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 25 of file LocalAlignmentStringKernel.h.

Inheritance diagram for CLocalAlignmentStringKernel:
Inheritance graph
[legend]

List of all members.

Public Member Functions

 CLocalAlignmentStringKernel (int32_t size)
 CLocalAlignmentStringKernel (CStringFeatures< char > *l, CStringFeatures< char > *r)
virtual ~CLocalAlignmentStringKernel ()
virtual bool init (CFeatures *l, CFeatures *r)
virtual void cleanup ()
virtual bool load_init (FILE *src)
virtual bool save_init (FILE *dest)
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 opening
int32_t extension
int32_t * scaled_blosum

Static Protected Attributes

static int32_t logsum_lookup [LOGSUM_TBL]
static const int32_t blosum []

Constructor & Destructor Documentation

CLocalAlignmentStringKernel::CLocalAlignmentStringKernel ( int32_t  size  ) 

constructor

Parameters:
size cache size

Definition at line 95 of file LocalAlignmentStringKernel.cpp.

CLocalAlignmentStringKernel::CLocalAlignmentStringKernel ( CStringFeatures< char > *  l,
CStringFeatures< char > *  r 
)

constructor

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

Definition at line 103 of file LocalAlignmentStringKernel.cpp.

CLocalAlignmentStringKernel::~CLocalAlignmentStringKernel (  )  [virtual]

Definition at line 113 of file LocalAlignmentStringKernel.cpp.


Member Function Documentation

void CLocalAlignmentStringKernel::cleanup (  )  [virtual]

clean up kernel

Reimplemented from CKernel.

Definition at line 125 of file LocalAlignmentStringKernel.cpp.

float64_t CLocalAlignmentStringKernel::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 CLocalAlignmentStringKernel::get_kernel_type (  )  [virtual]

return what type of kernel we are

Returns:
kernel type LOCALALIGNMENT

Implements CKernel.

Definition at line 72 of file LocalAlignmentStringKernel.h.

virtual const char* CLocalAlignmentStringKernel::get_name (  )  const [virtual]

return the kernel's name

Returns:
name LocalAlignment

Implements CSGObject.

Definition at line 81 of file LocalAlignmentStringKernel.h.

bool CLocalAlignmentStringKernel::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.

virtual bool CLocalAlignmentStringKernel::load_init ( FILE *  src  )  [virtual]

load kernel init_data

Parameters:
src file to load from
Returns:
if loading was successful

Implements CKernel.

Definition at line 59 of file LocalAlignmentStringKernel.h.

virtual bool CLocalAlignmentStringKernel::save_init ( FILE *  dest  )  [virtual]

save kernel init_data

Parameters:
dest file to save to
Returns:
if saving was successful

Implements CKernel.

Definition at line 66 of file LocalAlignmentStringKernel.h.


Member Data Documentation

correspondance between amino-acid letter and index

Definition at line 135 of file LocalAlignmentStringKernel.h.

const int32_t CLocalAlignmentStringKernel::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 145 of file LocalAlignmentStringKernel.h.

gap penalty extension

Definition at line 140 of file LocalAlignmentStringKernel.h.

if kernel is initialized

Definition at line 130 of file LocalAlignmentStringKernel.h.

int32_t* CLocalAlignmentStringKernel::isAA [protected]

indicates whether a char is an amino-acid

Definition at line 133 of file LocalAlignmentStringKernel.h.

int32_t CLocalAlignmentStringKernel::logsum_lookup [static, protected]

static logsum lookup

Definition at line 143 of file LocalAlignmentStringKernel.h.

gap penalty opening

Definition at line 138 of file LocalAlignmentStringKernel.h.

scaled blosum

Definition at line 147 of file LocalAlignmentStringKernel.h.


The documentation for this class was generated from the following files:

SHOGUN Machine Learning Toolbox - Documentation