Public

Allows to check if the data carried by an InteractionTag are already existing in
the IntAct node. 
R

alreadyExistsInIntact

areRangeEquals

Create an interaction shortlabel out of two shortlabels. 
Take care about the maximum length of the 

createInteractionShortLabels

Create an IntAct shortlabel for a given interaction (ie. a set of [protein,
role] ). - Stategy -

 P

createShortlabel

Assess if a IntAct Component's feature 'equals' a PSI definition. 
algo sketch: 
1. compare the feat

featureAreEquals

introspect a Protein object and pick up it's gene name. 
If it is not a UniProt protein, we use the 

getGeneName

Search for the first string (in alphabetical order).

getLabelFromCollection

Get an Intact Protein out of a ProteinInteractorTag.

getProtein

Retreive (if any) the PSI ID (MI:xxxx) of a Controlled Vocabulary item.

getPsiID

Persist the Interaction according to its PSI description. 
A Shortlabel is automatically generated b

persist

Search in IntAct for an Annotation having the a specific type and
annotationText.

searchIntactAnnotation

ScheduledThreadPoolExecutor

Making http post requests using okhttp

A file output stream is an output stream for writing data to aFile or to a 
FileDescriptor. Whether 

java.io.FileOutputStream

The Dictionary class is the abstract parent of any class, such as Hashtable,
which maps keys to valu

java.util.Dictionary

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

java.util.LinkedHashMap

Doubly-linked list implementation of the List and Dequeinterfaces. Implements
all optional list oper

java.util.LinkedList

Thrown when trying to retrieve an element past the end of an Enumeration or
Iterator.

java.util.NoSuchElementException

org.hibernate.mapping.Join

findViewById

startActivity

requestLocationUpdates

/**
     * Assess if a IntAct Component's feature 'equals' a PSI definition.
     * <p/>
     * <pre>
     * 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)
     * <p/>
     * 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.
     * <p/>
     * </pre>
     *
     * @param intactComponent an IntAct Component to compare with a PSI definition.
     * @param psiComponent    a PSI definition of a Component.
     *
     * @return true if the PSI definition reflects the content of the given component, otherwise false.
     */

// TODO when reading the PSI XML we could already load the FeatureTag with multiple Location based on the xref.id

// Component and proteinParticipant are different as soon as we discover one difference

// group PSI feature in order to reflect the relationship 1 feature -> 0..n Ranges

"\tAfter clustering, they don't have the same count of features"

"\tAfter clustering, they have the same count of features"

// now check that for each PSI cluster, there is one intact feature with the same Ranges.

// Check all PSI feature can be found in a single intact Feature (incl. Range Vs Location)

// We leave the loop as soon as one of them is not found.

"\t\tSelect an intact feature, shortlabel="

// Compare count of PSI Location and IntAct Range

"\t\tTheir count of range/Location is different, skip."

"\t\tTheir count of range/Location is identical, compare them."

// we have the same number of locations/ranges

// allow to leave the loop if one difference is found.

// Compare featureType, via MI reference (mandatory attribute in IntAct and PSI)

// this only works is the check step has been done before !!

// Compare featureIdentification, via MI reference (not mandatory in IntAct and PSI)

// The PSI feature doesn't have a feature detection

// TODO should we check as well the Xref of the Features ?

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

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