Namespaces
	anonymous_namespace{print_gdst.cpp}

Classes
struct	Branch

class	Children

struct	Common_subseq
	Common subsequence. More...

class	Depth_iter

class	Gdst
	Generalized DNA suffix tree. More...

struct	Gdst_stats

class	Leaf
	Store suffixes Each leaf is attached to a branch and stores suffixes that have the length of the branch' index. Since the length of the suffixes is known, only the sequence ID is stored. More...

struct	Match
	Results of matching pattern to suffix tree. More...

class	Pattern_iter
	Navigate suffix tree according to pattern. More...

class	Ukkonen_inserter
	According to: http://www.cise.ufl.edu/~sahni/dsaaj/enrich/c16/suffix.htm http://stackoverflow.com/questions/9452701. More...

Functions
std::ostream &	print (std::ostream &os, const Branch_id bid, Gdst const &st)

std::ostream &	operator<< (std::ostream &os, Gdst const &st)

std::ostream &	dot (std::ostream &os, Gdst const &st, const bool sl=true)

bool	mismatching_end (const unsigned start1, const unsigned len1, const unsigned start2, const unsigned len2, const unsigned match_len)

	VDJ_PIPE_OBJECT_ID (Leaf_id)

	VDJ_PIPE_OBJECT_ID (Branch_id)

	VDJ_PIPE_OBJECT_ID (Children_id)

Function Documentation

VDJ_PIPE_DECL std::ostream & vdj_pipe::gdst::dot	(	std::ostream &	os,
		Gdst const &	st,
		const bool	sl
	)

bool vdj_pipe::gdst::mismatching_end	(	const unsigned	start1,
		const unsigned	len1,
		const unsigned	start2,
		const unsigned	len2,
		const unsigned	match_len
	)

inline

Parameters

start1	start of the aligned region in the first sequence
len1	length of the first sequence
start2	start of the aligned region in the second sequence
len2	length of the second sequence
match_len	length of the aligned region

VDJ_PIPE_DECL std::ostream & vdj_pipe::gdst::operator<<	(	std::ostream &	os,
		Gdst const &	st
	)

VDJ_PIPE_DECL std::ostream & vdj_pipe::gdst::print	(	std::ostream &	os,
		const Branch_id	bid,
		Gdst const &	st
	)

vdj_pipe::gdst::VDJ_PIPE_OBJECT_ID ( Leaf_id )

vdj_pipe::gdst::VDJ_PIPE_OBJECT_ID ( Branch_id )

vdj_pipe::gdst::VDJ_PIPE_OBJECT_ID ( Children_id )

Namespaces