Public

getDefaultInteractionType

getDefaultInteractorTaxid

getInstance

hasDefaultInteractionType

hasDefaultInteractorTaxid

isGuiEnabled

reuseProtein

setDebugEnabled

setDefaultInteractionType

setDefaultInteractorTaxid

setGuiEnabled

setReuseExistingProtein

CommandLineOptions

Making http post requests using okhttp

A specialized Writer that writes to a file in the file system. All write
requests made by calling me

java.io.FileWriter

Uses a one-way hash function to turn an arbitrary number of bytes into a
fixed-length byte sequence.

java.security.MessageDigest

A class which can consume and produce dates in SQL Date format. Dates are
represented in SQL as yyyy

java.sql.Date

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

java.util.LinkedList

SortedSet is a Set which iterates over its elements in a sorted order. The order
is determined eithe

java.util.SortedSet

javax.swing.JPanel

getSystemService

scheduleAtFixedRate

onRequestPermissionsResult

/**
     * 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

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.util.CommandLineOptions.hasDefaultInteractorTaxid (Showing top 3 results out of 315)

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