本文整理汇总了Java中com.github.phenomics.ontolib.ontology.data.Term类的典型用法代码示例。如果您正苦于以下问题：Java Term类的具体用法？Java Term怎么用？Java Term使用的例子？那么, 这里精选的类代码示例或许可以为您提供帮助。
Term类属于com.github.phenomics.ontolib.ontology.data包，在下文中一共展示了Term类的1个代码示例，这些例子默认根据受欢迎程度排序。您可以为喜欢或者感觉有用的代码点赞，您的评价将有助于系统推荐出更棒的Java代码示例。
示例1: computeInformationContent
import com.github.phenomics.ontolib.ontology.data.Term; //导入依赖的package包/类
/**
* Perform the actual computation.
*
* <p>
* Note that {@code termLabels} must already contain the implicit ancestor annotations. You can
* achieve this using {@link TermIds#augmentWithAncestors(ImmutableOntology, Set, boolean)}.
* </p>
*
* @param <LabelT> Labels for objects from "the real world". This could, e.g., be
* <code>String</code>s with gene names. This type has to properly implement
* <code>equals(Object)</code> and <code>hashValue()</code> as it is to be used as keys in
* a {@link HashMap}.
*
* @param termLabels Labels for each {@link Term}, identified by {@link TermId}
* @return {@link Map} from {@link TermId} to information content.
*/
public <LabelT> Map<TermId, Double>
computeInformationContent(Map<TermId, ? extends Collection<LabelT>> termLabels) {
LOGGER.info("Computing IC of {} terms using {} labels...", new Object[] {ontology.countAllTerms(),
termLabels.values().stream().mapToInt(l -> l.size()).sum()});
// Build mapping from TermId -> absolute frequency
final TermId root = ontology.getRootTermId();
final Map<TermId, Integer> termToFrequency = new HashMap<>();
for (TermId termId : ontology.getNonObsoleteTermIds()) {
termToFrequency.put(termId, 0);
}
for (Entry<TermId, ? extends Collection<LabelT>> e : termLabels.entrySet()) {
termToFrequency.put(e.getKey(), e.getValue().size());
}
// Compute information content for each TermId
final int maxFreq = termToFrequency.get(root);
final Map<TermId, Double> termToInformationContent =
caculateInformationContent(maxFreq, termToFrequency);
// Fix terms with IC of zero, set it to IC of root
int countIcZero = 0;
final double dummyIc = -Math.log(1 / (double) maxFreq);
for (Term t : ontology.getTerms()) {
if (t.isObsolete()) {
continue;
}
if (!termToFrequency.containsKey(t.getId())) {
++countIcZero;
termToInformationContent.put(t.getId(), dummyIc);
}
}
if (countIcZero > 0) {
LOGGER.warn("Frequency of {} non-obsolete terms was zero! Their IC has been set to {} = "
+ "- log(1 / {}).", new Object[] {countIcZero, dummyIc, maxFreq});
}
LOGGER.info("Computing IC is complete.");
return termToInformationContent;
}