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.
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" |
CLocalAlignmentStringKernel | ( | int32_t | size = 0 |
) |
constructor
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
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.
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
idx_a | index a | |
idx_b | index b |
Implements CKernel.
Definition at line 358 of file LocalAlignmentStringKernel.cpp.
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
Implements CStringKernel< char >.
Definition at line 63 of file LocalAlignmentStringKernel.h.
virtual const char* get_name | ( | void | ) | const [virtual] |
return the kernel's name
Reimplemented from CStringKernel< char >.
Definition at line 72 of file LocalAlignmentStringKernel.h.
initialize kernel
l | features of left-hand side | |
r | features of right-hand side |
Reimplemented from CStringKernel< char >.
Definition at line 118 of file LocalAlignmentStringKernel.cpp.
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] |
{ 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.