Public

getDefaultInteractionType

getDefaultInteractorTaxid

getInstance

hasDefaultInteractionType

hasDefaultInteractorTaxid

isGuiEnabled

reuseProtein

setDebugEnabled

setDefaultInteractionType

setDefaultInteractorTaxid

setGuiEnabled

setReuseExistingProtein

CommandLineOptions

Running tasks concurrently on multiple threads

A component is an object having a graphical representation that can be displayed
on the screen and t

java.awt.Component

A Locale object represents a specific geographical, political, or cultural
region. An operation that

java.util.Locale

The Vector class implements a growable array of objects. Like an array, it
contains components that 

java.util.Vector

Provides Base64 encoding and decoding as defined by RFC 2045.This class
implements section 6.8. Base

org.apache.commons.codec.binary.Base64

General file manipulation utilities. Facilities are provided in the following
areas: * writing to a 

org.apache.commons.io.FileUtils

Used to perform Get operations on a single row. To get everything for a row,
instantiate a Get objec

org.apache.hadoop.hbase.client.Get

Return the original filename in the client's filesystem.This may contain path
information depending 

getOriginalFilename

runOnUiThread

getSharedPreferences

/**
     * Extract data from a <code>proteinInteractor</code> Element and produce an Intact <code>Protein</code>
     * <p/>
     * <pre>
     *  &lt;proteinInteractor id="hGHR"&gt;
     *      &lt;names&gt;
     *         &lt;shortLabel&gt;hGHR&lt;/shortLabel&gt;
     *         &lt;fullName&gt;Human growth hormone receptor&lt;/fullName&gt;
     *      &lt;/names&gt;
     *      &lt;xref&gt;
     *         &lt;primaryRef db="Swiss-Prot" id="P10912"/&gt;
     *      &lt;/xref&gt;
     *      &lt;organism ncbiTaxId="9606"&gt;
     *         &lt;names&gt;
     *            &lt;shortLabel&gt;Human&lt;/shortLabel&gt;
     *            &lt;fullName&gt;Homo sapiens&lt;/fullName&gt;
     *         &lt;/names&gt;
     *      &lt;/organism&gt;
     *      &lt;sequence&gt;MDLWQLLLTLALAGSSDAFSGSEATAAILSRAPWSLQSVNPGLKTNSSKEPKFTKCRSPERETFSCHWTDEVHHGTKNLGPIQLFYTRRNTQEWTQEWKECPDYVSAGENSCYFNSSFTSIWIPYCIKLTSNGGTVDEKCFSVDEIVQPDPPIALNWTLLNVSLTGIHADIQVRWEAPRNADIQKGWMVLEYELQYKEVNETKWKMMDPILTTSVPVYSLKVDKEYEVRVRSKQRNSGNYGEFSEVLYVTLPQMSQFTCEEDFYFPWLLIIIFGIFGLTVMLFVFLFSKQQRIKMLILPPVPVPKIKGIDPDLLKEGKLEEVNTILAIHDSYKPEFHSDDSWVEFIELDIDEPDEKTEESDTDRLLSSDHEKSHSNLGVKDGDSGRTSCCEPDILETDFNANDIHEGTSEVAQPQRLKGEADLLCLDQKNQNNSPYHDACPATQQPSVIQAEKNKPQPLPTEGAESTHQAAHIQLSNPSSLSNIDFYAQVSDITPAGSVVLSPGQKNKAGMSQCDMHPEMVSLCQENFLMDNAYFCEADAKKCIPVAPHIKVESHIQPSLNQEDIYITTESLTTAAGRPGTGEHVPGSEMPVPDYTSIHIVQSPQGLILNATALPLPDKEFLSSCGYVSTDQLNKIMP&lt;/sequence&gt;
     *  &lt;/proteinInteractor&gt;
     * </pre>
     *
     * @return an intact <code>Protein</code> or null if something goes wrong.
     *
     * @see uk.ac.ebi.intact.model.Protein
     */

// check if the proteinInteractor is existing in the global context

"The global definition will be used instead."

// the PSI file lacks a taxid, check if the user requested us to put a default value in such case.

// TODO we could optimize by checking if the primaryRef is UniProt, if so we can shortcut the data loading

// CAUTION - if names present, IT MAY NOT BE THERE

// Will contain the map: id ---> Protein definition

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

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