#! /bin/csh -f

#
# Edit pscoffee.tmpl, not pscoffee.
#

cat << ENDF > _lara2pairalign
#! /usr/bin/env ruby

gets
line = gets
nseq = line.to_i
gets

seq = []
len = []
for i in 0..(nseq-1)
	line = gets
	seq.push( line.split(' ').slice(2).to_s )
	len.push( line.split(' ').slice(1).to_i )
	gets
end

#p seq
#p len

while 1 
	line = gets
	mem1 = line.split(' ').slice(1).to_i - 1
	mem2 = line.split(' ').slice(2).to_i - 1

#	p mem1
#	p mem2

	gets

	aln1 = ""
	aln2 = ""

	pos1bk = len[mem1] - 1
	pos2bk = len[mem2] - 1

	while 1
		line = gets
		pos1 = line.split(' ').slice(0).to_i - 1
		pos2 = line.split(' ').slice(1).to_i - 1

		break if line.to_i == 0

#		puts "\npos = \n"
#		p pos1
#		p pos2

		next if pos1 == 0 && pos2 == 0

		if pos1bk > pos1 then
			j = pos1bk
			while j > pos1
#				puts "j1= " + j.to_s
				aln1 = seq[mem1][j..j] + aln1
				aln2 = '-' + aln2
				j -= 1
			end
		end
		if pos2bk > pos2 then
			j = pos2bk
			while j > pos2
#				puts "j2= " + j.to_s
				aln1 = '-' + aln1
				aln2 = seq[mem2][j..j] + aln2
				j -= 1
			end
		end


		aln1 = seq[mem1][pos1..pos1] + aln1
		aln2 = seq[mem2][pos2..pos2] + aln2

#		puts "\nadding nuc"
#		p aln1
#		p aln2

		pos1bk = pos1-1
		pos2bk = pos2-1

#		puts "\nposbk = \n"
#		p pos1bk
#		p pos2bk

	end
	if pos1bk >= 0 then
		j = pos1bk
		while j >= 0
			aln1 = seq[mem1][j..j] + aln1
			aln2 = '-' + aln2
			j -= 1
		end
	end
	if pos2bk >= 0 then
		j = pos2bk
		while j >= 0
			aln1 = '-' + aln1
			aln2 = seq[mem2][j..j] + aln2
			j -= 1
		end
	end

	puts ">#{mem1}"
	puts aln1
	puts ">#{mem2}"
	puts aln2


	break if line =~ /^!/ 
end
exit

ENDF

chmod guo+rx _lara2pairalign

echo "####### IN PSCOFFEE ######" 

set fname = `echo $1 | sed 's/-in=//'`
cp $fname larapairs.$$
./_lara2pairalign larapairs.$$ > larapairs
rm larapairs.$$