SHOGUN
v1.1.0
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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/StringKernel.h> 00016 #include <shogun/features/SimpleFeatures.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 CSimpleFeatures<uint16_t>* lpos, CSimpleFeatures<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 inline virtual const char* get_name() const { return "RegulatoryModulesStringKernel"; } 00079 00085 void set_motif_positions( 00086 CSimpleFeatures<uint16_t>* positions_lhs, CSimpleFeatures<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 CSimpleFeatures<uint16_t>* motif_positions_lhs; 00129 00131 CSimpleFeatures<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__ */