Nothing
deletecodongaps <- function(matrix){
if(length(which(matrix==5))==0 & length(which(matrix==6))==0){return(matrix)}
erg <- apply(matrix,2,del)
id <- which(erg==1)
if(length(id)==0){return(matrix)}
mod <- rep(-1,length(id))
codonid <- matrix(-1,length(id),3)
for(xx in 1:length(id)){
# x x gap
if(id[xx]%%3==0){
codonid[xx,1] <- id[xx] -2
codonid[xx,2] <- id[xx] -1
codonid[xx,3] <- id[xx]
}
if(id[xx]%%3==2){
codonid[xx,1] <- id[xx] -1
codonid[xx,2] <- id[xx]
codonid[xx,3] <- id[xx] +1
}
if(id[xx]%%3==1){
codonid[xx,1] <- id[xx]
codonid[xx,2] <- id[xx] +1
codonid[xx,3] <- id[xx] +2
}
}
d <- as.vector(codonid)
d <- unique(d)
matrix <- matrix[,-d]
return(matrix)
}
################
##Function######
################
del <- function(vek){
if(is.element(5,vek)|is.element(6,vek)){ # gaps or unknown_positions
return(1)
}else{return(0)}
}
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