本文整理了Java中org.opencb.opencga.core.results.VariantQueryResult.<init>()方法的一些代码示例，展示了VariantQueryResult.<init>()的具体用法。这些代码示例主要来源于Github/Stackoverflow/Maven等平台，是从一些精选项目中提取出来的代码，具有较强的参考意义，能在一定程度帮忙到你。VariantQueryResult.<init>()方法的具体详情如下：
包路径：org.opencb.opencga.core.results.VariantQueryResult
类名称：VariantQueryResult
方法名：<init>

VariantQueryResult.<init>介绍

暂无

代码示例

代码示例来源：origin: opencb/opencga

public VariantQueryResult<Variant> toQueryResult(Map<String, List<String>> samples) {
  return new VariantQueryResult<>(toQueryResult(), samples);
}

代码示例来源：origin: opencb/opencga

@Override
public VariantQueryResult<Variant> get(Query query, QueryOptions options) {
  logger.info("Query " + query.toJson());
  logger.info("QueryOptions " + options.toJson());
  logger.info("dbName " + dbName);
  List<Variant> variants = new ArrayList<>();
  iterator(query, options).forEachRemaining(variants::add);
  return new VariantQueryResult<>("", 0, variants.size(), variants.size(), "", "", variants, null,
      DummyVariantStorageEngine.STORAGE_ENGINE_ID);
}

代码示例来源：origin: opencb/opencga

@Override
public VariantQueryResult<Variant> get(Query query, QueryOptions options) {
  List<Variant> variants = new LinkedList<>();
  VariantDBIterator iterator = iterator(query, options);
  iterator.forEachRemaining(variants::add);
  long numTotalResults;
  String warn = "";
  String error = "";
  if (options == null) {
    numTotalResults = variants.size();
  } else {
    if (options.getInt(QueryOptions.LIMIT, -1) > 0) {
      if (options.getBoolean(QueryOptions.SKIP_COUNT, DEFAULT_SKIP_COUNT)) {
        numTotalResults = -1;
      } else {
        numTotalResults = count(query).first();
      }
    } else {
      // There are no limit. Do not count.
      numTotalResults = variants.size();
    }
  }
  Map<String, List<String>> samples = getSamplesMetadataIfRequested(query, options, getStudyConfigurationManager());
  return new VariantQueryResult<>("getVariants", ((int) iterator.getTimeFetching()), variants.size(), numTotalResults,
      warn, error, variants, samples, HadoopVariantStorageEngine.STORAGE_ENGINE_ID);
}

代码示例来源：origin: opencb/opencga

@Override
public VariantQueryResult<Variant> get(Query query, QueryOptions options) {
  if (options == null) {
    options = new QueryOptions();
  }
  SelectVariantElements selectVariantElements = VariantQueryUtils.parseSelectElements(query, options, studyConfigurationManager);
  Document mongoQuery = queryParser.parseQuery(query);
  Document projection = queryParser.createProjection(query, options, selectVariantElements);
  options.putIfAbsent(QueryOptions.SKIP_COUNT, DEFAULT_SKIP_COUNT);
  if (options.getBoolean("explain", false)) {
    Document explain = variantsCollection.nativeQuery()
        .find(mongoQuery, projection, options)
        .modifiers(new Document("$explain", true))
        .first();
    logger.debug("MongoDB Explain = {}", explain.toJson(new JsonWriterSettings(JsonMode.SHELL, true)));
  }
  DocumentToVariantConverter converter = getDocumentToVariantConverter(query, selectVariantElements);
  Map<String, List<String>> samples = getSamplesMetadataIfRequested(query, options, studyConfigurationManager);
  return new VariantQueryResult<>(variantsCollection.find(mongoQuery, projection, converter, options), samples);
}

代码示例来源：origin: opencb/opencga

return new VariantQueryResult<>("count", time, 1, 1, "", "", Collections.singletonList(count), null,
    SEARCH_ENGINE_ID + '+' + getStorageEngineId(), approxCount, approxCount ? sampling : null);

代码示例来源：origin: opencb/opencga

/**
 * Return the list of VariantSearchModel objects from a Solr core/collection
 * according a given query.
 *
 * @param collection   Collection name
 * @param query        Query
 * @param queryOptions Query options
 * @return List of VariantSearchModel objects
 * @throws VariantSearchException VariantSearchException
 * @throws IOException   IOException
 */
public VariantQueryResult<VariantSearchModel> nativeQuery(String collection, Query query, QueryOptions queryOptions)
    throws VariantSearchException, IOException {
  SolrQuery solrQuery = solrQueryParser.parse(query, queryOptions);
  SolrCollection solrCollection = solrManager.getCollection(collection);
  QueryResult<VariantSearchModel> queryResult;
  try {
    queryResult = solrCollection.query(solrQuery, VariantSearchModel.class);
  } catch (SolrServerException e) {
    throw new VariantSearchException("Error executing variant query (nativeQuery)", e);
  }
  return new VariantQueryResult<>("", queryResult.getDbTime(), queryResult.getNumResults(),
      queryResult.getNumTotalResults(), "", "", queryResult.getResult(), null, SEARCH_ENGINE_ID);
}

代码示例来源：origin: opencb/opencga

return new VariantQueryResult<>("getPhased", ((int) watch.getTime()), 0, 0, null, null, Collections.emptyList(), null,
    MongoDBVariantStorageEngine.STORAGE_ENGINE_ID);

代码示例来源：origin: opencb/opencga

/**
 * Return the list of Variant objects from a Solr core/collection
 * according a given query.
 *
 * @param collection   Collection name
 * @param query        Query
 * @param queryOptions Query options
 * @return List of Variant objects
 * @throws VariantSearchException VariantSearchException
 * @throws IOException   IOException
 */
public VariantQueryResult<Variant> query(String collection, Query query, QueryOptions queryOptions)
    throws VariantSearchException, IOException {
  SolrQuery solrQuery = solrQueryParser.parse(query, queryOptions);
  SolrCollection solrCollection = solrManager.getCollection(collection);
  QueryResult<Variant> queryResult;
  try {
    queryResult = solrCollection.query(solrQuery, VariantSearchModel.class,
        new VariantSearchToVariantConverter(VariantField.getIncludeFields(queryOptions)));
  } catch (SolrServerException e) {
    throw new VariantSearchException("Error executing variant query", e);
  }
  return new VariantQueryResult<>("", queryResult.getDbTime(), queryResult.getNumResults(),
      queryResult.getNumTotalResults(), "", "", queryResult.getResult(), null, SEARCH_ENGINE_ID);
}

代码示例来源：origin: opencb/opencga

@SuppressWarnings("unchecked")
public <T> VariantQueryResult<T> get(Query query, QueryOptions queryOptions, String sessionId, Class<T> clazz)
    throws CatalogException, IOException, StorageEngineException {
  VariantQueryResult<Variant> result = get(query, queryOptions, sessionId);
  List<T> variants;
  if (clazz == Variant.class) {
    return (VariantQueryResult<T>) result;
  } else if (clazz == org.ga4gh.models.Variant.class) {
    Ga4ghVariantConverter<org.ga4gh.models.Variant> converter = new Ga4ghVariantConverter<>(new AvroGa4GhVariantFactory());
    variants = (List<T>) converter.apply(result.getResult());
  } else if (clazz == ga4gh.Variants.Variant.class) {
    Ga4ghVariantConverter<ga4gh.Variants.Variant> converter = new Ga4ghVariantConverter<>(new ProtoGa4GhVariantFactory());
    variants = (List<T>) converter.apply(result.getResult());
  } else {
    throw new IllegalArgumentException("Unknown variant format " + clazz);
  }
  return new VariantQueryResult<>(
      result.getId(),
      result.getDbTime(),
      result.getNumResults(),
      result.getNumTotalResults(),
      result.getWarningMsg(),
      result.getErrorMsg(),
      variants,
      result.getSamples(),
      result.getSource(),
      result.getApproximateCount(),
      result.getApproximateCountSamplingSize());
}