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SNPFeatures.h
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1 /*
2  * This program is free software; you can redistribute it and/or modify
3  * it under the terms of the GNU General Public License as published by
4  * the Free Software Foundation; either version 3 of the License, or
5  * (at your option) any later version.
6  *
7  * Written (W) 2010 Soeren Sonnenburg
8  * Copyright (C) 2010 Berlin Institute of Technology
9  */
10 
11 #ifndef _SNPFEATURES_H___
12 #define _SNPFEATURES_H___
13 
14 #include <shogun/lib/common.h>
17 
18 namespace shogun
19 {
20 template <class ST> class CStringFeatures;
21 
27 class CSNPFeatures : public CDotFeatures
28 {
29  public:
31  CSNPFeatures();
32 
38 
40  CSNPFeatures(const CSNPFeatures & orig);
41 
43  virtual ~CSNPFeatures();
44 
52  virtual int32_t get_dim_feature_space() const;
53 
61  virtual float64_t dot(int32_t vec_idx1, CDotFeatures* df, int32_t vec_idx2);
62 
69  virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len);
70 
79  virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1,
80  float64_t* vec2, int32_t vec2_len, bool abs_val=false);
81 
87  virtual int32_t get_nnz_features_for_vector(int32_t num);
88 
98  virtual void* get_feature_iterator(int32_t vector_index);
99 
110  virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator);
111 
117  virtual void free_feature_iterator(void* iterator);
118 
123  virtual CFeatures* duplicate() const;
124 
129  virtual EFeatureType get_feature_type() const;
130 
135  virtual EFeatureClass get_feature_class() const;
136 
141  virtual int32_t get_num_vectors() const;
142 
146 
149 
154  void set_minor_base_string(const char* str);
155 
160  void set_major_base_string(const char* str);
161 
166  char* get_minor_base_string();
167 
172  char* get_major_base_string();
173 
179  void obtain_base_strings(CSNPFeatures* snp=NULL);
180 
182  virtual const char* get_name() const { return "SNPFeatures"; }
183 
186  virtual SGMatrix<float64_t> get_histogram(bool normalize=true);
187 
192 
193  private:
200  void find_minor_major_strings(uint8_t* minor, uint8_t* major);
201 
202  protected:
205 
207  int32_t string_length;
209  int32_t num_strings;
211  int32_t w_dim;
212 
215 
217  uint8_t* m_str_min;
219  uint8_t* m_str_maj;
220 };
221 }
222 #endif // _SNPFEATURES_H___
virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1, float64_t *vec2, int32_t vec2_len, bool abs_val=false)
virtual void free_feature_iterator(void *iterator)
virtual int32_t get_num_vectors() const
float64_t get_normalization_const()
virtual bool get_next_feature(int32_t &index, float64_t &value, void *iterator)
virtual int32_t get_nnz_features_for_vector(int32_t num)
Definition: SNPFeatures.cpp:89
void set_major_base_string(const char *str)
void obtain_base_strings(CSNPFeatures *snp=NULL)
virtual int32_t get_dim_feature_space() const
Definition: SNPFeatures.cpp:84
char * get_major_base_string()
Features that support dot products among other operations.
Definition: DotFeatures.h:41
virtual void * get_feature_iterator(int32_t vector_index)
EFeatureClass
shogun feature class
Definition: FeatureTypes.h:35
virtual EFeatureType get_feature_type() const
Definition: SNPFeatures.cpp:94
char * get_minor_base_string()
virtual const char * get_name() const
Definition: SNPFeatures.h:182
double float64_t
Definition: common.h:48
virtual CFeatures * duplicate() const
EFeatureType
shogun feature type
Definition: FeatureTypes.h:16
CStringFeatures< uint8_t > * strings
Definition: SNPFeatures.h:204
float64_t normalization_const
Definition: SNPFeatures.h:214
Features that compute the Weighted Degreee Kernel feature space explicitly.
Definition: SNPFeatures.h:27
void set_minor_base_string(const char *str)
virtual float64_t dense_dot(int32_t vec_idx1, const float64_t *vec2, int32_t vec2_len)
virtual SGMatrix< float64_t > get_histogram(bool normalize=true)
The class Features is the base class of all feature objects.
Definition: Features.h:62
void set_normalization_const(float64_t n=0)
static SGMatrix< float64_t > get_2x3_table(CSNPFeatures *pos, CSNPFeatures *neg)
virtual EFeatureClass get_feature_class() const
Definition: SNPFeatures.cpp:99
virtual float64_t dot(int32_t vec_idx1, CDotFeatures *df, int32_t vec_idx2)

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