Public

addToList

Classify experiments matching searchPattern into a data structure according to
species and experimen

classifyExperiments

Checks for a negative interaction. NB This will have to be done using SQL
otherwise we end up materi

classifyNegatives

createExpListItems

createExperimentListItems

Build the classification by dataset.
We keep the negative experiment separated from the non negative

createItemClassificationByDataset

Build the classification by pubmed id.
We keep the negative experiment separated from the non negati

createItemClassificationByPubmed

createItemClassificationBySpecies

generateClassificationByPublications

generateClassificationBySpecies

Given a set of Experiments, it returns the year of the date of creation of the
oldest experiment.

getCreatedYear

getDaoFactory

Fetch dataset information (if any) from experiment.

getDatasets

getExperiments

getFilteredExperimentAcs

getNegativeExperiments

Fetch publication primaryId from experiment.

getPubmedId

Retreive BioSources corresponding ot the target-species assigned to the given
experiment.

getTargetSpecies

interactionsForExperiment

Answers the following question: "Is the given shortlabel refering to a negative
experiment ?".

isNegative

OutputStreamWriter

Running tasks concurrently on multiple threads

The Font class represents fonts, which are used to render text in a visible way.
A font provides the

java.awt.Font

An "abstract" representation of a file system entity identified by a pathname.
The pathname may be a

java.io.File

Allows reading from and writing to a file in a random-access manner. This is
different from the uni-

java.io.RandomAccessFile

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

java.security.Permission

A compiled representation of a regular expression. A regular expression,
specified as a string, must

java.util.regex.Pattern

Main entry-point into the library.

Options represents a collection of Option objects, which describ

org.apache.commons.cli.Options

notifyDataSetChanged

runOnUiThread

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

getOriginalFilename

/**
     * Classify experiments matching searchPattern into a data structure according to species and experiment size.
     *
     * @return HashMap of HashMap of ArrayLists of Experiments: {species}{scale}[n]
     *
     * @throws uk.ac.ebi.intact.business.IntactException
     *
     */

// TODO separate classification - one method per type of classification !

// Obtain data, probably experiment by experiment, build

// PSI data for it then write it to a file....

// Split the list of experiments into species- and size-specific files

// Skip empty experiments and give a warning about'em

// 1. Get the species of one of the interactors of the experiment.

//    The bioSource of the Experiment is irrelevant, as it may be an auxiliary experimental system.

"ERROR: Experiment without target-species: "

// 3. create the classification by publication

// add the experiment to the set of experiments.

"ERROR: Could not find a pubmed ID for experiment: "

// if multiple target-species have been found, that experiment will be associated redundantly

// to each BioSource. only the publication classification is non redundant.

// not yet in the structure, create an entry

//    The classification is as follow: datasets/pmid.xml contains the list of corresponding experiments.

"ERROR: PubMed id was null when classifying experiment '"

"PubMed id was null when classifying experiment '"

How to use getPubmedIdmethodin uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator.getPubmedId (Showing top 3 results out of 315)

How to use
getPubmedId
method
in
uk.ac.ebi.intact.application.dataConversion.ExperimentListGenerator