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/**
 * Search for the first string (in alphabetical order).
 *
 * @param geneNames a collection of non ordered gene names.
 * @param failOnError if <code>true</code> throw an IntactException when no gene name is found, if
 * <code>false</code> sends back <code>null</code>.
 *
 * @return either a String or null according to the failOnError parameter.
 *
 * @throws IntactException thrown when the failOnError parameter is true and no string can be returned.
 * @see uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister.GeneNameIgnoreCaseComparator
 */

"You must give a non null collection of gene name."

// This should have been detected during step 1 or 2.

"Could not find gene name for that interaction."

/**
 * 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 useInteractionPersister$GeneNameIgnoreCaseComparator in uk.ac.ebi.intact.application.dataConversion.psiUpload.persister

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