/usr/include/shogun/features/ExplicitSpecFeatures.h is in libshogun-dev 1.1.0-4ubuntu2.
This file is owned by root:root, with mode 0o644.
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* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 3 of the License, or
* (at your option) any later version.
*
* Written (W) 2009 Soeren Sonnenburg
* Copyright (C) 2009 Fraunhofer Institute FIRST and Max-Planck-Society
*/
#ifndef _EXPLICITSPECFEATURES_H___
#define _EXPLICITSPECFEATURES_H___
#include <shogun/lib/common.h>
#include <shogun/features/DotFeatures.h>
#include <shogun/features/StringFeatures.h>
namespace shogun
{
template <class ST> class CStringFeatures;
/**@brief Features that compute the Spectrum Kernel feature space explicitly.
*
* \sa CCommWordStringKernel
*/
class CExplicitSpecFeatures : public CDotFeatures
{
public:
/** default constructor */
CExplicitSpecFeatures();
/** constructor
*
* @param str stringfeatures (of words)
* @param normalize whether to use sqrtdiag normalization
*/
CExplicitSpecFeatures(CStringFeatures<uint16_t>* str, bool normalize=true);
/** copy constructor */
CExplicitSpecFeatures(const CExplicitSpecFeatures & orig);
/** destructor */
virtual ~CExplicitSpecFeatures();
/** duplicate feature object
*
* @return feature object
*/
virtual CFeatures* duplicate() const;
/** obtain the dimensionality of the feature space
*
* (not mix this up with the dimensionality of the input space, usually
* obtained via get_num_features())
*
* @return dimensionality
*/
virtual int32_t get_dim_feature_space() const;
/** compute dot product between vector1 and vector2,
* appointed by their indices
*
* @param vec_idx1 index of first vector
* @param df DotFeatures (of same kind) to compute dot product with
* @param vec_idx2 index of second vector
*/
virtual float64_t dot(int32_t vec_idx1, CDotFeatures* df, int32_t vec_idx2);
/** compute dot product between vector1 and a dense vector
*
* @param vec_idx1 index of first vector
* @param vec2 pointer to real valued vector
* @param vec2_len length of real valued vector
*/
virtual float64_t dense_dot(int32_t vec_idx1, const float64_t* vec2, int32_t vec2_len);
/** add vector 1 multiplied with alpha to dense vector2
*
* @param alpha scalar alpha
* @param vec_idx1 index of first vector
* @param vec2 pointer to real valued vector
* @param vec2_len length of real valued vector
* @param abs_val if true add the absolute value
*/
virtual void add_to_dense_vec(float64_t alpha, int32_t vec_idx1,
float64_t* vec2, int32_t vec2_len, bool abs_val=false);
#ifndef DOXYGEN_SHOULD_SKIP_THIS
/** iterator for weighted spectrum features */
struct explicit_spec_feature_iterator
{
/** pointer to feature vector */
uint16_t* vec;
/** index of vector */
int32_t vidx;
/** length of vector */
int32_t vlen;
/** if we need to free the vector*/
bool vfree;
/** feature index */
int32_t index;
};
#endif
/** iterate over the non-zero features
*
* call get_feature_iterator first, followed by get_next_feature and
* free_feature_iterator to cleanup
*
* @param vector_index the index of the vector over whose components to
* iterate over
* @return feature iterator (to be passed to get_next_feature)
*/
virtual void* get_feature_iterator(int32_t vector_index);
/** iterate over the non-zero features
*
* call this function with the iterator returned by get_first_feature
* and call free_feature_iterator to cleanup
*
* @param index is returned by reference (-1 when not available)
* @param value is returned by reference
* @param iterator as returned by get_first_feature
* @return true if a new non-zero feature got returned
*/
virtual bool get_next_feature(int32_t& index, float64_t& value, void* iterator);
/** clean up iterator
* call this function with the iterator returned by get_first_feature
*
* @param iterator as returned by get_first_feature
*/
virtual void free_feature_iterator(void* iterator);
/** get number of non-zero features in vector
*
* @param num which vector
* @return number of non-zero features in vector
*/
virtual int32_t get_nnz_features_for_vector(int32_t num);
/** get feature type
*
* @return templated feature type
*/
virtual EFeatureType get_feature_type();
/** get feature class
*
* @return feature class
*/
virtual EFeatureClass get_feature_class();
/** get number of strings
*
* @return number of strings
*/
virtual int32_t get_num_vectors() const;
/** get size of one element
*
* @return size of one element
*/
virtual int32_t get_size();
/** @return object name */
inline virtual const char* get_name() const { return "ExplicitSpecFeatures"; }
protected:
/** obtain the k-spectrum from a list of strings
*
* @param str the string feature object already in k-mer format
*/
void obtain_kmer_spectrum(CStringFeatures<uint16_t>* str);
/** free kmer spectrum */
void delete_kmer_spectrum();
protected:
/** use sqrtdiag normalization */
bool use_normalization;
/** number of strings */
int32_t num_strings;
/** size of alphabet */
int32_t alphabet_size;
/** size of k-mer spectrum*/
int32_t spec_size;
/** k-mer counts for all strings */
float64_t** k_spectrum;
};
}
#endif // _EXPLICITSPECFEATURES_H___
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