accessors: multidna Accessors

Description

Accessors for slots in multidna and multiphyDat objects.

Usage

getNumInd(x, ...)
# S4 method for multidna
getNumInd(x, ...)
# S4 method for multiphyDat
getNumInd(x, ...)
getNumLoci(x, ...)
# S4 method for multidna
getNumLoci(x, ...)
# S4 method for multiphyDat
getNumLoci(x, ...)
getLocusNames(x, ...)
# S4 method for multidna
getLocusNames(x, ...)
# S4 method for multiphyDat
getLocusNames(x, ...)
setLocusNames(x) <- value
# S4 method for multidna
setLocusNames(x) <- value
# S4 method for multiphyDat
setLocusNames(x) <- value
getNumSequences(x, ...)
# S4 method for multidna
getNumSequences(x, exclude.gap.only = TRUE,
  loci = NULL, ...)
# S4 method for multiphyDat
getNumSequences(x, exclude.gap.only = TRUE,
  loci = NULL, ...)
getSequenceNames(x, ...)
# S4 method for multidna
getSequenceNames(x, exclude.gap.only = TRUE,
  loci = NULL, ...)
# S4 method for multiphyDat
getSequenceNames(x, exclude.gap.only = TRUE,
  loci = NULL, ...)
getSequences(x, ...)
# S4 method for multidna
getSequences(x, loci = NULL, ids = NULL,
  simplify = TRUE, exclude.gap.only = TRUE, ...)
# S4 method for multiphyDat
getSequences(x, loci = NULL, ids = NULL,
  simplify = TRUE, exclude.gap.only = TRUE, ...)

Value

returns the information stored in a slot, see details.

Arguments

x: a multidna or multiphyDat object.
...: further arguments passed on to other functions.
value: a replacement value for the slot.
exclude.gap.only: logical. Remove or ignore sequences containing all gaps?
loci: a character, numeric, or logical vector identifying which loci to return.
ids: a character, numeric, or logical vector identifying which sequences to return within a locus.
simplify: logical. If FALSE, always return a list of DNAbin sequences. If TRUE and only one locus has been requested, return a single DNAbin object.

Details

getNumInd: Returns the number of individuals.
getNumLoci: Returns the number of loci.
getLocusNames: Returns the names of each locus.
setLocusNames: Sets the names of each locus.
getNumSequences: Returns the number of sequences in each locus.
getSequenceNames: Returns the names of individual sequences at each locus.
getSequences: Returns sequences of specified loci and individuals.