Detailed Description

The LocalAlignmentString kernel compares two sequences through all possible local alignments between the two sequences.

The implementation is taken from http://www.mloss.org/software/view/40/ and only adjusted to work with shogun.

Definition at line 27 of file LocalAlignmentStringKernel.h.

Inheritance diagram for CLocalAlignmentStringKernel:

Public Member Functions
	CLocalAlignmentStringKernel (int32_t size=0)
	CLocalAlignmentStringKernel (CStringFeatures< char > l, CStringFeatures< char > r, float64_t opening=12, float64_t extension=2)
virtual	~CLocalAlignmentStringKernel ()
virtual bool	init (CFeatures l, CFeatures r)
virtual void	cleanup ()
virtual EKernelType	get_kernel_type ()
virtual const char *	get_name () const
Protected Member Functions
virtual float64_t	compute (int32_t idx_a, int32_t idx_b)
Protected Attributes
bool	initialized
int32_t *	isAA
int32_t *	aaIndex
int32_t	m_opening
int32_t	m_extension
int32_t *	scaled_blosum
Static Protected Attributes
static int32_t	logsum_lookup [LOGSUM_TBL]
static const int32_t	blosum []
static const char *	aaList = "ARNDCQEGHILKMFPSTWYV"

Constructor & Destructor Documentation

CLocalAlignmentStringKernel ( int32_t size = 0 )

constructor

Parameters:

size

cache size

Definition at line 94 of file LocalAlignmentStringKernel.cpp.

CLocalAlignmentStringKernel	(	CStringFeatures< char > *	l,
		CStringFeatures< char > *	r,
		float64_t	opening = `12`,
		float64_t	extension = `2`
	)

constructor

Parameters:

	l	features of left-hand side
	r	features of right-hand side
	opening	gap opening penalty
	extension	gap extension penalty

Definition at line 101 of file LocalAlignmentStringKernel.cpp.

~CLocalAlignmentStringKernel ( ) [virtual]

Definition at line 113 of file LocalAlignmentStringKernel.cpp.

Member Function Documentation

void cleanup ( ) [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 125 of file LocalAlignmentStringKernel.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 358 of file LocalAlignmentStringKernel.cpp.

virtual EKernelType get_kernel_type ( ) [virtual]

return what type of kernel we are

Returns:: kernel type LOCALALIGNMENT

Implements CStringKernel< char >.

Definition at line 63 of file LocalAlignmentStringKernel.h.

virtual const char* get_name ( void ) const [virtual]

return the kernel's name

Returns:: name LocalAlignment

Reimplemented from CStringKernel< char >.

Definition at line 72 of file LocalAlignmentStringKernel.h.

bool init	(	CFeatures *	l,
		CFeatures *	r
	)			`[virtual]`

initialize kernel

Parameters:

	l	features of left-hand side
	r	features of right-hand side

Returns:: if initializing was successful

Reimplemented from CStringKernel< char >.

Definition at line 118 of file LocalAlignmentStringKernel.cpp.

Member Data Documentation

int32_t* aaIndex [protected]

correspondance between amino-acid letter and index

Definition at line 130 of file LocalAlignmentStringKernel.h.

const char * aaList = "ARNDCQEGHILKMFPSTWYV" [static, protected]

List of amino acids

Definition at line 144 of file LocalAlignmentStringKernel.h.

const int32_t blosum [static, protected]

Initial value:

 {
  6,
 -2,   8,
 -2,  -1,   9,
  -3,  -2,   2,   9,
  -1,  -5,  -4,  -5,  13,
  -1,   1,   0,   0,  -4,   8,
  -1,   0,   0,   2,  -5,   3,   7,
  0,  -3,  -1,  -2,  -4,  -3,  -3,   8,
  -2,   0,   1,  -2,  -4,   1,   0,  -3,  11,
  -2,  -5,  -5,  -5,  -2,  -4,  -5,  -6,  -5,   6,
  -2,  -3,  -5,  -5,  -2,  -3,  -4,  -5,  -4,   2,   6,
  -1,   3,   0,  -1,  -5,   2,   1,  -2,  -1,  -4,  -4,   7,
  -1,  -2,  -3,  -5,  -2,  -1,  -3,  -4,  -2,   2,   3,  -2,   8,
  -3,  -4,  -5,  -5,  -4,  -5,  -5,  -5,  -2,   0,   1,  -5,   0,   9,
  -1,  -3,  -3,  -2,  -4,  -2,  -2,  -3,  -3,  -4,  -4,  -2,  -4,  -5,  11,
  2,  -1,   1,   0,  -1,   0,   0,   0,  -1,  -4,  -4,   0,  -2,  -4,  -1,   6,
  0,  -2,   0,  -2,  -1,  -1,  -1,  -2,  -3,  -1,  -2,  -1,  -1,  -3,  -2,   2,   7,
  -4,  -4,  -6,  -6,  -3,  -3,  -4,  -4,  -4,  -4,  -2,  -4,  -2,   1,  -6,  -4,  -4,  16,
  -3,  -3,  -3,  -5,  -4,  -2,  -3,  -5,   3,  -2,  -2,  -3,  -1,   4,  -4,  -3,  -2,   3,  10,
  0,  -4,  -4,  -5,  -1,  -3,  -4,  -5,  -5,   4,   1,  -3,   1,  -1,  -4,  -2,   0,  -4,  -2,   6}

static blosum

Definition at line 140 of file LocalAlignmentStringKernel.h.

bool initialized [protected]

if kernel is initialized

Definition at line 125 of file LocalAlignmentStringKernel.h.

int32_t* isAA [protected]

indicates whether a char is an amino-acid

Definition at line 128 of file LocalAlignmentStringKernel.h.

int32_t logsum_lookup [static, protected]

static logsum lookup

Definition at line 138 of file LocalAlignmentStringKernel.h.

int32_t m_extension [protected]