Examples of addAll()

Examples of org.broadinstitute.gatk.utils.activeregion.ActiveRegion.addAll()

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        final Cigar c = new Cigar();
        c.add(new CigarElement(refHaplotype.getBases().length, CigarOperator.M));
        refHaplotype.setCigar(c);

        final ActiveRegion activeRegion = new ActiveRegion(loc, null, true, genomeLocParser, 0);
        activeRegion.addAll(reads);
//        logger.warn("Assembling " + activeRegion + " with " + engine);
        final AssemblyResultSet assemblyResultSet =  assembler.runLocalAssembly(activeRegion, refHaplotype, refBases, loc, Collections.<VariantContext>emptyList(), null);
        return assemblyResultSet.getHaplotypeList();
    }
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Examples of org.broadinstitute.gatk.utils.collections.CountSet.addAll()

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                if (referenceWithinBoundaries.contains(v)) {
                    final CountSet previous = expectedRejoins.get(v);
                    if (previous == null)
                        expectedRejoins.put(v, depth.clone());
                    else
                        previous.addAll(depth);
                }
            } else {
                final CountSet depthPlusOne = depth.clone();
                depthPlusOne.incAll(1);
                final Set<MultiSampleEdge> nextEdges = backwards ? incomingEdgesOf(v) : outgoingEdgesOf(v);
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Examples of org.broadleafcommerce.openadmin.dto.CriteriaTransferObject.addAll()

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            throws ServiceException {
        PersistencePackage pkg = persistencePackageFactory.create(request);

        CriteriaTransferObject cto = getDefaultCto();
        if (request.getFilterAndSortCriteria() != null) {
            cto.addAll(Arrays.asList(request.getFilterAndSortCriteria()));
        }
       
        if (request.getStartIndex() == null) {
            cto.setFirstResult(0);
        } else {
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Examples of org.cfeclipse.cfml.parser.CFNodeList.addAll()

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      int matches = 0;
      int endMatches = 0;
     
      if(search.doChildNodes)
        result.addAll(currItem.selectNodes(search));
     
      //r2 added simple * node selection
      if(search.searchForTag
        && (currItem.getName().compareToIgnoreCase(search.tagName) == 0
                || search.tagName.equals("*"))
 
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Examples of org.cleartk.eval.AnnotationStatistics.addAll()

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      List<AnnotationStatistics> foldStats = evaluation.crossValidation(trainFiles, 2);
      //AnnotationStatistics overallStats = AnnotationStatistics.addAll(foldStats);
      AnnotationStatistics overallStats = new AnnotationStatistics();
      for (AnnotationStatistics singleFoldStats : foldStats)
      {
        overallStats.addAll(singleFoldStats);
      }
     
      System.err.println("overall:");
      System.err.print(overallStats);
      System.err.println(overallStats.confusions());
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Examples of org.codehaus.jackson.node.ArrayNode.addAll()

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            return NullNode.getInstance();
        case 1:
            return matching.get(0);
        default:
            final ArrayNode arrayNode = new ArrayNode(JsonNodeFactory.instance);
            arrayNode.addAll(matching);
            return arrayNode;
        }
    }

    private static void checkValue(final String path, final JsonNode node, final String requiredType) {
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Examples of org.cx4a.rsense.typing.TypeSet.addAll()

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                prevResult = result;
                SpecialMethod spec = graph.getSpecialMethod(name);
                if (spec != null) {
                    spec.call(graph.getRuntime(), receivers, argVertices, block, result);
                    if (result.getResultTypeSet() != null) {
                        accumulator.addAll(result.getResultTypeSet());
                    }
                    if (result.hasPrivateVisibility()) {
                        vertex.setPrivateVisibility(true);
                    }
                    if (result.isNeverCallAgain()) {
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Examples of org.dbunit.database.PrimaryKeyFilter.PkTableMap.addAll()

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            logger.debug("getDataset(connection={}, rootTable={}, allowedIds={}) - start",
                    new Object[] { connection, rootTable, allowedIds });
        }

        PkTableMap map = new PkTableMap();
        map.addAll(rootTable, allowedIds);
        return getDataset(connection, map);
    }

    public static IDataSet getDataset( IDatabaseConnection connection, PkTableMap rootTables )
    throws SearchException, SQLException, DataSetException
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Examples of org.dcm4che3.data.Attributes.addAll()

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    }

    private Attributes modify(Attributes original) {
        Attributes other = new Attributes(original.size()+2);
        other.setString("PrivateCreatorC", 0x00990002, VR.LO, "New0099xx02C");
        other.addAll(original);
        other.remove(Tag.AccessionNumber);
        other.setString(Tag.PatientName, VR.LO, "Added^Patient^Name");
        other.setString(Tag.PatientID, VR.LO, "ModifiedPatientID");
        other.getNestedDataset(Tag.OtherPatientIDsSequence)
                .setString(Tag.PatientID, VR.LO, "ModifiedOtherPatientID");
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Examples of org.drools.MockPersistentSet.addAll()

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        List list = new ArrayList();
        list.add( "example1" );
        list.add( "example2" );

        MockPersistentSet mockPersistentSet = new MockPersistentSet( false );
        mockPersistentSet.addAll( list );
        org.drools.ObjectWithSet objectWithSet = new ObjectWithSet();
        objectWithSet.setSet( mockPersistentSet );

        workingMemory.insert( objectWithSet );
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