Public

<init>

equals

getOrganism

getPrimaryXref

getSecondaryXrefs

getSequence

getShortlabel

hasUniProtXref

hashCode

ProteinInteractorTag

Creating JSON documents from java classes using gson

A Window object is a top-level window with no borders and no menubar. The
default layout for a windo

java.awt.Window

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

java.net.URLEncoder

A Set is a data structure which does not allow duplicate elements.

java.util.Set

This class provides access to implementations of cryptographic ciphers for
encryption and decryption

javax.crypto.Cipher

javax.naming.Reference

Defines methods that all servlets must implement. A servlet is a small Java
program that runs within

javax.servlet.Servlet

onCreateOptionsMenu

findViewById

getExternalFilesDir

/**
     * introspect a Protein object and pick up it's gene name. <br> If it is not a UniProt protein, we use the
     * shortlabel instead.
     *
     * @param proteinHolder container holding either a UniProt protein of an XML definition of the protein.
     *
     * @return the Protein's gene name.
     */

// if the protein is NOT a UniProt one, then use the shortlabel as we won't get a gene name.

// the gene name we want to extract from the protein.

// remove any _organism in case it exists

" does not have a gene name, we will use it's SPTR ID: "

/**
     * 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 getShortlabelmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinInteractorTag

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinInteractorTag.getShortlabel (Showing top 6 results out of 315)

How to use
getShortlabel
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.model.ProteinInteractorTag