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aligned_string <-function(data,para){
# data is a 2*n matrix containing two sequence of strings sampled from the data
# para is a m*12 matrix contains 12 random sampled sequence. The population size of the parameter should be fixed
string1<-vector()
string2<-vector()
### There are mistakes in this one. After testing, it comes from the difference in the input. Maybe raw.alignment can not handle some of the strings ###
for(i in 1:length(para[,1]))
{
for(j in 1:length(data[1,]))
{
T<-raw.alignment(c(as.character(data[1,j]),as.character(data[2,j])),para[i,1],para[i,2],para[i,3],para[i,4],para[i,5],para[i,6],para[i,7],para[i,8],para[i,9],para[i,10],para[i,11],para[i,12],para[i,13])
string1[j]<-T$alignment1
string2[j]<-T$alignment2
}
if(i==1)
{
sf1<-string1
sf2<-string2
}
else{
sf1<-rbind(sf1,string1)
sf2<-rbind(sf2,string2)
}
}
z<-list()
z[[1]]<-sf1
z[[2]]<-sf2
names(z)<-c("alignment1","alignment2")
colnames(z[[1]])<-data[1,]
colnames(z[[2]])<-data[2,]
return(z)
}
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