SHOGUN v0.9.0
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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.
在文件LocalAlignmentStringKernel.h第27行定义。
公有成员 | |
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 |
保护成员 | |
virtual float64_t | compute (int32_t idx_a, int32_t idx_b) |
保护属性 | |
bool | initialized |
int32_t * | isAA |
int32_t * | aaIndex |
int32_t | m_opening |
int32_t | m_extension |
int32_t * | scaled_blosum |
静态保护属性 | |
static int32_t | logsum_lookup [LOGSUM_TBL] |
static const int32_t | blosum [] |
static const char * | aaList = "ARNDCQEGHILKMFPSTWYV" |
CLocalAlignmentStringKernel | ( | int32_t | size = 0 | ) |
CLocalAlignmentStringKernel | ( | CStringFeatures< char > * | l, |
CStringFeatures< char > * | r, | ||
float64_t | opening = 12 , |
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float64_t | extension = 2 |
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) |
constructor
l | features of left-hand side |
r | features of right-hand side |
opening | gap opening penalty |
extension | gap extension penalty |
~CLocalAlignmentStringKernel | ( | ) | [virtual] |
void cleanup | ( | ) | [virtual] |
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 |
实现了CKernel。
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
在文件LocalAlignmentStringKernel.h第63行定义。
virtual const char* get_name | ( | void | ) | const [virtual] |
initialize kernel
l | features of left-hand side |
r | features of right-hand side |
int32_t* aaIndex [protected] |
correspondance between amino-acid letter and index
在文件LocalAlignmentStringKernel.h第130行定义。
const char * aaList = "ARNDCQEGHILKMFPSTWYV" [static, protected] |
List of amino acids
在文件LocalAlignmentStringKernel.h第144行定义。
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
在文件LocalAlignmentStringKernel.h第140行定义。
bool initialized [protected] |
if kernel is initialized
在文件LocalAlignmentStringKernel.h第125行定义。
int32_t* isAA [protected] |
indicates whether a char is an amino-acid
在文件LocalAlignmentStringKernel.h第128行定义。
int32_t logsum_lookup [static, protected] |
static logsum lookup
在文件LocalAlignmentStringKernel.h第138行定义。
int32_t m_extension [protected] |
gap penalty extension
在文件LocalAlignmentStringKernel.h第135行定义。
int32_t m_opening [protected] |
gap penalty opening
在文件LocalAlignmentStringKernel.h第133行定义。
int32_t* scaled_blosum [protected] |
scaled blosum
在文件LocalAlignmentStringKernel.h第142行定义。