Public Member Functions | Protected Member Functions | Protected Attributes | Static Protected Attributes

CLocalAlignmentStringKernel Class Reference


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:
Inheritance graph
[legend]

List of all members.

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 133 of file LocalAlignmentStringKernel.h.

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

List of amino acids

Definition at line 147 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 143 of file LocalAlignmentStringKernel.h.

bool initialized [protected]

if kernel is initialized

Definition at line 128 of file LocalAlignmentStringKernel.h.

int32_t* isAA [protected]

indicates whether a char is an amino-acid

Definition at line 131 of file LocalAlignmentStringKernel.h.

int32_t logsum_lookup [static, protected]

static logsum lookup

Definition at line 141 of file LocalAlignmentStringKernel.h.

int32_t m_extension [protected]

gap penalty extension

Definition at line 138 of file LocalAlignmentStringKernel.h.

int32_t m_opening [protected]

gap penalty opening

Definition at line 136 of file LocalAlignmentStringKernel.h.

int32_t* scaled_blosum [protected]

scaled blosum

Definition at line 145 of file LocalAlignmentStringKernel.h.


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