Public

Allows to check if the data carried by an InteractionTag are already existing in
the IntAct node. 
R

alreadyExistsInIntact

areRangeEquals

Create an interaction shortlabel out of two shortlabels. 
Take care about the maximum length of the 

createInteractionShortLabels

Create an IntAct shortlabel for a given interaction (ie. a set of [protein,
role] ). - Stategy -

 P

createShortlabel

Assess if a IntAct Component's feature 'equals' a PSI definition. 
algo sketch: 
1. compare the feat

featureAreEquals

introspect a Protein object and pick up it's gene name. 
If it is not a UniProt protein, we use the 

getGeneName

Search for the first string (in alphabetical order).

getLabelFromCollection

Get an Intact Protein out of a ProteinInteractorTag.

getProtein

Retreive (if any) the PSI ID (MI:xxxx) of a Controlled Vocabulary item.

getPsiID

Persist the Interaction according to its PSI description. 
A Shortlabel is automatically generated b

persist

Search in IntAct for an Annotation having the a specific type and
annotationText.

searchIntactAnnotation

ScheduledThreadPoolExecutor

Creating JSON documents from java classes using gson

Formats or parses dates and times.This class provides factories for obtaining
instances configured f

java.text.DateFormat

Formats and parses dates in a locale-sensitive manner. Formatting turns a Date
into a String, and pa

java.text.SimpleDateFormat

 Calendar is an abstract base class for converting between a Date object and a
set of integer fields

java.util.Calendar

A Set that further provides a total ordering on its elements. The elements are
ordered using their C

java.util.SortedSet

A reentrant mutual exclusion Lock with the same basic behavior and semantics as
the implicit monitor

java.util.concurrent.locks.ReentrantLock

The exception that is thrown when a handshake could not be completed
successfully.

javax.net.ssl.SSLHandshakeException

scheduleAtFixedRate

runOnUiThread

putExtra

/**
 * Create an IntAct shortlabel for a given interaction (ie. a set of [protein, role] ).
 * 
 * - Stategy -
 * 
 * Protein's role can be either: bait, prey or neutral the interaction shortlabel has the following patter: X-Y-Z
 * with a limit in length of 20 caracters. TODO: do not hard code that ! Could be fetched from the
 * DatabaseInspector.
 * 
 * X is (in order of preference): 1. the gene name of the bait protein 2. the gene name of a prey protein (the first
 * one in alphabetical order) 3. the gene name of a neutral protein (the first one in alphabetical order)
 * 
 * Y is : 1. the gene name of a prey protein (the first one in alphabetical order or second if the first has been
 * used already) 2. the gene name of a neutral protein (the first one in alphabetical order or second if the first
 * has been used already) Z is : an Integer that gives the number of occurence in intact.
 * 
 * eg. 1. bait(baaa), prey(paaa, pbbb, pccc), neutral(naaa) should gives us: baaa-paaa-1
 * 
 * 2. bait(baaa), prey(), neutral(naaa) should gives us: baaa-naaa-1
 * 
 * 3. bait(), prey(paaa, pbbb, pccc), neutral(naaa) should gives us: paaa-pbbb-1
 * 
 * 4. bait(), prey(paaa), neutral(naaa) should gives us: paaa-naaa-1
 *
 * @param interaction
 *
 * @throws IntactException
 */

/**
         * Search for a gene name in the set, if none exist, take the protein ID.
         */

// the gene name is held in the master protein, not the splice variant.

// TODO load default CVs via MI reference and use the CvObject.equals() !!!!

// most numerous role, cut down the number of test

// we have changed the name of that CV, from neutral to 'neutral component'

// for the time being allow both ... PSI 1.0 allow only neutral

// TODO program a switch, if the database contain only 'neutral component'

// we should never get in here if RoleChecker plays its role !

" which is not supported at the moment ("

"so far only bait, prey and 'neutral component' are). abort."

// we can have either 1..n bait with 1..n prey

// if more than 2 components, get one and add the cound of others.

// that updates the experiment collection and only leaves those for which we have to create a new interaction

How to use getGeneNamemethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister

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How to use
getGeneName
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister