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getExperiment

getShortlabel

hasShortlabel

setShortlabel

InteractionPersister$ExperimentWrapper

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/**
     * Create an interaction shortlabel out of two shortlabels. <br> Take care about the maximum length of the field.
     * <br> It checks as well if the generated shortlabel as already been associated to an other Interaction.
     *
     * @param psiInteraction The interaction we are investigating on.
     * @param experiments    Collection in which after processing we have all ExperimentWrapper (shortlabel +
     *                       experimentDescription) in which the interaction hasn't been created yet.
     * @param bait           the label for the bait (could be gene name or SPTR entry AC)
     * @param prey           the label for the prey (could be gene name or SPTR entry AC)
     */

// convert bad characters ('-', ' ', '.') to '_'

// check out the curation rules to know how to create an interaction shortlabel.

// http://www3.ebi.ac.uk/internal/seqdb/curators/intact/Intactcurationrules_000.htm

// if so, remove one character from the longest between bait and prey ... until the length is right.

// truncate, remove last charachter (from bait)

// truncate, remove last charachter (from prey)

// we have the right label's size now ... search for existing one !

// Give the remaining experiment a shortlabel.

// takes care of gaps in the shortlabel sequence (label-1, label-2, label-3 ...).

// could create new gaps if some already exists.

// we want to associate only one shortlabel per loop and check if there is at least one

"At least one more experiment to which we have to give a shortlabel"

" has been given the interaction shortlabel: "

"none has been set up to now and the current one has already a shortlabel"

"All experiment have been given an interaction shortlabel."

/**
                 * An interaction already exists in an experiment if:
                 *       (1) The shortlabel has the prefix bait-prey
                 *       (2) if components involved (Protein + Role) are identical.
                 *           If the components are somehow different, a new Interaction should be created
                 *           with the same prefix and a suffix that is not already in use.
                 *           eg.
                 *                We have 3 Proteins:
                 *                    - P1: gene-name -> gene1
                 *                    - P1-1: gene-name -> gene1 (got from P1)
                 *                    - P2: gene-name -> gene2
                 *
                 *                We have 2 interactions
                 *                    - Interaction 1 have interaction between P1(bait) and P2(prey)
                 *                      gives us the shortlabel gene1-gene2-1
                 *                    - Interaction 1 have interaction between P1-1(bait) and P2(prey)
                 *                      gives us the shortlabel gene1-gene2-2
                 *                      (!) the components involved are different even if the gene name are identical
                 *                          hence, we get same interaction name with suffixes 1 and 2.
                 */

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

How to use setShortlabelmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister$ExperimentWrapper

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