本文整理了Java中org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils.isNegated()方法的一些代码示例，展示了VariantQueryUtils.isNegated()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。VariantQueryUtils.isNegated()方法的具体详情如下：
包路径：org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils
类名称：VariantQueryUtils
方法名：isNegated

VariantQueryUtils.isNegated介绍

[英]Determines if the filter is negated.
[中]确定过滤器是否为反。

代码示例

代码示例来源：origin: opencb/opencga

protected List<String> getValuesToValidate(List<String> rawValues) {
  return rawValues.stream()
      .map(value -> {
        value = isNegated(value) ? removeNegation(value) : value;
        String[] strings = VariantQueryUtils.splitOperator(value);
        boolean withComparisionOperator = strings[0] != null;
        if (withComparisionOperator) {
          value = strings[0];
        }
        return value;
      })
      .collect(Collectors.toList());
}

代码示例来源：origin: opencb/opencga

private DBObject[] getFileFilterDBObjects(String key, List<String> filterValues) {
  DBObject[] regexList = new DBObject[filterValues.size()];
  for (int i = 0; i < filterValues.size(); i++) {
    String filter = filterValues.get(i);
    boolean negated = isNegated(filter);
    if (negated) {
      filter = removeNegation(filter);
    }
    if (filter.contains(VCFConstants.FILTER_CODE_SEPARATOR) || filter.equals(VCFConstants.PASSES_FILTERS_v4)) {
      if (!negated) {
        regexList[i] = new BasicDBObject(key, filter);
      } else {
        regexList[i] = new BasicDBObject(key, new BasicDBObject("$ne", filter));
      }
    } else {
      if (!negated) {
        regexList[i] = new BasicDBObject(key, new BasicDBObject("$regex", filter));
      } else {
        regexList[i] = new BasicDBObject(key, new BasicDBObject("$not", Pattern.compile(filter)));
      }
    }
  }
  return regexList;
}

代码示例来源：origin: opencb/opencga

public Integer getStudyId(Object studyObj, boolean skipNegated, Map<String, Integer> studies) {
  Integer studyId;
  if (studyObj instanceof Integer) {
    studyId = ((Integer) studyObj);
  } else {
    String studyName = studyObj.toString();
    if (isNegated(studyName)) { //Skip negated studies
      if (skipNegated) {
        return null;
      } else {
        studyName = removeNegation(studyName);
      }
    }
    if (StringUtils.isNumeric(studyName)) {
      studyId = Integer.parseInt(studyName);
    } else {
      Integer value = studies.get(studyName);
      if (value == null) {
        throw VariantQueryException.studyNotFound(studyName, studies.keySet());
      }
      studyId = value;
    }
  }
  if (!studies.containsValue(studyId)) {
    throw VariantQueryException.studyNotFound(studyId, studies.keySet());
  }
  return studyId;
}

代码示例来源：origin: opencb/opencga

/**
 * Parse the genotype filter.
 *
 * @param sampleGenotypes Genotypes filter value
 * @param map             Initialized map to be filled with the sample to list of genotypes
 * @return QueryOperation between samples
 */
public static QueryOperation parseGenotypeFilter(String sampleGenotypes, Map<Object, List<String>> map) {
  Pair<QueryOperation, Map<String, String>> pair = parseMultiKeyValueFilter(GENOTYPE, sampleGenotypes);
  for (Map.Entry<String, String> entry : pair.getValue().entrySet()) {
    List<String> gts = splitValue(entry.getValue(), QueryOperation.OR);
    boolean anyNegated = false;
    boolean allNegated = true;
    for (String gt : gts) {
      if (isNegated(gt)) {
        anyNegated = true;
      } else {
        allNegated = false;
      }
    }
    if (!allNegated && anyNegated) {
      throw VariantQueryException.malformedParam(GENOTYPE, sampleGenotypes);
    }
    map.put(entry.getKey(), gts);
  }
  return pair.getKey();
}

代码示例来源：origin: opencb/opencga

public static boolean isValidParam(Query query, QueryParam param, boolean discardNegated) {
  boolean validParam = isValidParam(query, param);
  if (!discardNegated || !validParam) {
    return validParam;
  } else {
    String strValue = query.getString(param.key());
    return splitValue(strValue, checkOperator(strValue))
        .stream()
        .anyMatch((v) -> !isNegated(v)); // Discard negated
  }
}

代码示例来源：origin: opencb/opencga

if (isNegated(str)) {
  str = removeNegation(str);

代码示例来源：origin: opencb/opencga

public static boolean isOutputMultiStudy(Query query, QueryOptions options, Collection<?> studies) {
  Set<VariantField> fields = VariantField.getIncludeFields(options);
  if (!fields.contains(VariantField.STUDIES)) {
    return false;
  } else if (isValidParam(query, INCLUDE_STUDY)) {
    String includeStudy = query.getString(VariantQueryParam.INCLUDE_STUDY.key());
    if (NONE.equals(includeStudy)) {
      return false;
    } else if (ALL.equals(includeStudy)) {
      return studies.size() > 1;
    } else {
      return query.getAsList(VariantQueryParam.INCLUDE_STUDY.key()).size() > 1;
    }
  } else if (isValidParam(query, STUDY)) {
    String value = query.getString(VariantQueryParam.STUDY.key());
    long numStudies = splitValue(value, checkOperator(value)).stream().filter(s -> !isNegated(s)).count();
    return numStudies > 1;
  } else {
    return studies.size() > 1;
  }
}

代码示例来源：origin: opencb/opencga

samples = splitValue(value, checkOperator(value))
    .stream()
    .filter((v) -> !isNegated(v)) // Discard negated
    .collect(Collectors.toList());

代码示例来源：origin: opencb/opencga

includeFiles = splitValue(files, checkOperator(files))
    .stream()
    .filter(value -> !isNegated(value))
    .collect(Collectors.toList());

代码示例来源：origin: opencb/opencga

if (elem instanceof String && isNegated((String) elem)) {
  T mapped = map.apply((S) removeNegation((String) elem));
  if (mapped instanceof Collection) {
List<Object> list = new ArrayList<>(values.size());
for (S elem : values) {
  if (elem instanceof String && isNegated((String) elem)) {
    throw new VariantQueryException("Unable to use negate (!) operator in OR sequences (<it_1>(,<it_n>)*)");
  } else {
  if (elem instanceof String && isNegated((String) elem)) {
    T mapped = map.apply((S) removeNegation((String) elem));
    if (mapped instanceof Collection) {

代码示例来源：origin: opencb/opencga

valid &= !isNegated(gt);

代码示例来源：origin: opencb/opencga

valid &= !isNegated(gt);
queryOperation = VariantQueryUtils.checkOperator(samplesStr);
List<String> samples = VariantQueryUtils.splitValue(samplesStr, queryOperation);
samples.stream().filter(s -> !isNegated(s)).forEach(sample -> samplesMap.put(sample, Collections.emptyList()));

代码示例来源：origin: opencb/opencga

String study = iterator.next();
  Integer studyId = studyConfigurationManager.getStudyId(study, false, studies);
  if (isNegated(study)) {
    sb.append("\"").append(getStudyColumn(studyId).column()).append("\" IS NULL ");
  } else {
  if (isNegated(file)) {
      for (int i = 0; i < filterValues.size(); i++) {
        String filter = checkStringValue(filterValues.get(i));
        boolean negated = isNegated(filter);
        if (negated) {
          filter = removeNegation(filter);
for (String cohort : query.getAsStringList(COHORT.key())) {
  boolean negated = false;
  if (isNegated(cohort)) {
    cohort = removeNegation(cohort);
    negated = true;

代码示例来源：origin: opencb/opencga

} else {
  String sampleStr = sampleObj.toString();
  if (isNegated(sampleStr)) {
    sampleStr = removeNegation(sampleStr);

代码示例来源：origin: opencb/opencga

} else {
  sampleIds = samples.stream()
      .map(sample -> isNegated(sample) ? removeNegation(sample) : sample)
      .map(sample -> studyConfigurationManager.getSampleId(sample, studyConfiguration)).collect(Collectors.toList());
  file = isNegated(file) ? removeNegation(file) : file;
  Integer fileId = StudyConfigurationManager.getFileIdFromStudy(file, studyConfiguration);
  if (fileId == null) {

代码示例来源：origin: opencb/opencga

.filter(value -> !isNegated(value))
  .map(value -> {
    Integer fileId = studyConfigurationManager.getFileIdPair(value, false, defaultStudyConfiguration).getValue();
if (isNegated(sample)) {
  throw VariantQueryException.malformedParam(SAMPLE, samples, "Unsupported negated samples");
  for (String genotype : genotypes) {
    if (isNegated(genotype)) {
      if (defaultGenotypes.contains(removeNegation(genotype))) {
        canFilterSampleByFile = true;
  boolean negated = isNegated(genotype);
  if (negated) {
    genotype = removeNegation(genotype);

代码示例来源：origin: opencb/opencga

if (isNegated(fileStr)) { //Skip negated studies
  if (skipNegated) {
    return null;

代码示例来源：origin: opencb/opencga

@Override
public Query preProcessQuery(Query originalQuery, QueryOptions options) throws StorageEngineException {
  Query query = super.preProcessQuery(originalQuery, options);
  List<String> studyNames = studyConfigurationManager.getStudyNames(QueryOptions.empty());
  CellBaseUtils cellBaseUtils = getCellBaseUtils();
  if (isValidParam(query, VariantQueryParam.STUDY)
      && studyNames.size() == 1
      && !isNegated(query.getString(VariantQueryParam.STUDY.key()))
      && !isValidParam(query, FILE)
      && !isValidParam(query, FILTER)
      && !isValidParam(query, QUAL)
      && !isValidParam(query, INFO)
      && !isValidParam(query, SAMPLE)
      && !isValidParam(query, FORMAT)
      && !isValidParam(query, GENOTYPE)) {
    query.remove(VariantQueryParam.STUDY.key());
  }
  convertGoToGeneQuery(query, cellBaseUtils);
  convertExpressionToGeneQuery(query, cellBaseUtils);
  return query;
}

代码示例来源：origin: opencb/opencga

Pair<Integer, Integer> fileIdPair = studyConfigurationManager.getFileIdPair(file, false, defaultStudyConfiguration);
byte[] column = buildFileColumnKey(fileIdPair.getKey(), fileIdPair.getValue());
if (isNegated(file)) {
  subFilters.addFilter(missingColumnFilter(column));
} else {
Integer studyId = studyConfigurationManager.getStudyId(studyStr, null);
byte[] column = VariantPhoenixHelper.getStudyColumn(studyId).bytes();
if (isNegated(studyStr)) {
  subFilters.addFilter(missingColumnFilter(column));
  scan.addColumn(family, column);