Public

getDefaultInteractionType

getDefaultInteractorTaxid

getInstance

hasDefaultInteractionType

hasDefaultInteractorTaxid

isGuiEnabled

reuseProtein

setDebugEnabled

setDefaultInteractionType

setDefaultInteractorTaxid

setGuiEnabled

setReuseExistingProtein

CommandLineOptions

Reactive rest calls using spring rest template

An input stream that reads bytes from a file.    
File file = ...finally  
if (in != null)  
in.clos

java.io.FileInputStream

A readable source of bytes.Most clients will use input streams that read data
from the file system (

java.io.InputStream

The abstract base class for all number formats. This class provides the
interface for formatting and

java.text.NumberFormat

HashSet is an implementation of a Set. All optional operations (adding and
removing) are supported. 

java.util.HashSet

A Handler object accepts a logging request and exports the desired messages to a
target, for example

java.util.logging.Handler

javax.swing.JFileChooser

requestLocationUpdates

addToBackStack

notifyDataSetChanged

/**
     * 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

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

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