详细描述
The Regulaty Modules kernel, based on the WD kernel, as published in Schultheiss et al., Bioinformatics (2009) on regulatory sequences.
构造及析构函数文档
| CRegulatoryModulesStringKernel | ( | void | ) |
default constructor
| CRegulatoryModulesStringKernel | ( | int32_t | size, |
| float64_t | width, | ||
| int32_t | degree, | ||
| int32_t | shift, | ||
| int32_t | window | ||
| ) |
constructor
- 参数:
-
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
- 参数:
-
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
成员函数文档
| 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
- 参数:
-
idx_a index a idx_b index b
- 返回:
- computed kernel function at indices a,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
- 参数:
-
avec vector a bvec vector b len length of string
- 返回:
- computed kernel function
| virtual EKernelType get_kernel_type | ( | ) | [virtual] |
return what type of kernel we are
- 返回:
- kernel type
| virtual const char* get_name | ( | void | ) | const [virtual] |
return the kernel's name
- 返回:
- name Regulatory Modules
initialize kernel
- 参数:
-
l features of left-hand side r features of right-hand side
- 返回:
- if initializing was successful
| void set_motif_positions | ( | CSimpleFeatures< uint16_t > * | positions_lhs, |
| CSimpleFeatures< uint16_t > * | positions_rhs | ||
| ) |
set motif positions
- 参数:
-
positions_lhs motif positions on lhs positions_rhs motif positions on rhs
| void set_wd_weights | ( | ) | [protected] |
set standard weighted degree kernel weighting
成员数据文档
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
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