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

Reading from database using SQL prepared statement

java.awt.image.Kernel

This exception is thrown when a timeout expired on a socket read or accept
operation.

java.net.SocketTimeoutException

This class is used to encode a string using the format required by
application/x-www-form-urlencoded

java.net.URLEncoder

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

java.util.Scanner

javax.swing.JButton

javax.swing.JLabel

onCreateOptionsMenu

addToBackStack

putExtra

/**
     * In case of Non uniprot protein, we check if it already exist in IntAct (based on biosource, primaryid and
     * CvDatabase) and if not we create it.
     *
     * @param proteinInteractor protein attributes.
     *
     * @return the created protein or null if it fails.
     */

//            System.out.println( ">>>>>>>>>>>" + proteins.size() + " protein found by Xref(" + proteinId + ")" );

// check that the Xref has the same CvDatabase.

//                    System.out.println( ">>>>>>>>>>> Protein: " + protein1.getAc() );

//                        System.out.println( ">>>>>>>>>>> Same BioSource" );

//                                System.out.println( ">>>>>>>>>>> Same Primary id" );

//                                    System.out.println( ">>>>>>>>>>> Same qualifier(identity)" );

//                                        System.out.println( ">>>>>>>>>>> Same CvDatabase" );

// more than one is an error that the user has to solve.

// that should never happen ... but who knows ...

"Could not find a unique instance of the protein having Biosource("

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

"Could not find a CvInteractorType by MI reference: "

"Could not find a BioSource using the definition: "

"Could not for the protein having Biosource("

How to use createXrefmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.checker.ProteinInteractorChecker

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

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