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git-svn-id: file:///home/git/hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/seqTools@128657 bc3139a8-67e5-0310-9ffc-ced21a209358

Wolfgang Kaisers authored on 13/04/2017 15:56:05
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+##                                                                           ##
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+##  Project   :   seqTools                                                   ##
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+##  Created   :   26.August.2013                                             ##
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+##  Author    :   W. Kaisers                                                 ##
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+##  File      :   allStatics.r                                               ##
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+##  Content   :   All static variables and (not directly object related )    ##
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+##                function declarations                                      ##
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+##                                                                           ##
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## Global variables:
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+strandlevels <- c("+", "-", "*")
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+iupac_chars <- c('a', 'c', 'g', 't', 'u', 'r', 'y', 's', 'w', 'k', 'm', 'b',
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+                'd', 'h', 'v', 'n', '.', '-', '=')
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## Although static array sizes would allow larger k (e.g. 15: 8 GB RAM), 
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+## exponential increase in run-time restricts usability to k values in 1:12
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+## 4^12 = 16.777.216 possible combinations.
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+## 'Hard' coded (in stat_defs.h: 15)
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+max_k <- 12
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## End global variables
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## Some useful functions for work with phred's
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+char2ascii <- function(c) { strtoi(charToRaw(c), base=16L) }
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+
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+ascii2char <- function(x, multiple=FALSE)
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+                                { rawToChar(as.raw(x), multiple=multiple) }
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+
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+phredTable <- function(phred=0:93)
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+{
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+    if(!is.numeric(phred))
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+        stop("phred must be numeric.")
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+    
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+    phred <- sort(unique(as.integer(phred)))
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+    
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+    if( (phred[1] < 0) || (max(phred) > 93) )
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+        stop("Only phred values in 0:93 are allowed.")
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+
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+    ascii <- phred + 33
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+    return(data.frame(ascii=ascii, phred=phred,
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+                    char=ascii2char(ascii, multiple=TRUE)))
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+}
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+# unexported functions,  do not check for x
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+rel_int  <- function(x) {return(.Call("rel_int", x, PACKAGE="seqTools"))}
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+rel_real <- function(x) {return(.Call("rel_real", x, PACKAGE="seqTools"))}
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+enlargeIntMat <- function(x, newDim){
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+    if(!is.matrix(x))
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+        stop("x must be matrix.")
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+
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+    if(!is.numeric(newDim))
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+        stop("newDim must be numeric.")
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+    
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+    newDim <- as.integer(newDim)
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+
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+    if(length(newDim) != 2)
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+        stop("newDim must have length 2.")
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+
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+    return(.Call("r_enlarge_int_mat", x, newDim, PACKAGE="seqTools"))
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+}
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+
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+kMerIndex <- function(kMers, k=nchar(kMers)[1], base=1)
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+{
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+    if(!is.character(kMers))
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+        stop("kMers must be character.")
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+
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+    if(!is.numeric(k))
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+        stop("k must be numeric.")
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+    k <- as.integer(k)
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+
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+    if(k<0 || k > max_k)
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+        stop("k must be in range 0, ... , ", max_k, ".")
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+
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+    if(!all(nchar(kMers) == k))
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+        stop("All kMers must have k characters!")
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+
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+    if(!is.numeric(base))
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+        stop("base must be numeric")
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+
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+    if(length(base) > 1)
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+        stop("base must have length 1.")
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+    base<-as.integer(base)
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+
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+    if(!(base %in% 0:1))
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+        stop("base must be 0 or 1.")
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+
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+    return(.Call("get_Kmer_Index", kMers, k, PACKAGE="seqTools") + base)
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+}
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+
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+
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##
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+## END OF FILE
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+## + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ##