Detailed Description

spectrum mismatch rbf kernel

Definition at line 42 of file SpectrumMismatchRBFKernel.h.

Inheritance diagram for CSpectrumMismatchRBFKernel:

Public Member Functions
	CSpectrumMismatchRBFKernel ()
	CSpectrumMismatchRBFKernel (int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width)
	CSpectrumMismatchRBFKernel (CStringFeatures< char > l, CStringFeatures< char > r, int32_t size, float64_t *AA_matrix_, int32_t nr_, int32_t nc_, int32_t degree, int32_t max_mismatch, float64_t width)
virtual	~CSpectrumMismatchRBFKernel ()
virtual bool	init (CFeatures l, CFeatures r)
virtual void	cleanup ()
virtual EKernelType	get_kernel_type ()
virtual const char *	get_name () const
bool	set_max_mismatch (int32_t max)
int32_t	get_max_mismatch () const
bool	set_degree (int32_t deg)
int32_t	get_degree () const
bool	set_AA_matrix (float64_t *AA_matrix_=NULL, int32_t nr=128, int32_t nc=128)
Protected Member Functions
float64_t	AA_helper (std::string &path, const char *joint_seq, unsigned int index)
float64_t	compute_helper (const char *joint_seq, std::vector< unsigned int > joint_index, std::vector< unsigned int > joint_mismatch, std::string path, unsigned int d, const int &alen)
void	compute_helper_all (const char *joint_seq, std::vector< struct joint_list_struct > &joint_list, std::string path, unsigned int d)
void	compute_all ()
float64_t	compute (int32_t idx_a, int32_t idx_b)
virtual void	remove_lhs ()
virtual void	register_params ()
void	register_alphabet ()
Protected Attributes
CAlphabet *	alphabet
int32_t	degree
int32_t	max_mismatch
float64_t *	AA_matrix
int32_t	AA_matrix_length
float64_t	width
bool	initialized
CArray2< float64_t >	kernel_matrix
int32_t	kernel_matrix_length
int32_t	target_letter_0

Constructor & Destructor Documentation

CSpectrumMismatchRBFKernel ( )

default constructor

Definition at line 36 of file SpectrumMismatchRBFKernel.cpp.

CSpectrumMismatchRBFKernel	(	int32_t	size,
		float64_t *	AA_matrix_,
		int32_t	nr_,
		int32_t	nc_,
		int32_t	degree,
		int32_t	max_mismatch,
		float64_t	width
	)

constructor

Parameters:

	size
	AA_matrix_
	nr_
	nc_
	degree
	max_mismatch
	width

Definition at line 43 of file SpectrumMismatchRBFKernel.cpp.

CSpectrumMismatchRBFKernel	(	CStringFeatures< char > *	l,
		CStringFeatures< char > *	r,
		int32_t	size,
		float64_t *	AA_matrix_,
		int32_t	nr_,
		int32_t	nc_,
		int32_t	degree,
		int32_t	max_mismatch,
		float64_t	width
	)

constructor

Parameters:

	l	features of left-hand side
	r	features of right-hand side
	size
	AA_matrix_
	nr_
	nc_
	degree
	max_mismatch
	width

Definition at line 58 of file SpectrumMismatchRBFKernel.cpp.

~CSpectrumMismatchRBFKernel ( ) [virtual]

destructor

Definition at line 70 of file SpectrumMismatchRBFKernel.cpp.

Member Function Documentation

float64_t AA_helper	(	std::string &	path,
		const char *	joint_seq,
		unsigned int	index
	)			`[protected]`

AA helper

Parameters:

	path
	joint_seq
	index

Returns:: AA helper

Definition at line 120 of file SpectrumMismatchRBFKernel.cpp.

void cleanup ( ) [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 111 of file SpectrumMismatchRBFKernel.cpp.

float64_t compute	(	int32_t	idx_a,
		int32_t	idx_b
	)			`[protected, virtual]`

compute kernel function for features a and b idx_{a,b} denote the index of the feature vectors in the corresponding feature object

Parameters:

	idx_a	index a
	idx_b	index b

Returns:: computed kernel function at indices a,b

Implements CKernel.

Definition at line 360 of file SpectrumMismatchRBFKernel.cpp.

void compute_all ( ) [protected]

computer all

Definition at line 324 of file SpectrumMismatchRBFKernel.cpp.

float64_t compute_helper	(	const char *	joint_seq,
		std::vector< unsigned int >	joint_index,
		std::vector< unsigned int >	joint_mismatch,
		std::string	path,
		unsigned int	d,
		const int &	alen
	)			`[protected]`