本文整理了Java中org.opencb.opencga.storage.core.variant.adaptors.VariantQueryUtils.parseConsequenceType()方法的一些代码示例，展示了VariantQueryUtils.parseConsequenceType()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.parseConsequenceType()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：parseConsequenceType

VariantQueryUtils.parseConsequenceType介绍

暂无

代码示例

代码示例来源：origin: opencb/opencga

/**
 * Build an OR/AND-condition with all consequence types from the input list. It uses the VariantDBAdaptorUtils
 * to parse the consequence type (accession or term) into an integer.
 *
 * @param cts   List of consequence types
 * @param op    Boolean operator (OR / AND)
 * @return      OR/AND-condition string
 */
private String buildConsequenceTypeOrAnd(List<String> cts, String op) {
  StringBuilder sb = new StringBuilder();
  for (String ct : cts) {
    if (sb.length() > 0) {
      sb.append(op);
    }
    sb.append("soAcc:\"").append(VariantQueryUtils.parseConsequenceType(ct)).append("\"");
  }
  return sb.toString();
}

代码示例来源：origin: opencb/opencga

/**
 * Build the condition: genes AND cts.
 *
 * @param genes    List of genes
 * @param cts      List of consequence types
 * @return         OR/AND condition string
 */
private String buildGeneAndConsequenceType(List<String> genes, List<String> cts) {
  // in the VariantSearchModel the (gene AND ct) is modeled in the field: geneToSoAcc:gene_ct
  // and if there are multiple genes and consequence types, we have to build the combination of all of them in a OR expression
  StringBuilder sb = new StringBuilder();
  for (String gene: genes) {
    for (String ct: cts) {
      if (sb.length() > 0) {
        sb.append(" OR ");
      }
      sb.append("geneToSoAcc:\"").append(gene).append("_").append(VariantQueryUtils.parseConsequenceType(ct))
          .append("\"");
    }
  }
  return sb.toString();
}

代码示例来源：origin: opencb/opencga

@Test
public void testParseSO() throws Exception {
  assertEquals(1587, parseConsequenceType("stop_gained"));
  assertEquals(1587, parseConsequenceType("1587"));
  assertEquals(1587, parseConsequenceType("SO:00001587"));
}

代码示例来源：origin: opencb/opencga

@Test
public void testParseWrongSONumber2() throws Exception {
  thrown.expect(VariantQueryException.class);
  parseConsequenceType("SO:9999999");
}

代码示例来源：origin: opencb/opencga

@Test
public void testParseWrongSOTerm() throws Exception {
  thrown.expect(VariantQueryException.class);
  parseConsequenceType("wrong_so");
}

代码示例来源：origin: opencb/opencga

@Test
public void testParseWrongSONumber() throws Exception {
  thrown.expect(VariantQueryException.class);
  parseConsequenceType("9999999");
}

代码示例来源：origin: opencb/opencga

for (String gene : genes) {
  for (String so : soList) {
    int soNumber = parseConsequenceType(so);
    gnSoSet.add(VariantAnnotationToPhoenixConverter.buildGeneSO(gene, soNumber));

代码示例来源：origin: opencb/opencga

for (SequenceOntologyTerm sequenceOntologyTerm : consequenceType.getSequenceOntologyTerms()) {
  String accession = sequenceOntologyTerm.getAccession();
  int so = parseConsequenceType(accession);
  addNotNull(soList, so);

代码示例来源：origin: opencb/opencga

for (String gene : variantQueryXref.getGenes()) {
  for (String so : soList) {
    int soNumber = parseConsequenceType(so);
    gnSo.add(DocumentToVariantAnnotationConverter.buildGeneSO(gene, soNumber));