass qc = new QueryClass(osw.getModel().getClassDescriptorByName("IntergenicRegion").getType());
    q.addFrom(qc);
    q.addToSelect(qc);
    SingletonResults res = os.executeSingleton(q);
    Iterator resIter = res.iterator();

    {
        Set intergenicRegions = new HashSet(IteratorUtils.toList(resIter));

        Iterator irIter = intergenicRegions.iterator();

        Set actualIdentifiers = new HashSet();

        while (irIter.hasNext()) {
            IntergenicRegion ir = (IntergenicRegion) irIter.next();

            assertNotNull(ir.getChromosome());
            assertNotNull(ir.getOrganism());
            assertNotNull(ir.getLength());
            assertTrue(ir.getLength().intValue() > 0);
            assertEquals(1, ir.getDataSets().size());

            Location loc = ir.getChromosomeLocation();
            assertNotNull(loc);
            assertNotNull(loc.getStart());
            assertNotNull(loc.getEnd());
            assertNotNull(loc.getStrand());
            assertEquals(1, loc.getDataSets().size());

            int locStart = loc.getStart().intValue();
            if (locStart > 0) {
                Integer newLoc = new Integer(locStart - 1);
                Collection prevGeneIds;
                if (ir.getChromosome().getId().equals(chr1Id)) {
                    prevGeneIds = getByLoc(newLoc, chr1locMap);
                } else {
                    prevGeneIds = getByLoc(newLoc, chrXlocMap);
                }
                Iterator prevGeneIdsIter = prevGeneIds.iterator();

                while (prevGeneIdsIter.hasNext()) {
                    Gene prevGene = (Gene) os.getObjectById((Integer) prevGeneIdsIter.next());

                    assertTrue(prevGene.getUpstreamIntergenicRegion() != null
                            || prevGene.getDownstreamIntergenicRegion() != null);

                    Set adjacentGenes = new HashSet(ir.getAdjacentGenes());
                    assertTrue(adjacentGenes.contains(prevGene));
                    if ("1".equals(loc.getStrand())) {
                        IntergenicRegion nextIntergenicRegion = prevGene.getDownstreamIntergenicRegion();
                        Integer id = nextIntergenicRegion.getId();
                        assertEquals(id, ir.getId());
                    } else {
                        assertEquals(prevGene.getUpstreamIntergenicRegion().getId(), ir.getId());
                    }
                }
            }

            int locEnd = loc.getEnd().intValue();
            if (locEnd < ir.getChromosome().getLength().intValue()) {
                Integer newLoc = new Integer(locEnd + 1);
                Collection nextGeneIds;
                if (ir.getChromosome().getId().equals(chr1Id)) {
                    nextGeneIds = getByLoc(newLoc, chr1locMap);
                } else {
                    nextGeneIds = getByLoc(newLoc, chrXlocMap);
                }
                assertTrue(nextGeneIds.size() > 0);
                Iterator nextGeneIdsIter = nextGeneIds.iterator();

                while (nextGeneIdsIter.hasNext()) {
                    Gene nextGene = (Gene) os.getObjectById((Integer) nextGeneIdsIter.next());

                    if ("1".equals(loc.getStrand())) {
                        assertTrue(ir.getAdjacentGenes().contains(nextGene));
                        assertEquals(nextGene.getUpstreamIntergenicRegion().getId(), ir.getId());
                    } else {
                        assertTrue(ir.getAdjacentGenes().contains(nextGene));
                        assertEquals(nextGene.getDownstreamIntergenicRegion().getId(), ir.getId());
                    }
                }
            }
            actualIdentifiers.add(ir.getPrimaryIdentifier());
        }

        Set expectedIdentifiers = new HashSet(
                Arrays.asList(new Object[] { "intergenic_region_chrX_1..100", "intergenic_region_chrX_201..300",
                        "intergenic_region_chrX_401..500", "intergenic_region_chrX_601..700",
                        "intergenic_region_chrX_951..1000", "intergenic_region_chrI_101..300",
                        "intergenic_region_chrI_401..500", "intergenic_region_chrI_901..1800", }));

        assertEquals(expectedIdentifiers, actualIdentifiers);
    }
}

---

From source file:org.intermine.bio.postprocess.CreateIntronFeaturesProcessTest.java

public void testCreateIntronFeaturesRef() throws Exception {
    CreateIntronFeaturesProcess iru = new CreateIntronFeaturesProcess(osw);

    createTranscriptT1(100);/*from   w  ww .j a v a  2  s  .c  o m*/
    createTranscriptT2(100);

    iru.postProcess();

    ObjectStore os = osw.getObjectStore();
    os.flushObjectById();

    Query q = new Query();

    QueryClass qc = new QueryClass(Intron.class);
    q.addFrom(qc);
    q.addToSelect(qc);
    SingletonResults res = os.executeSingleton(q);
    Iterator resIter = res.iterator();

    Set introns = new HashSet(IteratorUtils.toList(resIter));

    Iterator irIter = introns.iterator();

    Set actualIdentifiers = new HashSet();

    while (irIter.hasNext()) {
        Intron ir = (Intron) irIter.next();

        assertNotNull(ir.getChromosome());
        assertNotNull(ir.getOrganism());
        assertNotNull(ir.getLength());

        assertTrue(ir.getLength().intValue() > 0);
        assertEquals(1, ir.getDataSets().size());

        Location loc = ir.getChromosomeLocation();
        assertNotNull(loc);
        assertNotNull(loc.getStart());
        assertNotNull(loc.getEnd());
        assertNotNull(loc.getStrand());
        assertEquals(1, loc.getDataSets().size());

        Set<Gene> genes = ir.getGenes();
        assertFalse(genes.isEmpty());
        assertEquals(1, genes.size());

        //            assertEquals(1, ir.getSynonyms().size());
        //            Synonym synonym = (Synonym) ir.getSynonyms().iterator().next();
        //            assertEquals(ir.getPrimaryIdentifier(), synonym.getValue());
        //
        actualIdentifiers.add(ir.getPrimaryIdentifier());
    }

    Set expectedIdentifiers = new HashSet(Arrays
            .asList(new Object[] { "intron_chrX_201..300", "intron_chrX_501..600", "intron_chrX_501..700", }));

    assertEquals(expectedIdentifiers, actualIdentifiers);

}

---

From source file:org.intermine.bio.postprocess.IntergenicRegionsTest.java

public void testCreateIntergenicRegionFeatures() throws Exception {
    IntergenicRegionUtil iru = new IntergenicRegionUtil(osw);

    List chrXgeneLocList = new ArrayList();
    Map chrXlocMap = new HashMap();
    Integer chrXId = createChrX(chrXgeneLocList, chrXlocMap, 1000);
    Iterator irIter = iru.createIntergenicRegionFeatures(new HashSet(chrXgeneLocList), chrXlocMap, chrXId);

    {/*  w ww .  j  ava  2  s.c om*/
        Set intergenicRegions = new HashSet(IteratorUtils.toList(irIter));

        assertEquals(5, intergenicRegions.size());
    }

    List chr1geneLocList = new ArrayList();
    Map chr1locMap = new HashMap();
    Integer chr1Id = createChr1(chr1geneLocList, chr1locMap, 2000);
    irIter = iru.createIntergenicRegionFeatures(new HashSet(chr1geneLocList), chr1locMap, chr1Id);

    {
        Set intergenicRegions = new HashSet(IteratorUtils.toList(irIter));

        assertEquals(3, intergenicRegions.size());
    }
}

---

From source file:org.intermine.bio.postprocess.IntergenicRegionsTest.java

public void testCreateIntergenicRegionFeaturesRefs() throws Exception {
    IntergenicRegionUtil iru = new IntergenicRegionUtil(osw);

    List chrXgeneLocList = new ArrayList();
    Map chrXlocMap = new HashMap();
    createChrX(chrXgeneLocList, chrXlocMap, 3000);
    List chr1geneLocList = new ArrayList();
    Map chr1locMap = new HashMap();
    Integer chr1Id = createChr1(chr1geneLocList, chr1locMap, 4000);

    iru.createIntergenicRegionFeatures();

    ObjectStore os = osw.getObjectStore();
    os.flushObjectById();// www  .  j  av  a  2 s .com

    Query q = new Query();

    QueryClass qc = new QueryClass(IntergenicRegion.class);
    q.addFrom(qc);
    q.addToSelect(qc);
    SingletonResults res = os.executeSingleton(q);
    Iterator resIter = res.iterator();

    {
        Set intergenicRegions = new HashSet(IteratorUtils.toList(resIter));

        Iterator irIter = intergenicRegions.iterator();

        Set actualIdentifiers = new HashSet();

        while (irIter.hasNext()) {
            IntergenicRegion ir = (IntergenicRegion) irIter.next();

            assertNotNull(ir.getChromosome());
            assertNotNull(ir.getOrganism());
            assertNotNull(ir.getLength());
            assertTrue(ir.getLength().intValue() > 0);
            assertEquals(1, ir.getDataSets().size());

            Location loc = ir.getChromosomeLocation();
            assertNotNull(loc);
            assertNotNull(loc.getStart());
            assertNotNull(loc.getEnd());
            assertNotNull(loc.getStrand());
            assertEquals(1, loc.getDataSets().size());

            int locStart = loc.getStart().intValue();
            if (locStart > 0) {
                Integer newLoc = new Integer(locStart - 1);
                Collection prevGeneIds;
                if (ir.getChromosome().getId().equals(chr1Id)) {
                    prevGeneIds = getByLoc(newLoc, chr1locMap);
                } else {
                    prevGeneIds = getByLoc(newLoc, chrXlocMap);
                }
                Iterator prevGeneIdsIter = prevGeneIds.iterator();

                while (prevGeneIdsIter.hasNext()) {
                    Gene prevGene = (Gene) os.getObjectById((Integer) prevGeneIdsIter.next());

                    assertTrue(prevGene.getUpstreamIntergenicRegion() != null
                            || prevGene.getDownstreamIntergenicRegion() != null);

                    Set adjacentGenes = new HashSet(ir.getAdjacentGenes());
                    assertTrue(adjacentGenes.contains(prevGene));
                    if ("1".equals(loc.getStrand())) {
                        IntergenicRegion nextIntergenicRegion = prevGene.getDownstreamIntergenicRegion();
                        Integer id = nextIntergenicRegion.getId();
                        assertEquals(id, ir.getId());
                    } else {
                        assertEquals(prevGene.getUpstreamIntergenicRegion().getId(), ir.getId());
                    }
                }
            }

            int locEnd = loc.getEnd().intValue();
            if (locEnd < ir.getChromosome().getLength().intValue()) {
                Integer newLoc = new Integer(locEnd + 1);
                Collection nextGeneIds;
                if (ir.getChromosome().getId().equals(chr1Id)) {
                    nextGeneIds = getByLoc(newLoc, chr1locMap);
                } else {
                    nextGeneIds = getByLoc(newLoc, chrXlocMap);
                }
                assertTrue(nextGeneIds.size() > 0);
                Iterator nextGeneIdsIter = nextGeneIds.iterator();

                while (nextGeneIdsIter.hasNext()) {
                    Gene nextGene = (Gene) os.getObjectById((Integer) nextGeneIdsIter.next());

                    if ("1".equals(loc.getStrand())) {
                        assertTrue(ir.getAdjacentGenes().contains(nextGene));
                        assertEquals(nextGene.getUpstreamIntergenicRegion().getId(), ir.getId());
                    } else {
                        assertTrue(ir.getAdjacentGenes().contains(nextGene));
                        assertEquals(nextGene.getDownstreamIntergenicRegion().getId(), ir.getId());
                    }
                }
            }
            actualIdentifiers.add(ir.getPrimaryIdentifier());
        }

        Set expectedIdentifiers = new HashSet(
                Arrays.asList(new Object[] { "intergenic_region_chrX_1..100", "intergenic_region_chrX_201..300",
                        "intergenic_region_chrX_401..500", "intergenic_region_chrX_601..700",
                        "intergenic_region_chrX_951..1000", "intergenic_region_chrI_101..300",
                        "intergenic_region_chrI_401..500", "intergenic_region_chrI_901..1800", }));

        assertEquals(expectedIdentifiers, actualIdentifiers);
    }
}

---

From source file:org.intermine.bio.postprocess.IntronTest.java

public void testCreateIntronFeaturesRef() throws Exception {
    IntronUtil iru = new IntronUtil(osw);

    createTranscriptT1(100);/*from   ww w .j  av  a2 s . c  o  m*/
    createTranscriptT2(100);

    iru.createIntronFeatures();

    ObjectStore os = osw.getObjectStore();
    os.flushObjectById();

    Query q = new Query();

    QueryClass qc = new QueryClass(Intron.class);
    q.addFrom(qc);
    q.addToSelect(qc);
    SingletonResults res = os.executeSingleton(q);
    Iterator resIter = res.iterator();

    Set introns = new HashSet(IteratorUtils.toList(resIter));

    Iterator irIter = introns.iterator();

    Set actualIdentifiers = new HashSet();

    while (irIter.hasNext()) {
        Intron ir = (Intron) irIter.next();

        assertNotNull(ir.getChromosome());
        assertNotNull(ir.getOrganism());
        assertNotNull(ir.getLength());

        assertTrue(ir.getLength().intValue() > 0);
        assertEquals(1, ir.getDataSets().size());

        Location loc = ir.getChromosomeLocation();
        assertNotNull(loc);
        assertNotNull(loc.getStart());
        assertNotNull(loc.getEnd());
        assertNotNull(loc.getStrand());
        assertEquals(1, loc.getDataSets().size());

        Set<Gene> genes = ir.getGenes();
        assertFalse(genes.isEmpty());
        assertEquals(1, genes.size());

        //            assertEquals(1, ir.getSynonyms().size());
        //            Synonym synonym = (Synonym) ir.getSynonyms().iterator().next();
        //            assertEquals(ir.getPrimaryIdentifier(), synonym.getValue());
        //
        actualIdentifiers.add(ir.getPrimaryIdentifier());
    }

    Set expectedIdentifiers = new HashSet(Arrays
            .asList(new Object[] { "intron_chrX_201..300", "intron_chrX_501..600", "intron_chrX_501..700", }));

    assertEquals(expectedIdentifiers, actualIdentifiers);

}

---

From source file:org.jasig.portlet.survey.service.jpa.JpaSurveyDao.java

@Override
@SuppressWarnings("unchecked")
public List<JpaSurvey> getAllSurveys() {
    Iterable<?> surveyIter = surveyRepository.findAll();
    List<JpaSurvey> surveyList = IteratorUtils.toList(surveyIter.iterator());
    return surveyList;
}

---

From source file:org.jasig.portlet.survey.service.jpa.JpaSurveyDao.java

@Override
public List<JpaResponse> getResponseByUser(String user) {
    Iterable<JpaResponse> responseIter = responseRepository.findByUser(user);
    return IteratorUtils.toList(responseIter.iterator());
}

---

From source file:org.jbpm.bpel.integration.soap.SoapUtilTest.java

public void testCopyVisibleNamespaces_soapDom_targetMatch() throws Exception {
    String xml = "<part xmlns:produce='urn:example:produce'>"
            + " <lunch produce:lettuce='0.1lb' fish:fillet='0.25lb' "
            + "  xmlns:fish='urn:example:fish' xmlns='urn:example:meal'/>" + "</part>";
    Element source = XmlUtil.getElement(XmlUtil.parseText(xml), "urn:example:meal", "lunch");

    String targetXml = "<soap:Envelope xmlns:soap='" + SOAPConstants.URI_NS_SOAP_ENVELOPE + "'>"
            + " <soap:Body>"
            + "  <other:Operation xmlns:produce='urn:example:produce' xmlns:meal='urn:example:meal'"
            + "   xmlns:other='urn:example:other'>" + "   <lunch />" + "  </other:Operation>" + " </soap:Body>"
            + "</soap:Envelope>";
    SOAPMessage soapMessage = parseSoap(targetXml);
    SOAPElement operation = SoapUtil.getElement(soapMessage.getSOAPBody(), "urn:example:other", "Operation");
    SOAPElement target = SoapUtil.getElement(operation, "lunch");

    // in the WS4EE stack, target contains the *visible* namespace after parsing
    target.removeNamespaceDeclaration("produce");
    target.removeNamespaceDeclaration("meal");

    // perform the copy
    SoapUtil.copyVisibleNamespaces(target, source);
    List prefixes = IteratorUtils.toList(target.getNamespacePrefixes());

    // prefixed declaration
    assertTrue(prefixes.contains("fish"));
    assertEquals("urn:example:fish", target.getNamespaceURI("fish"));
    // parent prefixed declaration
    assertFalse(prefixes.contains("produce"));
    assertEquals("urn:example:produce", target.getNamespaceURI("produce"));
    // default declaration (reassigned)
    assertFalse(prefixes.contains("meal"));
    assertEquals("urn:example:meal", target.getNamespaceURI("meal"));
}

---

From source file:org.jgrades.lic.service.LicenceManagingServiceImpl.java

@Override
public List<Licence> getAll() {
    LOGGER.debug("Getting all licences in system");
    List<Licence> licences = Lists.newArrayList();
    List<LicenceEntity> entitiesList = IteratorUtils.toList(licenceRepository.findAll().iterator());
    for (LicenceEntity entity : entitiesList) {
        licences.add(mapper.map(entity, Licence.class));
    }//  w  ww. j av a 2 s . c om
    LOGGER.trace("Returning all licences in system: {}", licences);
    return licences;
}

---

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