HostUtils::Sequence Namespace Reference

Functions
int	base_to_num (char base)
	Map a single base to a number. A: 0, C: 1, G: 2, T: 3, _: 4. More...
char	num_to_base (int num)
char	num_to_aa (int num)
int	aa_to_num (char aa)
template<typename T >
string	nav_to_string (T nav)
template<typename T , size_t MAX_QRY_LENGTH, size_t MAX_REF_LENGTH>
std::vector< string >	ReconstructTracebackProfile (std::vector< string > querys, std::vector< string > references, int query_start_idx, int reference_start_idx, T(&tb_streams)[MAX_REF_LENGTH+MAX_QRY_LENGTH])
	Reconstruct the traceback for profile alignmetnt from the array of traceback navigations. More...
std::vector< std::array< int, 5 > >	MultipleSequencesToProfileAlign (std::vector< string > seq, int len)
	Given a array of sequences, convert them to the format of the input of profile alignment. More...
template<typename T , size_t MAX_QRY_LENGTH, size_t MAX_REF_LENGTH>
std::map< string, string >	ReconstructTraceback (string query, string reference, int query_start_idx, int reference_start_idx, T(&tb_streams)[MAX_REF_LENGTH+MAX_QRY_LENGTH])
	Fucntion to reconstruct the alignment result from the an array of traceback navigations. More...
template<typename T , size_t MAX_QRY_LENGTH, size_t MAX_REF_LENGTH>
std::map< string, string >	ReconstructTracebackSemiglobal (string query, string reference, int query_start_idx, int reference_start_idx, T(&tb_streams)[MAX_REF_LENGTH+MAX_QRY_LENGTH])
template<typename T , size_t MAX_QRY_LENGTH, size_t MAX_REF_LENGTH>
std::map< string, string >	ReconstructTracebackOverlapSuffixPrefix (string query, string reference, int query_start_idx, int reference_start_idx, T(&tb_streams)[MAX_REF_LENGTH+MAX_QRY_LENGTH])
template<typename T , int LEN>
string	NavigationToString (T nav[LEN])
template<typename T , int NB, int MAX_QRY_LENGTH, int MAX_REF_LENGTH>
array< map< string, string >, NB >	ReconstructTracebackBlocks (string query[NB], string reference[NB], int query_start_idx[NB], int reference_start_idx[NB], T(&tb_streams)[NB][MAX_REF_LENGTH+MAX_QRY_LENGTH])
	Function to reconstruct the alignment result from the array of the traceback navigations for all blocks. More...
template<typename T , int NB, int MAX_QRY_LENGTH, int MAX_REF_LENGTH>
array< map< string, string >, NB >	ReconstructTracebackSemiglobalBlocks (string query[NB], string reference[NB], int query_start_idx[NB], int reference_start_idx[NB], T(&tb_streams)[NB][MAX_REF_LENGTH+MAX_QRY_LENGTH])
template<typename T , int NB, int MAX_QRY_LENGTH, int MAX_REF_LENGTH>
array< map< string, string >, NB >	ReconstructTracebackOverlapSuffixPrefixBlocks (string query[NB], string reference[NB], int query_start_idx[NB], int reference_start_idx[NB], T(&tb_streams)[NB][MAX_REF_LENGTH+MAX_QRY_LENGTH])

Function Documentation

int HostUtils::Sequence::aa_to_num

(

char

aa

)

int HostUtils::Sequence::base_to_num

(

char

base

)

Map a single base to a number. A: 0, C: 1, G: 2, T: 3, _: 4.

Parameters

base

Returns

int

std::vector<std::array<int, 5> > HostUtils::Sequence::MultipleSequencesToProfileAlign	(	std::vector< string >	seq,
		int	len
	)

Given a array of sequences, convert them to the format of the input of profile alignment.

Parameters

seq	Sequences
len	Length of Sequences

Returns

std::vector<std::array<int, 5>>

template<typename T >

string HostUtils::Sequence::nav_to_string

(

T

nav

)

template<typename T , int LEN>

string HostUtils::Sequence::NavigationToString

(

T

nav[LEN]

)

char HostUtils::Sequence::num_to_aa

(

int

num

)

char HostUtils::Sequence::num_to_base

(

int

num

)

template<typename T , size_t MAX_QRY_LENGTH, size_t MAX_REF_LENGTH>

std::map<string, string> HostUtils::Sequence::ReconstructTraceback	(	string	query,
		string	reference,
		int	query_start_idx,
		int	reference_start_idx,
		T(&)	tb_streams[MAX_REF_LENGTH+MAX_QRY_LENGTH]
	)

Fucntion to reconstruct the alignment result from the an array of traceback navigations.

Template Parameters

T

Parameters

query
reference

template<typename T , int NB, int MAX_QRY_LENGTH, int MAX_REF_LENGTH>

array<map<string, string>, NB> HostUtils::Sequence::ReconstructTracebackBlocks	(	string	query[NB],
		string	reference[NB],
		int	query_start_idx[NB],
		int	reference_start_idx[NB],
		T(&)	tb_streams[NB][MAX_REF_LENGTH+MAX_QRY_LENGTH]
	)

Function to reconstruct the alignment result from the array of the traceback navigations for all blocks.

Template Parameters

NB	Number of Blocks

Parameters

query
reference

template<typename T , size_t MAX_QRY_LENGTH, size_t MAX_REF_LENGTH>

std::map<string, string> HostUtils::Sequence::ReconstructTracebackOverlapSuffixPrefix	(	string	query,
		string	reference,
		int	query_start_idx,
		int	reference_start_idx,
		T(&)	tb_streams[MAX_REF_LENGTH+MAX_QRY_LENGTH]
	)

template<typename T , int NB, int MAX_QRY_LENGTH, int MAX_REF_LENGTH>

array<map<string, string>, NB> HostUtils::Sequence::ReconstructTracebackOverlapSuffixPrefixBlocks	(	string	query[NB],
		string	reference[NB],
		int	query_start_idx[NB],
		int	reference_start_idx[NB],
		T(&)	tb_streams[NB][MAX_REF_LENGTH+MAX_QRY_LENGTH]
	)

template<typename T , size_t MAX_QRY_LENGTH, size_t MAX_REF_LENGTH>

std::vector<string> HostUtils::Sequence::ReconstructTracebackProfile	(	std::vector< string >	querys,
		std::vector< string >	references,
		int	query_start_idx,
		int	reference_start_idx,
		T(&)	tb_streams[MAX_REF_LENGTH+MAX_QRY_LENGTH]
	)

Reconstruct the traceback for profile alignmetnt from the array of traceback navigations.

Parameters

querys
references
query_start_idx
reference_start_idx

Returns

std::vector<string>

template<typename T , size_t MAX_QRY_LENGTH, size_t MAX_REF_LENGTH>

std::map<string, string> HostUtils::Sequence::ReconstructTracebackSemiglobal	(	string	query,
		string	reference,
		int	query_start_idx,
		int	reference_start_idx,
		T(&)	tb_streams[MAX_REF_LENGTH+MAX_QRY_LENGTH]
	)

template<typename T , int NB, int MAX_QRY_LENGTH, int MAX_REF_LENGTH>

array<map<string, string>, NB> HostUtils::Sequence::ReconstructTracebackSemiglobalBlocks	(	string	query[NB],
		string	reference[NB],
		int	query_start_idx[NB],
		int	reference_start_idx[NB],
		T(&)	tb_streams[NB][MAX_REF_LENGTH+MAX_QRY_LENGTH]
	)