Public

<init>

getExperiment

getShortlabel

hasShortlabel

setShortlabel

InteractionPersister$ExperimentWrapper

Reading from database using SQL prepared statement

ObjectMapper provides functionality for reading and writing JSON, either to and
from basic POJOs (Pl

com.fasterxml.jackson.databind.ObjectMapper

The Color class is used to encapsulate colors in the default sRGB color space or
colors in arbitrary

java.awt.Color

A flow layout arranges components in a left-to-right flow, much like lines of
text in a paragraph. F

java.awt.FlowLayout

A Rectangle specifies an area in a coordinate space that is enclosed by the 
Rectangle object's top-

java.awt.Rectangle

A Map is a data structure consisting of a set of keys and values in which each
key is mapped to a si

java.util.Map

The annotation structure.An instance of this class is returned bygetAnnotations() in AnnotationsAttr

javassist.bytecode.annotation.Annotation

setScale

setContentView

getSupportFragmentManager

/**
 * Persist the Interaction according to its PSI description. A Shortlabel is automatically generated based on
 * the gene names of the participant, if no gene name are available we use the protein AC. An Interaction
 * can be linked to multiple experiment in PSI, we do take it into account and we manages cases where an interaction
 * already exists, attached to one Experiment (let's call it E1) and the same interaction is also declared in the
 * PSI file as interacting in E1 and E2, in which case we just create an extra interaction and link it to E2. 
 * So far, we do not automatically link several Experiment to a single Interaction using the PSI loader. 
 *
 * @param interactionTag the PSI definition of the Interaction
 *
 * @return the collection of created IntAct Interaction.
 *
 * @throws IntactException if an error occurs while persisting the data in IntAct.
 */

// that updates the experiment collection and only leaves those for which we have to create a new interaction

// LOOP HERE OVER THE RESULT COLLECTION(shortlabel, experiment)

/* Components
            * The way to create an Interaction is NOT TRIVIAL: we have firstly to create an
            * Interaction Object with an empty collection of Component. and Then we have to
            * use the interaction.addComponent( Component c ) to fill it up.
            */

// check if there is a Kd value available

// search for an annotation to re-use, instead of creating a new one.

// doesn't exist, then create a new Annotation

// no need for an else, the additional annotation topic have been controlled by the checker.

// TODO clean that thing. Right now we are most of the time stuffing the author confidence as annotation

// TODO look after that unit parameter, we might have to adapt the CvTopic accordingly later.

// check if that annotation could not be shared.

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uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister$ExperimentWrapper
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