详细描述
The Regulaty Modules kernel, based on the WD kernel, as published in Schultheiss et al., Bioinformatics (2009) on regulatory sequences.
在文件RegulatoryModulesStringKernel.h第25行定义。
所有成员的列表。
公有成员 |
| CRegulatoryModulesStringKernel (int32_t size, float64_t width, int32_t degree, int32_t shift, int32_t window) |
| 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) |
virtual | ~CRegulatoryModulesStringKernel () |
virtual bool | init (CFeatures *l, CFeatures *r) |
virtual EKernelType | get_kernel_type () |
virtual const char * | get_name () const |
void | set_motif_positions (CSimpleFeatures< uint16_t > *positions_lhs, CSimpleFeatures< uint16_t > *positions_rhs) |
保护成员 |
virtual float64_t | compute (int32_t idx_a, int32_t idx_b) |
float64_t | compute_wds (char *avec, char *bvec, int32_t len) |
void | set_wd_weights () |
保护属性 |
float64_t | width |
int32_t | degree |
int32_t | shift |
int32_t | window |
CSimpleFeatures< uint16_t > * | motif_positions_lhs |
CSimpleFeatures< uint16_t > * | motif_positions_rhs |
float64_t * | position_weights |
float64_t * | weights |
构造及析构函数文档
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 |
在文件RegulatoryModulesStringKernel.cpp第19行定义。
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 |
在文件RegulatoryModulesStringKernel.cpp第26行定义。
成员函数文档
float64_t compute |
( |
int32_t |
idx_a, |
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int32_t |
idx_b |
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) |
| [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。
在文件RegulatoryModulesStringKernel.cpp第75行定义。
float64_t compute_wds |
( |
char * |
avec, |
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char * |
bvec, |
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int32_t |
len |
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) |
| [protected] |
virtual const char* get_name |
( |
) |
const [virtual] |
void set_wd_weights |
( |
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[protected] |
成员数据文档
int32_t shift [protected] |
该类的文档由以下文件生成: