Public

check

getCvComponentRole

getCvExperimentalRole

getDefaultCvBiologicalRole

Gson

Reading from database using SQL prepared statement

An exception that indicates a failed JDBC operation. It provides the following
information about pro

java.sql.SQLException

MessageFormat provides a means to produce concatenated messages in
language-neutral way. Use this to

java.text.MessageFormat

 Collection is the root of the collection hierarchy. It defines operations on
data collections and t

java.util.Collection

This class consists exclusively of static methods that operate on or return
collections. It contains

java.util.Collections

Defines a general exception a servlet can throw when it encounters difficulty.

javax.servlet.ServletException

 This is the main interface of a Quartz Scheduler.

 A Scheduler maintains a registery of org.quartz

org.quartz.Scheduler

requestLocationUpdates

addToBackStack

Returns a stream for the resource with the specified name. See
#getResource(String) for a descriptio

getResourceAsStream

/**
 * Allows to check if the data carried by an InteractionTag are already existing in the IntAct node.
 * <pre>
 * Reminder:
 * - an interaction (as a set of components) must be unique in the experiment scope.
 * - the shortlabel of an interaction must be unique in the database scope.
 * 
 * Logic sketch:
 * If there is an experiment in commons between the data declare in PSI and those existing in Intact
 * - Compare the conponent of the two interactions
 * - if the same: the PSI interaction has already an instance in IntAct for that experiment
 * - if not the same: compare with the next interaction (if there is one)
 * - if no more interaction: the PSI interaction doesn't have an instance in IntAct
 * for that experiment.
 * </pre>
 *
 * @param psi the PSI data materialised as an Object.
 * @param intactInteraction an Intact Interaction.
 * @param experiments it reflects the collection of experiments linked to the PSI interaction and we will
 * update it in order to leave only those for which we need to create a new interaction.
 */

// this is in theory a pretty heavy computation but in practice an interaction rarely have many experiments

// and few interaction have a lot of components.

// compare two experiments using their shortlabel as they should be unique.

// they are the same ... check on the conponents

"They are equals ! Check on their participants..."

"Before intactComponent.getBindingDomains().size() = "

//WARNING : if we do not reload the Component using the helper, it does not find

// the feature on the component (intactComponent.getBindingDomains.size() return null)

// even if in the dabase the Component is associated to a Feature

// special case, a same protein can be bait and prey in the same interaction.

// Hence, we have to browse the whole intact Component set until we find the

// no need to carry on to check the psi component set because now, we know that

// there is already an instance of that interaction in intact

"All component(protein+role+feature) have been found, hence there "

"is an instance of that interaction in intact"

"and involving the following components: "

// TODO process the <confidence> tag here

How to use getCvComponentRolemethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.RoleChecker

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How to use
getCvComponentRole
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.RoleChecker