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org.opencb.biodata.models.variant.avro.Xref类的使用及代码示例

转载 作者:知者 更新时间:2024-03-18 23:34:40 27 4
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本文整理了Java中org.opencb.biodata.models.variant.avro.Xref类的一些代码示例,展示了Xref类的具体用法。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。Xref类的具体详情如下:
包路径:org.opencb.biodata.models.variant.avro.Xref
类名称:Xref

Xref介绍

暂无

代码示例

代码示例来源:origin: opencb/cellbase

private List<Xref> getXrefs(Map<String, String> sourceMap, int variationId) throws IOException, SQLException {
  List<String[]> variationSynonyms = variationSynonymFile.getVariationRelatedLines(variationId);
  List<Xref> xrefs = null;
  if (variationSynonyms != null && variationSynonyms.size() > 0) {
    String[] arr;
    for (String[] variationSynonymFields : variationSynonyms) {
      // TODO: use constans to identify the fields
      if (sourceMap.get(variationSynonymFields[3]) != null) {
        arr = sourceMap.get(variationSynonymFields[3]).split(",");
        if (xrefs == null) {
          xrefs = new ArrayList<>();
        }
        xrefs.add(new Xref(variationSynonymFields[4], arr[0]));
      }
    }
  }
  return xrefs;
}

代码示例来源:origin: opencb/opencga

xrefs.add(convertXrefToStorage(xref.getId(), xref.getSource()));

代码示例来源:origin: opencb/opencga

variantAnnotation.getXrefs().forEach(xref -> {
  if (xref != null) {
    xrefs.add(xref.getId());

代码示例来源:origin: opencb/cellbase

VariantAnnotationProto.VariantAnnotation.Xref.Builder xrefBuilder =
    VariantAnnotationProto.VariantAnnotation.Xref.newBuilder()
        .setId(xref.getId())
        .setSource(xref.getSource());
builder.addXrefs(xrefBuilder.build());

代码示例来源:origin: opencb/opencga

if (variantAnnotation.getXrefs() != null) {
  for (Xref xref : variantAnnotation.getXrefs()) {
    addNotNull(xrefs, xref.getId());

代码示例来源:origin: org.opencb.biodata/biodata-models

@Override
 public Xref build() {
  try {
   Xref record = new Xref();
   record.id = fieldSetFlags()[0] ? this.id : (java.lang.String) defaultValue(fields()[0]);
   record.source = fieldSetFlags()[1] ? this.source : (java.lang.String) defaultValue(fields()[1]);
   return record;
  } catch (Exception e) {
   throw new org.apache.avro.AvroRuntimeException(e);
  }
 }
}

代码示例来源:origin: opencb/opencga

xrefs.add(new Xref(xref, "dbSNP"));
continue;
xrefs.add(new Xref(xref, "ensemblGene"));
continue;
xrefs.add(new Xref(xref, "ensemblTranscript"));

代码示例来源:origin: opencb/opencga

va.setId(id);
xrefs.add(new Xref(id, source));

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