Ncount4<-function(seq,w){
#w=length of word
tcount<-array(rep(0,4^w), rep(4,w))
# array[4x4x4x4] to hold word counts, elements set to zero
ncount<-array(rep(0,4^w), rep(4,w))
# array[4x4x4x4] holds number of sequences with one or
# more of each k-word
N<-length(seq[1,]) #Length of each sequence
M<-length(seq[,1]) #Number of sequences
#######################################################
#Count total number of word occurrences
for(j in 1:M){ #looping over sequences
jcount<-array(rep(0,4^w), rep(4,w))
#array to hold word counts for sequence j
for(k in 1:(N-w+1)){ #looping over positions
jcount[seq[j,k],seq[j,k+1],seq[j,k+2],seq[j,k+3]]<-
jcount[seq[j,k],seq[j,k+1],seq[j,k+2],seq[j,k+3]]+1
#adds 1 if word at k,k+1,k+2,k+3 appears in sequence j
}
tcount<-tcount+jcount
#Add contribution of j to total
#######################################################
#Plug-in: add 1 to ncount if word occurs >= once in j
for(k in 1:4){
for(l in 1:4){
for(m in 1:4){
for(n in 1:4){
if(jcount[k,l,m,n]!=0){
ncount[k,l,m,n]<-ncount[k,l,m,n]+1}
}
}
}
}
#######################################################
}
return(tcount,ncount)
}