Nothing
#############################################
# This code is subject to the license as stated in DESCRIPTION.
# Using this software implies acceptance of the license terms:
# - GPL 2
#
# (C) by F. Hoffgaard, P. Weil, and K. Hamacher in 2009.
#
# keul(AT)bio.tu-darmstadt.de
#
#
# http://www.kay-hamacher.de
#############################################
get.entropy<-function(aln,bool=FALSE,gapchar="NOGAPCHAR",verbose=FALSE){
aln<-toupper(aln)
entropy<-function(i,aln,bool,gc){
ss<-summary(as.factor(aln[,i]))
if(bool){
ss[grep(gc,names(ss))]<-0
}
sum<-sum(ss)
ss<-ss/sum
ss<-ss[which(ss>0)]
if(length(ss)==0){
ret<-0
if(verbose){
cat("No Non-Gap Character.\n")
}
}else{
ret<- -1*sum(ss*log2(ss))
}
return(ret)
}
gc<-paste(gapchar,collapse="|")
l<-ncol(aln)
indizes<-1:l
H<-apply(as.array(indizes),1,entropy,aln,bool,gc)
return(H)
}
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