Public

displayUsage

It take an interactions Collection and remove from it all the interactions
having a NucleicAcid as c

filterInteractions

Convert a list of experiment into PSI XML

generateData

Generates a PSI MI formatted file for a searchPattern. Large scale Experiments
will typically be a s

generatePsiData

Obtains the data from the dataSource, in preparation for the flat file
generation.

getExperiments

processLargeExperiment

setupCommandLineOptions

Write an Element (supposingly the root of a document) into a file.

write

Gson

Reading from database using SQL prepared statement

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

java.net.URLEncoder

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

java.sql.Date

A NavigableSet implementation based on a TreeMap. The elements are ordered using
their Comparable, o

java.util.TreeSet

An Executor that provides methods to manage termination and methods that can
produce a Future for tr

java.util.concurrent.ExecutorService

javax.swing.JCheckBox

 This is the main interface of a Quartz Scheduler.

 A Scheduler maintains a registery of org.quartz

org.quartz.Scheduler

setContentView

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

getOriginalFilename

getSharedPreferences

/**
     * Main method for the PSI application. The application is typically run twice - firstly with a wildcard ('%')
     * argument to generate a file containing classifications into species of experiment labels, then secondly to use
     * that file to generate the PSI XML data for each classification. This second step is handled via a perl script
     * which repeatedly calls this application to generate the files. Note that the exceptions to the species
     * classification are large-scale experiments (as defined by the SMALLSCALELIMIIT constant) - these cannot be put
     * into XML files with other experiments due to size and memory constraints, and so they are generated in 'chunks'
     * of data divided by 'chunks' of interactions.
     *
     * @param args
     *
     * @throws Exception
     */

"The given file doesn't exist. ignore it."

"The given file is not readable. ignore it."

"You must provide the filename of the PSI file to generate."

// Check and create all missing parent directory.

// check that all parent directory exist in the given filename

// 2. replace all slash by plateform specific file separator (if necessary)

// 3. make sure that the parent directories exists before to create the file.

"Total time to build and generate file: "

How to use displayUsagemethodin uk.ac.ebi.intact.application.dataConversion.FileGenerator

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