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

Start an intent from android

Wraps an existing Reader and buffers the input. Expensive interaction with the
underlying reader is 

java.io.BufferedReader

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

java.io.FileInputStream

An interface for an object which represents a database table entry, returned as
the result of the qu

java.sql.ResultSet

The BitSet class implements abit array [http://en.wikipedia.org/wiki/Bit_array].
Each element is eit

java.util.BitSet

This class provides methods that return pseudo-random values.It is dangerous to
seed Random with the

java.util.Random

Used to perform Get operations on a single row. To get everything for a row,
instantiate a Get objec

org.apache.hadoop.hbase.client.Get

getSystemService

requestLocationUpdates

scheduleAtFixedRate

// Need to process the big ones chunk by chunk -

// do this by splitting the Interactions into manageable pieces (LARGE_SCALE_CHUNK_SIZE each),

// then building and writing some XML to seperate files....

// filename in which the chunk will be saved

"generating Interaction files for experiment "

// create the session, and if required, set a CV mapping.

// in order to have them in that order, experimentList, then interactorList, at last interactionList.

//now build the XML and generate a file for it...

//add a leading zero to the chunk count and use the fileName

//if it is given - otherwise use the shortlabel

// we look for the suffix .xml otherwise if a directory has a . in its name we would truncate there.

//This will only NOT be a List if someone changes the model

"the Collection of Interactions must be a List but is instead "

/**
     * Generates a PSI MI formatted file for a searchPattern. Large scale Experiments will typically be a searchpattern
     * of a single shortlabel, and these are processed as chunks. Small scale ones will generally have a searchpattern
     * consisting of multiple shortlabels, and these will be placed into a single file.
     *
     * @param searchPattern a comma separated list of experiment's shortlabel.
     * @param fileName      the file in which we will store the generated XML.
     * @param version       the PSI version of the generated XML output.
     *
     * @throws Exception
     */

//get all of the Experiment shortlabels and process them according

//to the size of their interaction list..

//NB this currently means that if the search result size

//is one and the number of interactions is large then we process seperately.

//may be a large experiment - check and process if necessary

//not a large experiment - may be a single small one or a set of small ones,

//so process 'normally' into a single file...

// When generating psi1 xml files, we remove all the interactions having a Nucleic Acid as participant

// we can end up in having a psiDocument containing no experimentList tag as all the Experiments where

// only composed of interactions having Nucleic Acid as Participants. In this case we don't want to print

// out and xml file without any experimentList tag, therefore we do this check on the count of experimentList

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

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