SHOGUN v0.9.0
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The Regulaty Modules kernel, based on the WD kernel, as published in Schultheiss et al., Bioinformatics (2009) on regulatory sequences.
CRegulatoryModulesStringKernel | ( | void | ) |
default constructor
CRegulatoryModulesStringKernel | ( | int32_t | size, |
float64_t | width, | ||
int32_t | degree, | ||
int32_t | shift, | ||
int32_t | window | ||
) |
constructor
size | cache size |
width | width of gaussian kernel |
degree | degree of wds kernel |
shift | shift of wds kernel |
window | size of window around motifs to compute wds kernels on |
CRegulatoryModulesStringKernel | ( | CStringFeatures< char > * | lstr, |
CStringFeatures< char > * | rstr, | ||
CSimpleFeatures< uint16_t > * | lpos, | ||
CSimpleFeatures< uint16_t > * | rpos, | ||
float64_t | width, | ||
int32_t | degree, | ||
int32_t | shift, | ||
int32_t | window, | ||
int32_t | size = 10 |
||
) |
constructor
lstr | string features of left-hand side |
rstr | string features of right-hand side |
lpos | motif positions on lhs |
rpos | motif positions on rhs |
width | width of gaussian kernel |
degree | degree of wds kernel |
shift | shift of wds kernel |
window | size of window around motifs to compute wds kernels on |
size | cache size |
~CRegulatoryModulesStringKernel | ( | ) | [virtual] |
default destructor
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。
float64_t compute_wds | ( | char * | avec, |
char * | bvec, | ||
int32_t | len | ||
) | [protected] |
compute WDS kernel for features a and b
avec | vector a |
bvec | vector b |
len | length of string |
virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
virtual const char* get_name | ( | void | ) | const [virtual] |
return the kernel's name
initialize kernel
l | features of left-hand side |
r | features of right-hand side |
void set_motif_positions | ( | CSimpleFeatures< uint16_t > * | positions_lhs, |
CSimpleFeatures< uint16_t > * | positions_rhs | ||
) |
set motif positions
positions_lhs | motif positions on lhs |
positions_rhs | motif positions on rhs |
void set_wd_weights | ( | ) | [protected] |
set standard weighted degree kernel weighting
int32_t degree [protected] |
degree of Weighted Degree kernel part
CSimpleFeatures<uint16_t>* motif_positions_lhs [protected] |
Matrix of motif positions from sequences left-hand side
CSimpleFeatures<uint16_t>* motif_positions_rhs [protected] |
Matrix of motif positions from sequences right-hand side
float64_t* position_weights [protected] |
scaling weights in window
int32_t shift [protected] |
shift of Weighted Degree with Shifts kernel part
weights of WD kernel
width of Gaussian kernel part
int32_t window [protected] |
size of window around motifs