Public

<init>

addMessage

createElement

createTextNode

Declare in the session that the given protein has been already converted in XML.

declareAlreadyDefined

Load all CvTopic and check which one have been flagged 'obsolete'. Those CvTopic
are automatically a

filterObsoleteAnnotationTopic

Return the availabilityList element under the entry of the PSI document. If the
element doesn't exis

getAvailabilityListElement

getCvObjectCache

Return the entry element of the PSI document. If the element doesn't exist, it
is created.

getEntryElement

Get a specific identifier for the given experiemnt. If an identifier had already
been affected for t

getExperimentIdentifier

Return the experimentList element under the entry of the PSI document. If the
element doesn't exist,

getExperimentListElement

Get a specific identifier for the given feature. If an identifier had already
been affected for that

getFeatureIdentifier

getHostOrganismCache

Get a specific identifier for the given interaction. If an identifier had
already been affected for 

getInteractionIdentifier

Return the interactionList element under the entry of the PSI document. If the
element doesn't exist

getInteractionListElement

Get a specific identifier for the given interactor. If an identifier had already
been affected for t

getInteractorIdentifier

Return the interactorList element under the entry of the PSI document. If the
element doesn't exist,

getInteractorListElement

getMessages

return the current cluster ID suffix and increment it by 1.

getNextClusterIdSuffix

Return the next unique identifier required by most PSI-MI objects

getNextObjectIdentifier

UserSessionDownload

Running tasks concurrently on multiple threads

Abstract class for representing access to a system resource. All permissions
have a name (whose inte

java.security.Permission

This class generates cryptographically secure pseudo-random numbers. It is best
to invoke SecureRand

java.security.SecureRandom

Hash table and linked list implementation of the Map interface, with predictable
iteration order. Th

java.util.LinkedHashMap

javax.swing.JComboBox

Operations on java.lang.String that arenull safe.

 * IsEmpty/IsBlank - checks if a String contains 

org.apache.commons.lang.StringUtils

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

onRequestPermissionsResult

putExtra

requestLocationUpdates

/**
     * 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 printMessageReportmethodin uk.ac.ebi.intact.application.dataConversion.psiDownload.UserSessionDownload

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How to use
printMessageReport
method
in
uk.ac.ebi.intact.application.dataConversion.psiDownload.UserSessionDownload