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src
shogun
features
SNPFeatures.h
Go to the documentation of this file.
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/*
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* This program is free software; you can redistribute it and/or modify
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* it under the terms of the GNU General Public License as published by
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* the Free Software Foundation; either version 3 of the License, or
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* (at your option) any later version.
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*
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* Written (W) 2010 Soeren Sonnenburg
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* Copyright (C) 2010 Berlin Institute of Technology
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*/
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#ifndef _SNPFEATURES_H___
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#define _SNPFEATURES_H___
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#include <
shogun/lib/common.h
>
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#include <
shogun/features/DotFeatures.h
>
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#include <
shogun/features/StringFeatures.h
>
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namespace
shogun
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{
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template
<
class
ST>
class
CStringFeatures;
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class
CSNPFeatures
:
public
CDotFeatures
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{
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public
:
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CSNPFeatures
();
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CSNPFeatures
(
CStringFeatures<uint8_t>
* str);
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CSNPFeatures
(
const
CSNPFeatures
& orig);
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virtual
~CSNPFeatures
();
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virtual
int32_t
get_dim_feature_space
()
const
;
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virtual
float64_t
dot
(int32_t vec_idx1,
CDotFeatures
* df, int32_t vec_idx2);
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virtual
float64_t
dense_dot
(int32_t vec_idx1,
const
float64_t
* vec2, int32_t vec2_len);
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virtual
void
add_to_dense_vec
(
float64_t
alpha, int32_t vec_idx1,
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float64_t
* vec2, int32_t vec2_len,
bool
abs_val=
false
);
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virtual
int32_t
get_nnz_features_for_vector
(int32_t num);
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virtual
void
*
get_feature_iterator
(int32_t vector_index);
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virtual
bool
get_next_feature
(int32_t& index,
float64_t
& value,
void
* iterator);
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virtual
void
free_feature_iterator
(
void
* iterator);
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virtual
CFeatures
*
duplicate
()
const
;
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virtual
EFeatureType
get_feature_type
()
const
;
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virtual
EFeatureClass
get_feature_class
()
const
;
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virtual
int32_t
get_num_vectors
()
const
;
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void
set_normalization_const
(
float64_t
n=0);
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float64_t
get_normalization_const
();
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void
set_minor_base_string
(
const
char
* str);
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void
set_major_base_string
(
const
char
* str);
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char
*
get_minor_base_string
();
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char
*
get_major_base_string
();
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void
obtain_base_strings
(
CSNPFeatures
* snp=NULL);
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virtual
const
char
*
get_name
()
const
{
return
"SNPFeatures"
; }
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virtual
SGMatrix<float64_t>
get_histogram
(
bool
normalize=
true
);
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static
SGMatrix<float64_t>
get_2x3_table
(
CSNPFeatures
* pos,
CSNPFeatures
* neg);
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private
:
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void
find_minor_major_strings(uint8_t* minor, uint8_t* major);
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protected
:
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CStringFeatures<uint8_t>
*
strings
;
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int32_t
string_length
;
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int32_t
num_strings
;
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int32_t
w_dim
;
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float64_t
normalization_const
;
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uint8_t*
m_str_min
;
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uint8_t*
m_str_maj
;
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};
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}
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#endif // _SNPFEATURES_H___
SHOGUN
Machine Learning Toolbox - Documentation