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

Start an intent from android

This class represents proxy server settings. A created instance of Proxy stores
a type and an addres

java.net.Proxy

ArrayList is an implementation of List, backed by an array. All optional
operations including adding

java.util.ArrayList

Note: Do not use this class since it is obsolete. Please use the Map interface
for new implementatio

java.util.Dictionary

An int value that may be updated atomically. See the java.util.concurrent.atomic
package specificati

java.util.concurrent.atomic.AtomicInteger

javax.swing.JFileChooser

org.openjdk.jmh.runner.Runner

compareTo

getResourceAsStream

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 getLabelFromCollectionmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister

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