Public

check

getCvComponentRole

getCvExperimentalRole

getDefaultCvBiologicalRole

Gson

Creating JSON documents from java classes using gson

Thrown when a program encounters the end of a file or stream during an input
operation.

java.io.EOFException

Wraps either an existing OutputStream or an existing Writerand provides
convenience methods for prin

java.io.PrintWriter

java.security.Permission

A concrete subclass of NumberFormat that formats decimal numbers. It has a
variety of features desig

java.text.DecimalFormat

This class provides access to implementations of cryptographic ciphers for
encryption and decryption

javax.crypto.Cipher

Factory that creates instances of DateTimeFormatter from patterns and styles. 
Datetime formatting i

org.joda.time.format.DateTimeFormat

startActivity

notifyDataSetChanged

scheduleAtFixedRate

/**
 * 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