Package org.intermine.web.logic.widget

Class EnrichmentWidgetImplLdr

java.lang.Object

org.intermine.web.logic.widget.WidgetLdr

org.intermine.web.logic.widget.EnrichmentWidgetImplLdr

public class EnrichmentWidgetImplLdr
extends WidgetLdr

Implement methods to access data an enrichment calculation needs to be provided with.

Author:

Daniela Butano

Field Summary

Fields inherited from class org.intermine.web.logic.widget.WidgetLdr

bag, filter, ids, os, queryClassInQuery, startClass

Constructor Summary

Constructors

Constructor	Description
EnrichmentWidgetImplLdr(InterMineBag bag, InterMineBag populationBag, ObjectStore os, EnrichmentWidgetConfig config, java.lang.String filter, boolean extraCorrectionCoefficient, CorrectionCoefficient correctionCoefficient, java.lang.String ids, java.lang.String populationIds)	Construct an Enrichment widget loader, which performs the queries needed for enrichment statistics.

Method Summary

Modifier and Type	Method	Description
Query	getExportQuery(java.util.List<java.lang.String> keys)
Query	getPopulationQuery(boolean calcTotal)
Query	getQuery(java.lang.String action, java.util.List<java.lang.String> keys)	Returns the relevant query.
Query	getSampleQuery(boolean calcTotal)

Methods inherited from class org.intermine.web.logic.widget.WidgetLdr

addReference, buildQueryValue, createAttributePath, createQueryFieldByPath

Methods inherited from class java.lang.Object

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

Constructor Detail

EnrichmentWidgetImplLdr

public EnrichmentWidgetImplLdr(InterMineBag bag,
                               InterMineBag populationBag,
                               ObjectStore os,
                               EnrichmentWidgetConfig config,
                               java.lang.String filter,
                               boolean extraCorrectionCoefficient,
                               CorrectionCoefficient correctionCoefficient,
                               java.lang.String ids,
                               java.lang.String populationIds)

Construct an Enrichment widget loader, which performs the queries needed for enrichment statistics.

Parameters:

bag - The bag containing the items we are interested in examining.

populationBag - The bag containing the background population for this test (MAY BE NULL).

os - The connection to the Object Store database.

config - The configuration detailing the kind of enrichment to do.

filter - An optional filter value.

extraCorrectionCoefficient - if true correction coefficient has been selected

correctionCoefficient - a instance of correction coefficient

applyCorrectionCoefficient -

ids - list of IDs to analyse, use instead of intermine bag if bag is NULL

populationIds - use instead of populationBag

Method Detail

getQuery

public Query getQuery(java.lang.String action,
                      java.util.List<java.lang.String> keys)

Returns the relevant query. this method is used for 6 widget queries. export query: select identifier and term where key = what the user selected on the widget analysed query: select object.id where object is used in query the results of this query are used as a NOT_IN constraint in a pathquery. the pathquery is run when the user clicks on the 'not analysed' number on the widget. population query: M = total annotated with this term in reference population annotated population query: N = total annotated with any term in reference population sample query: k = total annotated with this term in bag annotated sample query: n = total annotated with any term in bag (used to be bag.count)

Parameters:

keys - the keys of the records to be exported

action - which query to be built.

Returns:

query to return the correct result set for this widget

getSampleQuery

public Query getSampleQuery(boolean calcTotal)

Parameters:

calcTotal - whether or not to calculate the total number of annotated objects in the sample

Returns:

the query representing the sample population (the list)

getPopulationQuery

public Query getPopulationQuery(boolean calcTotal)

Parameters:

calcTotal - whether or not to calculate the total number of annotated objects in the database

Returns:

the query representing the entire population (all the items in the database)

getExportQuery

public Query getExportQuery(java.util.List<java.lang.String> keys)

Parameters:

keys - the keys to the records to be exported

Returns:

the query representing the records to be exported