Examples of SampleList

com.iggroup.oss.sample.domain.SampleList
List of samples.
org.broadinstitute.gatk.tools.walkers.genotyper.SampleList
A indexed set of samples.
Implementing classes must guarantee that the sample list will remain constant through the life of the object.

Examples of com.iggroup.oss.sample.domain.SampleList

  @ResponseBody
  public SampleList findAllSamples() {


    LOGGER.info("getSamples ");


    return new SampleList(service.findAllSamples());


  }

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Examples of com.iggroup.oss.sample.domain.SampleList

  @ResponseBody
  public SampleList findSamplesByName(@RequestParam String name) {


    LOGGER.info("getSamplesByName " + name);


    return new SampleList(service.findSamplesByName(name));


  }

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Examples of com.iggroup.oss.sample.domain.SampleList


    LOGGER.info("getSamplesByType " + type);


    validate(type);


    return new SampleList(service.findSamplesByType(type));


  }

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Examples of com.iggroup.oss.sample.domain.SampleList


   @Profiled
   @Override
   public SampleList findSamplesByName(String nameFragment) {


      return new SampleList(sampleDAO.findSamples(nameFragment));


   }

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Examples of com.iggroup.oss.sample.domain.SampleList


   @Profiled
   @Override
   public SampleList findSamplesByType(SampleType type) {


      return new SampleList(sampleDAO.findSamples(type));
   }

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Examples of com.iggroup.oss.sample.domain.SampleList


   @Profiled
   @Override
   public SampleList findAllSamples() {


      return new SampleList(sampleDAO.findSamples());
   }

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Examples of org.broadinstitute.gatk.tools.walkers.genotyper.SampleList

        UAC.genotypingOutputMode = GenotypingOutputMode.GENOTYPE_GIVEN_ALLELES;


        String trackName = variantCollection.variants.getName();


        final GenomeAnalysisEngine toolkit = getToolkit();
        final SampleList samples =
                new IndexedSampleList(SampleUtils.getSampleListWithVCFHeader(getToolkit(), Arrays.asList(trackName)));
        final Set<String> sampleNameSet = SampleListUtils.asSet(samples);
        UG_engine = new UnifiedGenotypingEngine(UAC, samples,toolkit.getGenomeLocParser(),
                FixedAFCalculatorProvider.createThreadSafeProvider(toolkit,UAC,logger),
                toolkit.getArguments().BAQMode);

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Examples of org.broadinstitute.gatk.tools.walkers.genotyper.SampleList

 */
public class SampleListUtilsUnitTest {


    @Test(dataProvider = "singleSampleListData")
    public void testAsList(final List<String> samples) {
         final SampleList sampleList = new IndexedSampleList(samples);
         final List<String> asList = SampleListUtils.asList(sampleList);
         Assert.assertEquals(samples, asList);
    }

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Examples of org.broadinstitute.gatk.tools.walkers.genotyper.SampleList

         Assert.assertEquals(samples, asList);
    }


    @Test(dataProvider = "twoSampleListData", dependsOnMethods={"testAsList"})
    public void testEquals(final List<String> sample2, final List<String> samples2) {
        final SampleList sampleList1 = new IndexedSampleList(sample2);
        final SampleList sampleList2 = new IndexedSampleList(samples2);
        Assert.assertTrue(SampleListUtils.equals(sampleList1, sampleList1));
        Assert.assertTrue(SampleListUtils.equals(sampleList2,sampleList2));
        Assert.assertEquals(SampleListUtils.equals(sampleList1, sampleList2),
                Arrays.equals(SampleListUtils.asList(sampleList1).toArray(new String[sampleList1.sampleCount()]),
                        SampleListUtils.asList(sampleList2).toArray(new String[sampleList2.sampleCount()]))
        );
        Assert.assertEquals(SampleListUtils.equals(sampleList1,sampleList2),
                            SampleListUtils.equals(sampleList2,sampleList1));
    }

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