add annotation mapping for SummarizedExperiment and subclasses

[axelklenk]

This PR adds annotation mapping for SummarizedExperiment data containers and its subclasses SingleCellExperiment and SpatialExperiment.

This will work if gene sets are stored in a GeneSetCollection with geneIdType set to a valid value e.g. by importing them using GSEABase::getGmt() or GSVA::readGMT(). The container classes above need an geneIdType with an OrgDb as its annotation() set as the annotation element of their metadata, e.g.

metadata(sce)$annotation <- ENSEMBLIdentifier("org.Hs.eg.db")

and any gene set IDs supported by org.Hs.eg.db will be automatically converted to ENSEMBL IDs.

Annotation mapping for Biobase::ExpressionSet containers has been verified to continue working where annotation(ES) is not a geneIdType but only a character containing the name of the annotation database package.

Annotation mapping for simpler container types such as matrix or dgCMatrix or with gene sets stored in lists is not supported.

For performing/testing annotation mapping, it is sufficient to call geneSets(par) on a valid parameter object as described above, without running a complete gene set analysis.