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 "lib/common.h"
00015 #include "kernel/StringKernel.h"
00016 #include "features/SimpleFeatures.h"
00017 
00018 namespace shogun
00019 {
00025 class CRegulatoryModulesStringKernel: public CStringKernel<char>
00026 {
00027     public:
00036         CRegulatoryModulesStringKernel(int32_t size, float64_t width, int32_t degree, int32_t shift, int32_t window);
00037 
00050         CRegulatoryModulesStringKernel(CStringFeatures<char>* lstr, CStringFeatures<char>* rstr, 
00051             CSimpleFeatures<uint16_t>* lpos, CSimpleFeatures<uint16_t>* rpos, 
00052             float64_t width, int32_t degree, int32_t shift, int32_t window, int32_t size=10);
00053 
00055         virtual ~CRegulatoryModulesStringKernel();
00056 
00063         virtual bool init(CFeatures* l, CFeatures* r);
00064 
00069         virtual EKernelType get_kernel_type() { return K_REGULATORYMODULES; }
00070 
00075         inline virtual const char* get_name() const { return "RegulatoryModulesStringKernel"; }
00076         
00082         void set_motif_positions(
00083             CSimpleFeatures<uint16_t>* positions_lhs, CSimpleFeatures<uint16_t>* positions_rhs);
00084         
00085     protected:
00094         virtual float64_t compute(int32_t idx_a, int32_t idx_b);
00095         
00103         float64_t compute_wds(char* avec, char* bvec, int32_t len);
00104 
00105         
00107         void set_wd_weights();
00108 
00109     protected:
00111         float64_t width;
00112 
00114         int32_t degree; 
00116         int32_t shift;
00117         
00119         int32_t window;
00120 
00122         CSimpleFeatures<uint16_t>* motif_positions_lhs;
00123 
00125         CSimpleFeatures<uint16_t>* motif_positions_rhs;
00126 
00128         float64_t* position_weights;
00129 
00131         float64_t* weights;
00132 };
00133 }
00134 #endif /* _REGULATORYMODULESSTRINGKERNEL_H__ */

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