CLocalAlignmentStringKernel Class Reference
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 () |
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 [] |
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 23 of file LocalAlignmentStringKernel.h.
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 70 of file LocalAlignmentStringKernel.h.
| virtual const char* CLocalAlignmentStringKernel::get_name | ( | ) | [virtual] |
return the kernel's name
- Returns:
- name LocalAlignment
Implements CKernel.
Definition at line 79 of file LocalAlignmentStringKernel.h.
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 57 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 64 of file LocalAlignmentStringKernel.h.
Member Data Documentation
int32_t* CLocalAlignmentStringKernel::aaIndex [protected] |
correspondance between amino-acid letter and index
Definition at line 136 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}
Definition at line 146 of file LocalAlignmentStringKernel.h.
int32_t CLocalAlignmentStringKernel::extension [protected] |
gap penalty extension
Definition at line 141 of file LocalAlignmentStringKernel.h.
bool CLocalAlignmentStringKernel::initialized [protected] |
if kernel is initialized
Definition at line 131 of file LocalAlignmentStringKernel.h.
int32_t* CLocalAlignmentStringKernel::isAA [protected] |
indicates whether a char is an amino-acid
Definition at line 134 of file LocalAlignmentStringKernel.h.
int32_t CLocalAlignmentStringKernel::logsum_lookup [static, protected] |
static logsum lookup
Definition at line 144 of file LocalAlignmentStringKernel.h.
int32_t CLocalAlignmentStringKernel::opening [protected] |
gap penalty opening
Definition at line 139 of file LocalAlignmentStringKernel.h.
int32_t* CLocalAlignmentStringKernel::scaled_blosum [protected] |
scaled blosum
Definition at line 148 of file LocalAlignmentStringKernel.h.
The documentation for this class was generated from the following files: