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 
00020 class CLocalAlignmentStringKernel: public CStringKernel<CHAR>
00021 {
00022     public:
00026         CLocalAlignmentStringKernel(INT size);
00027 
00033         CLocalAlignmentStringKernel(
00034             CStringFeatures<CHAR>* l, CStringFeatures<CHAR>* r);
00035 
00036         virtual ~CLocalAlignmentStringKernel();
00037 
00044         virtual bool init(CFeatures* l, CFeatures* r);
00045 
00047         virtual void cleanup();
00048 
00054         virtual bool load_init(FILE* src) { return false; }
00055 
00061         virtual bool save_init(FILE* dest) { return false; }
00062 
00067         virtual EKernelType get_kernel_type()
00068         {
00069             return K_LOCALALIGNMENT;
00070         }
00071 
00076         virtual const CHAR* get_name()
00077         {
00078             return "LocalAlignment";
00079         }
00080 
00081     private:
00083         void init_logsum();
00084 
00091         int LogSum(int p1, int p2);
00092 
00099         float LogSum2(float p1, float p2);
00100 
00102         void initialize();
00103 
00112         DREAL LAkernelcompute(int* aaX, int* aaY, int nX, int nY);
00113 
00114     protected:
00123         virtual DREAL compute(INT idx_a, INT idx_b);
00124 
00125     protected:
00127         bool initialized;
00128 
00130         int *isAA;
00132         int *aaIndex;
00133 
00135         int opening;
00137         int extension;
00138 
00140         static int logsum_lookup[LOGSUM_TBL];
00142         static const int blosum[];
00144         int* scaled_blosum;
00145 };
00146 
00147 #endif /* _LOCALALIGNMENTSTRINGKERNEL_H__ */
00148 

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