Java HpoDiseaseAnnotation类代码示例

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
@Test
public void testParseHpoDiseaseAnnotationHead()
    throws IOException, TermAnnotationParserException {
  final HpoDiseaseAnnotationParser parser =
      new HpoDiseaseAnnotationParser(hpoDiseaseAnnotationHeadFile);

  // Read and check first record.
  final HpoDiseaseAnnotation firstRecord = parser.next();
  assertEquals(
      "HPODiseaseAnnotation [db=DECIPHER, dbObjectId=1, dbName=Wolf-Hirschhorn Syndrome, qualifier=, hpoId=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0000252], dbReference=DECIPHER:1, evidenceDescription=IEA, onsetModifier=, frequencyModifier=, with=, aspect=O, synonym=WOLF-HIRSCHHORN SYNDROME, date=Wed May 29 00:00:00 UTC 2013, assignedBy=HPO:skoehler]",
      firstRecord.toString());

  // Read remaining records and check count.
  int count = 1;
  while (parser.hasNext()) {
    parser.next();
    count += 1;
  }
  assertEquals(10, count);

  parser.close();
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
@Test
public void testParseHpoDiseaseAnnotationHead()
    throws IOException, TermAnnotationParserException {
  final HpoDiseaseAnnotationParser parser =
      new HpoDiseaseAnnotationParser(hpoDiseaseAnnotationHeadFile);

  // Read and check first record.
  final HpoDiseaseAnnotation firstRecord = parser.next();
  assertEquals(
      "HPODiseaseAnnotation [db=OMIM, dbObjectId=101000, dbName=#101000 NEUROFIBROMATOSIS, TYPE II; NF2;;NEUROFIBROMATOSIS, CENTRAL TYPE;;ACOUSTIC SCHWANNOMAS, BILATERAL;;BILATERAL ACOUSTIC NEUROFIBROMATOSIS; BANF;;ACOUSTIC NEURINOMA, BILATERAL; ACN, qualifier=NOT, hpoId=ImmutableTermId [prefix=ImmutableTermPrefix [value=HP], id=0009737], dbReference=OMIM:101000, evidenceDescription=IEA, onsetModifier=, frequencyModifier=, with=, aspect=O, synonym=, date=Fri Jun 18 00:00:00 UTC 2010, assignedBy=HPO:skoehler]",
      firstRecord.toString());

  // Read remaining records and check count.
  int count = 1;
  while (parser.hasNext()) {
    parser.next();
    count += 1;
  }
  assertEquals(10, count);

  parser.close();
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
/**
 * Perform basic checks on the first line of the file.
 *
 * @throws TermAnnotationParserException In case of problems with the first line in the file.
 */
private void checkFirstLine() throws TermAnnotationParserException {
  final String[] arr = nextLine.split("\t");
  if (arr.length != 14) {
    throw new TermAnnotationParserException(
        "Does not look like HPO disease annotation file. Invalid number of fields in first "
            + "line, expected 14, was " + arr.length);
  }
  if (!Enums.getIfPresent(HpoDiseaseAnnotation.DatabaseSource.class, arr[0]).isPresent()) {
    throw new TermAnnotationParserException(
        "Does not look like HPO disease annotation file. First field value was " + arr[0]
            + " but was expected to be one of "
            + Arrays.toString(HpoDiseaseAnnotation.DatabaseSource.values()));
  }
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
@Override
public HpoDiseaseAnnotation next() throws TermAnnotationParserException, IOException {
  final String[] arr = nextLine.split("\t");
  if (arr.length != 14) {
    throw new TermAnnotationParserException(
        "Does not look like HPO disease annotation file. Invalid number of fields, expected "
            + "14 but was " + arr.length);
  }

  final String db = arr[0];
  final String dbObjectId = arr[1];
  final String dbName = arr[2];
  final String qualifier = arr[3];
  final ImmutableTermId hpoId = ImmutableTermId.constructWithPrefix(arr[4]);
  final String dbReference = arr[5];
  final String evidenceCode = arr[6];
  final String onsetModifier = arr[7];
  final String frequencyModifier = arr[8];
  final String with = arr[9];
  final String aspect = arr[10];
  final String synonym = arr[11];
  final String dateStr = arr[12];
  final String assignedBy = arr[13];

  nextLine = reader.readLine();

  final SimpleDateFormat format = new SimpleDateFormat("yyyy-MM-dd");
  Date date;
  try {
    date = format.parse(dateStr);
  } catch (ParseException e) {
    throw new TermAnnotationParserException(
        "There was a problem parsing the date value " + dateStr, e);
  }

  return new HpoDiseaseAnnotation(db, dbObjectId, dbName, qualifier, hpoId, dbReference,
      evidenceCode, onsetModifier, frequencyModifier, with, aspect, synonym, date, assignedBy);
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
/**
 * Add a new {@link HpoDiseaseAnnotation} object with advanced logic.
 *
 * <p>
 * All the other functions for adding and setting are relatively "dumb" and directly work on the
 * members.
 * </p>
 *
 * <p>
 * In contrast, this function does a more advanced processing and can be used to fill a
 * {@link AnnotatedDiseaseBuilder} step by step from a list of positive and negative annotations.
 * It will ensure that only one annotation for each HPO {@link TermId} is created and set the
 * disease ID and name.
 * </p>
 *
 * @param anno The {@link HpoDiseaseAnnotation} to process.
 */
public void processAnnotation(HpoDiseaseAnnotation anno) {
  if (diseaseId == null) {
    setDiseaseId(new DiseaseId(DiseaseDatabase.valueOf(anno.getDb()), anno.getDbObjectId()));
  } else {
    if (!diseaseId
        .equals(new DiseaseId(DiseaseDatabase.valueOf(anno.getDb()), anno.getDbObjectId()))) {
      throw new IllegalArgumentException("HpoDiseaseAnnotation has conflicting disease ID "
          + anno.getDbReference() + " vs. " + diseaseId);
    }
  }

  if (name == null) {
    setName(anno.getDbName());
  } else {
    if (!name.equals(anno.getDbName())) {
      throw new IllegalArgumentException("HpoDiseaseAnnotation has conflicting disease name "
          + anno.getDbName() + " vs. " + name);
    }
  }

  // TODO: what about alternative names?!
  // TODO: what about handling of "references" as Sebastian's code does?

  if ("NOT".equals(anno.getQualifier())) {
    negativeAnnotations.add(anno);
  } else {
    positiveAnnotations.add(anno);
  }
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
@Override
public HpoDiseaseAnnotation next() throws TermAnnotationParserException, IOException {
  final String[] arr = nextLine.split("\t");
  if (arr.length != 14) {
    throw new TermAnnotationParserException(
        "Does not look like HPO disease annotation file. Invalid number of fields, expected "
            + "14 but was " + arr.length);
  }

  final String db = arr[0];
  final String dbObjectId = arr[1];
  final String dbName = arr[2];
  final String qualifier = arr[3];
  final ImmutableTermId hpoId = ImmutableTermId.constructWithPrefix(arr[4]);
  final String dbReference = arr[5];
  final String evidenceCode = arr[6];
  final String onsetModifier = arr[7];
  final String frequencyModifier = arr[8];
  final String with = arr[9];
  final String aspect = arr[10];
  final String synonym = arr[11];
  final String dateStr = arr[12];
  final String assignedBy = arr[13];

  nextLine = reader.readLine();

  final ImmutableList<String> formatStrings = ImmutableList.of("yyyy.MM.dd", "yyyy-MM-dd");
  Date date = null;
  for (String formatString : formatStrings) {
    final SimpleDateFormat format = new SimpleDateFormat(formatString);
    try {
      date = format.parse(dateStr);
      break;
    } catch (ParseException e) {
      continue; // swallow
    }
  }
  if (date == null) {
    throw new TermAnnotationParserException(
        "There was a problem parsing the date value " + dateStr);
  }

  return new HpoDiseaseAnnotation(db, dbObjectId, dbName, qualifier, hpoId, dbReference,
      evidenceCode, onsetModifier, frequencyModifier, with, aspect, synonym, date, assignedBy);
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
/**
 * @return Positive disease annotations.
 */
public ImmutableList<HpoDiseaseAnnotation> getPositiveAnnotations() {
  return positiveAnnotations;
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
/**
 * @return Negative disease annotations.
 */
public ImmutableList<HpoDiseaseAnnotation> getNegativeAnnotations() {
  return negativeAnnotations;
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
/**
 * Constructor.
 *
 * <p>
 * The alternative disease names will be sorted on construction.
 * </p>
 *
 * @param diseaseId The disease ID.
 * @param name The name of the disease.
 * @param alternativeNames Alternative disease names.
 * @param positiveAnnotations Positive disease annotations.
 * @param negativeAnnotations Negative disease annotations.
 */
public AnnotatedDisease(DiseaseId diseaseId, String name, Collection<String> alternativeNames,
    Collection<HpoDiseaseAnnotation> positiveAnnotations,
    Collection<HpoDiseaseAnnotation> negativeAnnotations) {
  this.diseaseId = diseaseId;
  this.name = name;
  this.alternativeNames = ImmutableList.sortedCopyOf(alternativeNames);
  this.positiveAnnotations = ImmutableList.copyOf(positiveAnnotations);
  this.negativeAnnotations = ImmutableList.copyOf(negativeAnnotations);
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
/**
 * Add positive disease annotation.
 *
 * @param anno The {@link HpoDiseaseAnnotation} to add.
 */
public void addPositiveAnnotation(HpoDiseaseAnnotation anno) {
  this.positiveAnnotations.add(anno);
}
 

import com.github.phenomics.ontolib.formats.hpo.HpoDiseaseAnnotation; //导入依赖的package包/类
/**
 * Add positive disease annotation.
 *
 * @param anno The {@link HpoDiseaseAnnotation} to add.
 */
public void addNegativeAnnotation(HpoDiseaseAnnotation anno) {
  this.negativeAnnotations.add(anno);
}