Public

getDefaultInteractionType

getDefaultInteractorTaxid

getInstance

hasDefaultInteractionType

hasDefaultInteractorTaxid

isGuiEnabled

reuseProtein

setDebugEnabled

setDefaultInteractionType

setDefaultInteractorTaxid

setGuiEnabled

setReuseExistingProtein

CommandLineOptions

Reading from database using SQL prepared statement

A FileInputStream obtains input bytes from a file in a file system. What files
are available depends

java.io.FileInputStream

A writable sink for bytes.Most clients will use output streams that write data
to the file system ( 

java.io.OutputStream

This class represents proxy server settings. A created instance of Proxy stores
a type and an addres

java.net.Proxy

 Collection is the root of the collection hierarchy. It defines operations on
data collections and t

java.util.Collection

Doubly-linked list implementation of the List and Dequeinterfaces. Implements
all optional list oper

java.util.LinkedList

Encapsulate an XML parse error or warning.This exception may include information
for locating the er

org.xml.sax.SAXParseException

getSystemService

runOnUiThread

getApplicationContext

/**
     * 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 getDefaultInteractorTaxidmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.util.CommandLineOptions

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