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# Copyright (c) 2015 by Sean Downey
# Authors: Sean Downey (sean@codexdata.com) and Guowei Sun (gwsun@umd.edu)
# This software is distributed under GPL-3.
decode.ALINE <-
function(x,y,m1=NULL,m2=NULL) {
map<-map(m1,m2)
splitx<-strsplit(x,"")
splity<-strsplit(y,"")
t<-splitx[[1]]
for(j in 1:length(splitx[[1]])){
catch<-FALSE
for(i in 1:length(map$U.Val)){
if(splitx[[1]][j]==intToUtf8(map$U.Val[i])){
catch=TRUE
break
}
}
if(!catch){
message(paste("Invalid character:",splitx[[1]][j],"dropped in alignment"))
t<-splitx[[1]][-j]
}
}
splitx[[1]]<-t
num<-length(splity[[1]])
J<-rep(NA,length(splitx[[1]]))
j=1
for( i in 1:num-1)
{
if (!splity[[1]][i]==" " && splity[[1]][i+1]==" ")
{
J[j]=i
j=j+1
}
}
aligned_y=rep(" ",num)
p=0
for (i in 1:(length(J)))
{
if(splity[[1]][J[i]]=="|"||splity[[1]][J[i]]=="<"||splity[[1]][J[i]]=="-")
{
aligned_y[J[i]]<-splity[[1]][J[i]]
p=p+1
}
else{
aligned_y[J[i]]=splitx[[1]][(i-p)]
}
}
z<-paste(aligned_y,sep=' ',collapse='')
return(z)
}
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