Public

getDefaultInteractionType

getDefaultInteractorTaxid

getInstance

hasDefaultInteractionType

hasDefaultInteractorTaxid

isGuiEnabled

reuseProtein

setDebugEnabled

setDefaultInteractionType

setDefaultInteractorTaxid

setGuiEnabled

setReuseExistingProtein

CommandLineOptions

Creating JSON documents from java classes using gson

Allows reading from and writing to a file in a random-access manner. This is
different from the uni-

java.io.RandomAccessFile

This class contains various methods for manipulating arrays (such as sorting and
searching). This cl

java.util.Arrays

A parser that parses a text string of primitive types and strings with the help
of regular expressio

java.util.Scanner

SortedSet is a Set which iterates over its elements in a sorted order. The order
is determined eithe

java.util.SortedSet

java.util.stream.Collectors

Factory for creating Log instances, with discovery and configuration features
similar to that employ

org.apache.commons.logging.LogFactory

getContentResolver

requestLocationUpdates

onCreateOptionsMenu

/**
     * @param proteinInteractor
     * @param proteinFactory
     * @param bioSourceFactory
     */

// if it has already been check, skip here.

// check that the CvInteractorType( interaction is available ).

/**
         * We have to deal with 3 different cases:
         *
         *  (1) the protein has a UniProt Xref in which case we use the UpdateProteins
         *      to do the job.
         *
         *  (2) The protein doesn't have a UniProt ID and we create it by hand using
         *      the data found in the XML file (Xrefs, Aliases, shorltabel, fullName)
         *
         *  (3) The protein doesn't have any Xrefs, we show an error message.
         */

"########## PROTEIN WITH NO UNIPROT ID ("

"Checking non UniProt protein's Xrefs ... "

// check the CvDatabases of the primary and secondary Xrefs

// TODO search in IntAct by primaryXref and BioSource !!! give Tag only if not found.

// only create the Protein is the CvDatabase of the primary Id is valid.

// a protein has been foudn in the database or created.

/**
             * -STATEGY-
             *
             * 2 cases: the user can have requested
             *              (1) to reuse existing protein in which case the UpdateProtein
             *                  is only called if the protein is not found in the IntAct node.
             *              (2) to force update, in which case the UpdateProteins is called
             *                  for every single ID in order to have up-to-date data.
             *
             * BEWARE: the uniprot ID given in the XML file can refer to either a protein or a splice variant
             *         and we link that ID to the relevant objects.
             */

/**
             * 1. retreive either protein or splice variant from IntAct
             *    getIntactObject( Object[2] prot_and_sv,  )
             *    1a. if something as been found, cache it and finish
             *    1b. if not, use UpdateProteins to get the data and search again.
             *
             * 2. do as in 1.
             *    2a. if found ok
             *    2b. if not, error.
             *
             *
             *
             * 1. details
             * ----------
             *
             * ID could be P12345 (Protein) or Q87264-2 (Splice variant)
             *
             * if (ID is splice variant) {
             *     search by shortlabel (lowercase(ID))
             *     get also the master protein using the xref to its AC.
             * } else {
             *    search by xref
             * }
             *
             */

// cache:  [uniprotID, taxid] -> [protein, spliceVariant] or [protein, null]

// if we ask for reuse of protein, and let's say a Protein A is already in IntAct but the entry

// in SRS has now 2 proteins (A and B). If no taxid is specified and reuseProtein requested, we might

// happily take A instead of throwing an error because of the existence of B that make the case ambiguous.

// Hence, reuse protein must be used only if taxid is not null !

// taxid is not null here so no exception can be thrown.

// we should never get here ! but just in case ...

// retreived by ID having different taxid

// always null if taxId == null or no reuseProtein requested.

"Protein not found in intact, updating..."

// there was exception during update, the proteins hasn't been updated.

" using UpdateProteins, a parsing error occured."

"============================================"

"Could not find Protein for uniprot ID: "

How to use reuseProteinmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.util.CommandLineOptions

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How to use
reuseProtein
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.util.CommandLineOptions