AAString objects

Description

An AAString object allows efficient storage and manipulation of a long amino acid sequence.

Usage

AAString(x="", start=1, nchar=NA)

## Predefined constants:
AA_ALPHABET       # full Amino Acid alphabet
AA_STANDARD       # first 20 letters only
AA_PROTEINOGENIC  # first 22 letters only

Arguments

Details

The AAString class is a direct XString subclass (with no additional slot). Therefore all functions and methods described in the XString man page also work with an AAString object (inheritance).

Unlike the BString container that allows storage of any single string (based on a single-byte character set) the AAString container can only store a string based on the Amino Acid alphabet (see below).

The Amino Acid alphabet

This alphabet contains all letters from the Single-Letter Amino Acid Code (see ?AMINO_ACID_CODE) plus "*" (the stop letter), "-" (the gap letter), "+" (the hard masking letter), and "." (the not a letter or not available letter). It is stored in the AA_ALPHABET predefined constant (character vector).

The alphabet() function returns AA_ALPHABET when applied to an AAString object.

Constructor-like functions and generics

In the code snippet below, x can be a single string (character vector of length 1) or a BString object.

AAString(x="", start=1, nchar=NA): Tries to convert x into an AAString object by reading nchar letters starting at position start in x.

Accessor methods

In the code snippet below, x is an AAString object.

alphabet(x): If x is an AAString object, then return the Amino Acid alphabet (see above). See the corresponding man pages when x is a BString, DNAString or RNAString object.

Author(s)

H. Pag<c3><83><c2><a8>s

See Also

AMINO_ACID_CODE, letter, XString-class, alphabetFrequency

Examples

  AA_ALPHABET
  a <- AAString("MARKSLEMSIR*")
  length(a)
  alphabet(a)

Results

R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
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> library(Biostrings)
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
    get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
    match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
    rbind, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Loading required package: S4Vectors
Loading required package: stats4

Attaching package: 'S4Vectors'

The following objects are masked from 'package:base':

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: IRanges
Loading required package: XVector
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/Biostrings/AAString-class.Rd_%03d_medium.png", width=480, height=480)
> ### Name: AAString-class
> ### Title: AAString objects
> ### Aliases: class:AAString AAString-class AA_ALPHABET AA_STANDARD
> ###   AA_PROTEINOGENIC AAString
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>   AA_ALPHABET
 [1] "A" "R" "N" "D" "C" "Q" "E" "G" "H" "I" "L" "K" "M" "F" "P" "S" "T" "W" "Y"
[20] "V" "U" "O" "B" "J" "Z" "X" "*" "-" "+" "."
>   a <- AAString("MARKSLEMSIR*")
>   length(a)
[1] 12
>   alphabet(a)
 [1] "A" "R" "N" "D" "C" "Q" "E" "G" "H" "I" "L" "K" "M" "F" "P" "S" "T" "W" "Y"
[20] "V" "U" "O" "B" "J" "Z" "X" "*" "-" "+" "."
> 
> 
> 
> 
> 
> dev.off()
null device 
          1 
>