Package org.intermine.web.logic.widget

Class EnrichmentInputWidgetLdr

  • All Implemented Interfaces:
    EnrichmentInput
    public class EnrichmentInputWidgetLdr
extends java.lang.Object
implements EnrichmentInput
    Executes queries and summarises data for a specific EnrichmentWidgetLdr ready for calculation.
    Author:
    Richard Smith, Daniela Butano

    • Method Summary

      All Methods Instance Methods Concrete 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.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Constructor Detail

      • EnrichmentInputWidgetLdr

        public EnrichmentInputWidgetLdr​(ObjectStore os,
                                EnrichmentWidgetImplLdr ldr)
        Construct with an EnrichmentWidgetLdr that contains queries needed for specific widget tests. This class executes queries and summarises data ready for calculation.
        Parameters:
        os - the ObjectStore to execute queries in
        ldr - queries to fetch data for a specific widget

    • Method Detail

      • getAnnotatedCountsInPopulation

        public java.util.Map<java.lang.String,​PopulationInfo> getAnnotatedCountsInPopulation()
        Description copied from interface: EnrichmentInput
        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.
        Specified by:
        getAnnotatedCountsInPopulation in interface EnrichmentInput
        Returns:
        a map from attribute value to the count of items in the population with that value

      • getAnnotatedCountsInSample

        public java.util.Map<java.lang.String,​java.lang.Integer> getAnnotatedCountsInSample()
        Description copied from interface: EnrichmentInput
        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.
        Specified by:
        getAnnotatedCountsInSample in interface EnrichmentInput
        Returns:
        a map from attribute value to the count of items in the sample with that value

      • getLabels

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

      • getPopulationInfo

        public PopulationInfo getPopulationInfo()
        Description copied from interface: EnrichmentInput
        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.
        Specified by:
        getPopulationInfo in interface EnrichmentInput
        Returns:
        the population info instance

      • getSampleSize

        public int getSampleSize()
        Description copied from interface: EnrichmentInput
        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.
        Specified by:
        getSampleSize in interface EnrichmentInput
        Returns:
        the sample size

      • getTestCount

        public int getTestCount()
        Description copied from interface: EnrichmentInput
        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.
        Specified by:
        getTestCount in interface EnrichmentInput
        Returns:
        the number of tests to be performed