\HeaderA{interactionEntry-class}{Class "interactionEntry"}{interactionEntry.Rdash.class}
\aliasA{bait,interactionEntry-method}{interactionEntry-class}{bait,interactionEntry.Rdash.method}
\aliasA{interactions,interactionEntry-method}{interactionEntry-class}{interactions,interactionEntry.Rdash.method}
\aliasA{interactors,interactionEntry-method}{interactionEntry-class}{interactors,interactionEntry.Rdash.method}
\aliasA{organismName,interactionEntry-method}{interactionEntry-class}{organismName,interactionEntry.Rdash.method}
\aliasA{prey,interactionEntry-method}{interactionEntry-class}{prey,interactionEntry.Rdash.method}
\aliasA{releaseDate,interactionEntry-method}{interactionEntry-class}{releaseDate,interactionEntry.Rdash.method}
\aliasA{show,interactionEntry-method}{interactionEntry-class}{show,interactionEntry.Rdash.method}
\aliasA{taxId,interactionEntry-method}{interactionEntry-class}{taxId,interactionEntry.Rdash.method}
\keyword{models}{interactionEntry-class}
\begin{Description}\relax
A class representing the interaction data extracted from an IntAct data file
in PSI-MI 2.5 format.
\end{Description}
\begin{Section}{Objects from the Class}
Objects are usually created by \code{psi25interaction}.
\end{Section}
\begin{Section}{Slots}
\describe{
\item[\code{releaseDate}:] character, release date of the data entry, 
recorded in the \code{entry} element of the XML file.
\item[\code{organismName}:] character, the unique organism name(s) of
the interactors.
\item[\code{taxId}:] character, the unique NCBI taxonomy ID(s) of
the interactors.
\item[\code{interactors}:] matrix, Each row represents one interactor. IntAct
IDs are used as row names. Each column represents one annotation. 
Annotations include: UniProt ID, gene symbol, full name, locus name, ORF name,
organism name, and NCBI taxonomy ID.
\item[\code{interactiones}:] list, a list of \code{intactInteraction} objects, 
each represents one interaction. 
}
\end{Section}
\begin{Section}{Methods}
\describe{
\item[show] \code{signature(object = "interactionEntry")}: a print method
\item[bait] \code{signature(object = "interactionEntry")}: a method to find all the
baits within the interactionEntry and print them
\item[prey] \code{signature(object = "interactionEntry")}: a method to find all the 
prey within the interactionEntry and print them
\item[interactions] \code{signature(object = "interactionEntry")}: a method to find
all the interactions within the interactionEntry and print them
\item[interactors] \code{signature(object = "interactionEntry")}: a method to find 
all the interactors within the interactionEntry and print them

\item[organismName] \code{signature(object = "interactionEntry")}: a method to print
all the unique organism names that are of the interactors 
\item[taxId] \code{signature(object = "interactionEntry")}: a method to print
each taxonomy id for each organism
\item[releaseDate] \code{signature(object = "interactionEntry")}: a method to print 
the updated release date of the PSI-MI 2.5 XML file; it serves as a proxy for versioning.
}
\end{Section}
\begin{Author}\relax
Nianhua Li
\end{Author}
\begin{References}\relax
The IntAct Database: \url{http://www.ebi.ac.uk/intact/site/contents/downloads.jsf}.
\end{References}
\begin{SeeAlso}\relax
\code{\LinkA{intactInteraction-class}{intactInteraction.Rdash.class}}, \code{\LinkA{psi25interaction}{psi25interaction}}
\end{SeeAlso}

