Package org.intermine.web.logic.widget

Interface EnrichmentInput

  • All Known Implementing Classes:
    EnrichmentInputWidgetLdr
    public interface EnrichmentInput
    Define methods to access data an enrichment calculation needs to be provided with. Implementations may have their own variations of the sample and population. An example would be calculating the enrichment of certain departments in a sample companies (where each company may contains several departments). The population is all companies (or all that have any departments) and the sample is a subset of interest of those companies.
    Author:
    Richard Smith, Daniela Butano

    • Method Summary

      All Methods Instance Methods Abstract Methods 
      Modifier and Type Method Description
      java.util.Map<java.lang.String,​PopulationInfo> getAnnotatedCountsInPopulation()
      For each attribute give a count of items in the whole population that have that attribute assigned to them, M.
      java.util.Map<java.lang.String,​java.lang.Integer> getAnnotatedCountsInSample()
      For each attribute give a count of items in the sample that have that attribute assigned to them, k.
      java.util.Map<java.lang.String,​java.lang.String> getLabels()
      Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.
      PopulationInfo getPopulationInfo()
      Return a population info instance contanining the population size, N (In our example this is the total number of companies, or possibly the total number of companies that have at least one Department) and the average length of the genes in the whole population.
      int getSampleSize()
      The sample size, n.
      int getTestCount()
      The test count represents the number of tests that will be performed.

    • Method Detail

      • getPopulationInfo

        PopulationInfo getPopulationInfo()
        Return a population info instance contanining the population size, N (In our example this is the total number of companies, or possibly the total number of companies that have at least one Department) and the average length of the genes in the whole population.
        Returns:
        the population info instance

      • getSampleSize

        int getSampleSize()
        The sample size, n. The number of items from the whole population that are in the sample, in our example this is the number of companies in the subset.
        Returns:
        the sample size

      • getAnnotatedCountsInSample

        java.util.Map<java.lang.String,​java.lang.Integer> getAnnotatedCountsInSample()
        For each attribute give a count of items in the sample that have that attribute assigned to them, k. In our example: for each department the count of companies in the sample that contain the department.
        Returns:
        a map from attribute value to the count of items in the sample with that value

      • getAnnotatedCountsInPopulation

        java.util.Map<java.lang.String,​PopulationInfo> getAnnotatedCountsInPopulation()
        For each attribute give a count of items in the whole population that have that attribute assigned to them, M. In our example: for each department the count of companies that contain the department.
        Returns:
        a map from attribute value to the count of items in the population with that value

      • getLabels

        java.util.Map<java.lang.String,​java.lang.String> getLabels()
        Get additional display labels for attribute values in the enrichment analysis, these may be names where the values analysed were identifiers.
        Returns:
        labels for each attribute value in the sample

      • getTestCount

        int getTestCount()
        The test count represents the number of tests that will be performed. This is the number of unique attribute values applied across all items in the population. For example, a count of the unique departments observed in all companies in the population.
        Returns:
        the number of tests to be performed