Public

getDefaultInteractionType

getDefaultInteractorTaxid

getInstance

hasDefaultInteractionType

hasDefaultInteractorTaxid

isGuiEnabled

reuseProtein

setDebugEnabled

setDefaultInteractionType

setDefaultInteractorTaxid

setGuiEnabled

setReuseExistingProtein

CommandLineOptions

Updating database using SQL prepared statement

A Rectangle specifies an area in a coordinate space that is enclosed by the 
Rectangle object's top-

java.awt.Rectangle

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

java.net.URLEncoder

A TimeUnit represents time durations at a given unit of granularity and provides
utility methods to 

java.util.concurrent.TimeUnit

Defines the contract between a returned instance and the runtime when an
application needs to provid

javax.ws.rs.core.Response

Factory for creating Log instances, with discovery and configuration features
similar to that employ

org.apache.commons.logging.LogFactory

org.hibernate.mapping.Table

getContentResolver

setRequestProperty

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