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-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-##                                                                           ##

-##  Project   :   seqTools                                                   ##

-##  Created   :   26.August.2013                                             ##

-##  Author    :   W. Kaisers                                                 ##

-##  File      :   allStatics.r                                               ##

-##  Content   :   All static variables and (not directly object related )    ##

-##                function declarations                                      ##

-##                                                                           ##

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## Global variables:

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-

-strandlevels <- c("+", "-", "*")

-iupac_chars <- c('a', 'c', 'g', 't', 'u', 'r', 'y', 's', 'w', 'k', 'm', 'b',

-                'd', 'h', 'v', 'n', '.', '-', '=')

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## Although static array sizes would allow larger k (e.g. 15: 8 GB RAM), 

-## exponential increase in run-time restricts usability to k values in 1:12

-## 4^12 = 16.777.216 possible combinations.

-## 'Hard' coded (in stat_defs.h: 15)

-max_k <- 12

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## End global variables

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## Some useful functions for work with phred's

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-

-char2ascii <- function(c) { strtoi(charToRaw(c), base=16L) }

-

-ascii2char <- function(x, multiple=FALSE)

-                                { rawToChar(as.raw(x), multiple=multiple) }

-

-phredTable <- function(phred=0:93)

-{

-    if(!is.numeric(phred))

-        stop("phred must be numeric.")

-    

-    phred <- sort(unique(as.integer(phred)))

-    

-    if( (phred[1] < 0) || (max(phred) > 93) )

-        stop("Only phred values in 0:93 are allowed.")

-

-    ascii <- phred + 33

-    return(data.frame(ascii=ascii, phred=phred,

-                    char=ascii2char(ascii, multiple=TRUE)))

-}

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-

-# unexported functions,  do not check for x

-rel_int  <- function(x) {return(.Call("rel_int", x, PACKAGE="seqTools"))}

-rel_real <- function(x) {return(.Call("rel_real", x, PACKAGE="seqTools"))}

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-enlargeIntMat <- function(x, newDim){

-    if(!is.matrix(x))

-        stop("x must be matrix.")

-

-    if(!is.numeric(newDim))

-        stop("newDim must be numeric.")

-    

-    newDim <- as.integer(newDim)

-

-    if(length(newDim) != 2)

-        stop("newDim must have length 2.")

-

-    return(.Call("r_enlarge_int_mat", x, newDim, PACKAGE="seqTools"))

-}

-

-kMerIndex <- function(kMers, k=nchar(kMers)[1], base=1)

-{

-    if(!is.character(kMers))

-        stop("kMers must be character.")

-

-    if(!is.numeric(k))

-        stop("k must be numeric.")

-    k <- as.integer(k)

-

-    if(k<0 || k > max_k)

-        stop("k must be in range 0, ... , ", max_k, ".")

-

-    if(!all(nchar(kMers) == k))

-        stop("All kMers must have k characters!")

-

-    if(!is.numeric(base))

-        stop("base must be numeric")

-

-    if(length(base) > 1)

-        stop("base must have length 1.")

-    base<-as.integer(base)

-

-    if(!(base %in% 0:1))

-        stop("base must be 0 or 1.")

-

-    return(.Call("get_Kmer_Index", kMers, k, PACKAGE="seqTools") + base)

-}

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-

-

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##

-## END OF FILE

-## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##