RegulatoryModulesStringKernel.h

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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) 2009 Sebastian J. Schultheiss and Soeren Sonnenburg
00008  * Copyright (C) 2009 Max-Planck-Society
00009  */
00010 
00011 #ifndef _REGULATORYMODULESSTRINGKERNEL_H___
00012 #define _REGULATORYMODULESSTRINGKERNEL_H___
00013 
00014 #include <shogun/lib/common.h>
00015 #include <shogun/kernel/string/StringKernel.h>
00016 #include <shogun/features/DenseFeatures.h>
00017 
00018 namespace shogun
00019 {
00025 class CRegulatoryModulesStringKernel: public CStringKernel<char>
00026 {
00027     public:
00029         CRegulatoryModulesStringKernel();
00030 
00039         CRegulatoryModulesStringKernel(int32_t size, float64_t width, int32_t degree, int32_t shift, int32_t window);
00040 
00053         CRegulatoryModulesStringKernel(CStringFeatures<char>* lstr, CStringFeatures<char>* rstr,
00054             CDenseFeatures<uint16_t>* lpos, CDenseFeatures<uint16_t>* rpos,
00055             float64_t width, int32_t degree, int32_t shift, int32_t window, int32_t size=10);
00056 
00058         virtual ~CRegulatoryModulesStringKernel();
00059 
00066         virtual bool init(CFeatures* l, CFeatures* r);
00067 
00072         virtual EKernelType get_kernel_type() { return K_REGULATORYMODULES; }
00073 
00078         virtual const char* get_name() const { return "RegulatoryModulesStringKernel"; }
00079 
00085         void set_motif_positions(
00086             CDenseFeatures<uint16_t>* positions_lhs, CDenseFeatures<uint16_t>* positions_rhs);
00087         /* register the parameters
00088          */
00089         virtual void register_params();
00090 
00091     protected:
00100         virtual float64_t compute(int32_t idx_a, int32_t idx_b);
00101 
00109         float64_t compute_wds(char* avec, char* bvec, int32_t len);
00110 
00111 
00113         void set_wd_weights();
00114 
00115     protected:
00117         float64_t width;
00118 
00120         int32_t degree;
00122         int32_t shift;
00123 
00125         int32_t window;
00126 
00128         CDenseFeatures<uint16_t>* motif_positions_lhs;
00129 
00131         CDenseFeatures<uint16_t>* motif_positions_rhs;
00132 
00134         int32_t alen;
00136         int32_t blen;
00137 
00139         float64_t* position_weights;
00140 
00142         float64_t* weights;
00143 };
00144 }
00145 #endif /* _REGULATORYMODULESSTRINGKERNEL_H__ */
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