LocalAlignmentStringKernel.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) 1999-2008 Soeren Sonnenburg
00008  * Copyright (C) 1999-2008 Fraunhofer Institute FIRST and Max-Planck-Society
00009  */
00010 
00011 #ifndef _LOCALALIGNMENTSTRINGKERNEL_H___
00012 #define _LOCALALIGNMENTSTRINGKERNEL_H___
00013 
00014 #include "lib/common.h"
00015 #include "kernel/StringKernel.h"
00016 
00017 #define LOGSUM_TBL 10000      /* span of the logsum table */
00018 
00023 class CLocalAlignmentStringKernel: public CStringKernel<char>
00024 {
00025     public:
00029         CLocalAlignmentStringKernel(int32_t size);
00030 
00036         CLocalAlignmentStringKernel(
00037             CStringFeatures<char>* l, CStringFeatures<char>* r);
00038 
00039         virtual ~CLocalAlignmentStringKernel();
00040 
00047         virtual bool init(CFeatures* l, CFeatures* r);
00048 
00050         virtual void cleanup();
00051 
00057         virtual bool load_init(FILE* src) { return false; }
00058 
00064         virtual bool save_init(FILE* dest) { return false; }
00065 
00070         virtual EKernelType get_kernel_type()
00071         {
00072             return K_LOCALALIGNMENT;
00073         }
00074 
00079         virtual const char* get_name()
00080         {
00081             return "LocalAlignment";
00082         }
00083 
00084     private:
00086         void init_logsum();
00087 
00094         int32_t LogSum(int32_t p1, int32_t p2);
00095 
00102         float32_t LogSum2(float32_t p1, float32_t p2);
00103 
00105         void initialize();
00106 
00115         float64_t LAkernelcompute(
00116             int32_t* aaX, int32_t* aaY, int32_t nX, int32_t nY);
00117 
00118     protected:
00127         virtual float64_t compute(int32_t idx_a, int32_t idx_b);
00128 
00129     protected:
00131         bool initialized;
00132 
00134         int32_t *isAA;
00136         int32_t *aaIndex;
00137 
00139         int32_t opening;
00141         int32_t extension;
00142 
00144         static int32_t logsum_lookup[LOGSUM_TBL];
00146         static const int32_t blosum[];
00148         int32_t* scaled_blosum;
00149 };
00150 
00151 #endif /* _LOCALALIGNMENTSTRINGKERNEL_H__ */
00152 

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