OligoStringKernel.h

Go to the documentation of this file.
00001 /*
00002  * This program is free software; you can redistribute it and/or modify
00003  * it under the terms of the GNU General Public License as published by
00004  * the Free Software Foundation; either version 3 of the License, or
00005  * (at your option) any later version.
00006  *
00007  * Written (W) 2008 Christian Igel, Tobias Glasmachers
00008  * Copyright (C) 2008 Christian Igel, Tobias Glasmachers
00009  *
00010  * Shogun adjustments (W) 2008-2009 Soeren Sonnenburg
00011  * Copyright (C) 2008-2009 Fraunhofer Institute FIRST and Max-Planck-Society
00012  */
00013 #ifndef _OLIGOSTRINGKERNEL_H_
00014 #define _OLIGOSTRINGKERNEL_H_
00015 
00016 #include "kernel/StringKernel.h"
00017 
00018 #include <vector>
00019 #include <string>
00020 
00021 namespace shogun
00022 {
00041 class COligoStringKernel : public CStringKernel<char>
00042 {
00043     public:
00049         COligoStringKernel(int32_t cache_size, int32_t k, float64_t width);
00050 
00052         virtual ~COligoStringKernel();
00053 
00060         virtual bool init(CFeatures* l, CFeatures* r);
00061 
00066         virtual EKernelType get_kernel_type() { return K_OLIGO; }
00067 
00072         virtual const char* get_name() const { return "Oligo"; }
00073 
00074 
00075         virtual float64_t compute(int32_t x, int32_t y);
00076 
00079         virtual void cleanup();
00080 
00081     protected:
00095         static void encodeOligo(
00096             const std::string& sequence, uint32_t k_mer_length,
00097             const std::string& allowed_characters,
00098             std::vector< std::pair<int32_t, float64_t> >&   values);
00099 
00107         static void getSequences(
00108             const std::vector<std::string>& sequences,
00109             uint32_t k_mer_length, const std::string& allowed_characters,
00110             std::vector< std::vector< std::pair<int32_t, float64_t> > >& encoded_sequences);
00111 
00127         float64_t kernelOligoFast(
00128             const std::vector< std::pair<int32_t, float64_t> >& x,
00129             const std::vector< std::pair<int32_t, float64_t> >& y,
00130             int32_t max_distance = -1);
00131 
00132     private: 
00143         void getExpFunctionCache(uint32_t sequence_length);
00144 
00145         static inline bool cmpOligos_(std::pair<int32_t, float64_t> a,
00146                 std::pair<int32_t, float64_t> b )
00147         {
00148             return (a.second < b.second);
00149         }
00150 
00151     protected:
00153         int32_t k;
00155         float64_t width;
00157         float64_t* gauss_table;
00158 };
00159 }
00160 #endif // _OLIGOSTRINGKERNEL_H_

SHOGUN Machine Learning Toolbox - Documentation