How to use
featureAreEquals
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister.featureAreEquals (Showing top 3 results out of 315)

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}

if ( featureAreEquals( intactComponent, psiComponent ) ) {

if ( featureAreEquals( intactComponent, psiComponent ) ) {

if ( featureAreEquals( intactComponent, psiComponent ) ) {

Javadoc

Assess if a IntAct Component's feature 'equals' a PSI definition.

algo sketch: 1. compare the features (all of them shoul dbe found identical to assess that the components are equals) 1.1. check feature type 1.2. check detection type 1.3. check the Range (IntAct) against Location (PSI)

Remark: in PSI version 1 a feature contains a single Location (Range in IntAct) although Intact's Feature ------ can have multiple Ranges, in order to map that we assume that if the user wants to store multiple Range into an IntAct's Feature he will add an Xref at the feature level, that xref id will be used to group multiple Location. Hence we can create from PSI a Feature having multiple Ranges. Hopefully, PSI version 2 fixes that problem and introduce the needed types.

Popular methods of InteractionPersister

alreadyExistsInIntact
Allows to check if the data carried by an InteractionTag are already existing in the IntAct node. R
areRangeEquals
compare two ranges.
createInteractionShortLabels
Create an interaction shortlabel out of two shortlabels. Take care about the maximum length of the
createShortlabel
Create an IntAct shortlabel for a given interaction (ie. a set of [protein, role] ). - Stategy - P
getGeneName
introspect a Protein object and pick up it's gene name. If it is not a UniProt protein, we use the
getLabelFromCollection
Search for the first string (in alphabetical order).
getProtein
Get an Intact Protein out of a ProteinInteractorTag.
getPsiID
Retreive (if any) the PSI ID (MI:xxxx) of a Controlled Vocabulary item.
persist
Persist the Interaction according to its PSI description. A Shortlabel is automatically generated b
searchIntactAnnotation
Search in IntAct for an Annotation having the a specific type and annotationText.

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How to use featureAreEqualsmethodin uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister

Best Java code snippets using uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister.featureAreEquals (Showing top 3 results out of 315)

How to use
featureAreEquals
method
in
uk.ac.ebi.intact.application.dataConversion.psiUpload.persister.InteractionPersister