Public

buildID

check

checkCvInteractorType

createXref

Remove from a collection of Protein all those that are not related to the given
taxid.

filterByTaxid

Get Protein from IntAct from its ID. If this is ID refers to (1) a protein, we
send back a Protein o

getIntactProtein

In case of Non uniprot protein, we check if it already exist in IntAct (based on
biosource, primaryi

getOrCreateNonUniprotProtein

getProtein

Check if the set of proteins is related to more than one biosource.

hasMultipleBioSource

Answer the question: is that protein a Splice Variant ? One (quick) way is to
check if the shortlabe

isSpliceVariant

ScheduledThreadPoolExecutor

Creating JSON documents from java classes using gson

An Internet Protocol (IP) address. This can be either an IPv4 address or an IPv6
address, and in pra

java.net.InetAddress

 KeyStore is responsible for maintaining cryptographic keys and their owners. 
The type of the syste

java.security.KeyStore

A plug-in replacement for JDK1.5 java.util.concurrent.ConcurrentHashMap. This
version is based on or

java.util.concurrent.ConcurrentHashMap

A synchronization aid that allows one or more threads to wait until a set of
operations being perfor

java.util.concurrent.CountDownLatch

javax.swing.JButton

This is the central class in the log4j package. Most logging operations, except
configuration, are d

org.apache.log4j.Logger

Return the contained value, if present, otherwise throw an exception to be
created by the provided s

orElseThrow

runOnUiThread

notifyDataSetChanged

/**
     * @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 getOrCreateNonUniprotProteinmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ProteinInteractorChecker

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ProteinInteractorChecker.getOrCreateNonUniprotProtein (Showing top 3 results out of 315)

How to use
getOrCreateNonUniprotProtein
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ProteinInteractorChecker