"""Classes for storing matches between sequences and genomic locations
built from lists of matches."""

class Match:
	"Track similar segments between two sequences."

	def __init__(self, src, dst):
		"src and dst are 3-tuples of (sequenceId, start, end)"
		self.srcSequenceId, self.srcStart, self.srcEnd = src
		self.dstSequenceId, self.dstStart, self.dstEnd = dst

	def __str__(self):
		return "<%s[%d..%d]=%s[%d..%d]>" % (
			self.srcSequenceId, self.srcStart, self.srcEnd,
			self.dstSequenceId, self.dstStart, self.dstEnd )

	def __repr__(self):
		return str(self)

class GenomicLocation:
	"Track location of one sequence on another as a series of matches."

	def __init__(self, matches=None):
		"matches is an optional initializer list of matches"
		if matches is None:
			self.matches = []
		else:
			# Note that we make a copy rather than using
			# the same list as passed in
			self.matches = matches[:]

	def addMatch(self, match):
		self.matches.append(match)

if __name__ == "__main__":
	def main():
		ml = [ Match(("abc", 1, 3), ("xyz", 12, 14)),
			Match(("abc", 4, 12), ("xyz", 70, 78)),
			Match(("abc", 14, 30), ("xyz", 100, 116)) ]
		gl = GenomicLocation(ml)
		print gl.matches
	main()