How to use
classifyNegatives
method
in
uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator.classifyNegatives (Showing top 3 results out of 315)

public Set<Experiment> getNegativeExperiments() {
  if ( negativeExperiments == null ) {
    classifyNegatives();
  }
  return negativeExperiments;
}

public Set<Experiment> getNegativeExperiments() {
  if ( negativeExperiments == null ) {
    classifyNegatives();
  }
  return negativeExperiments;
}

public Set<Experiment> getNegativeExperiments() {
  if ( negativeExperiments == null ) {
    classifyNegatives();
  }
  return negativeExperiments;
}

Javadoc

Checks for a negative interaction. NB This will have to be done using SQL otherwise we end up materializing all interactions just to do the check.

Also the new intact curation rules specify that an Experiment should ONLY contain negative Interactions if it is annotated as 'negative'. Thus to decide if an Experiment is classified as 'negative', the Annotations of that Experiment need to be checked for one with a 'negative' Controlled Vocab attached to it as a topic.

However at some point in the future there may be a possibility that only the Interactions will be marked as 'negative' (not the Experiment), and so these should be checked also, with duplicate matches being ignored.

This method has to be static because it is called by the static 'classifyExperiments'.

Popular methods of ExperimentListGenerator

addToList
classifyExperiments
Classify experiments matching searchPattern into a data structure according to species and experimen
createExpListItems
createExperimentListItems
createItemClassificationByDataset
Build the classification by dataset. We keep the negative experiment separated from the non negative
createItemClassificationByPubmed
Build the classification by pubmed id. We keep the negative experiment separated from the non negati
createItemClassificationBySpecies
generateClassificationByPublications
generateClassificationBySpecies
getCreatedYear
Given a set of Experiments, it returns the year of the date of creation of the oldest experiment.
getDaoFactory
getDatasets
Fetch dataset information (if any) from experiment.

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How to use classifyNegativesmethodin uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator.classifyNegatives (Showing top 3 results out of 315)

How to use
classifyNegatives
method
in
uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator