gpu_module.h

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/*
swsharp - CUDA parallelized Smith Waterman with applying Hirschberg's and 
Ukkonen's algorithm and dynamic cell pruning.
Copyright (C) 2013 Matija Korpar, contributor Mile Šikić

This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.

This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
GNU General Public License for more details.

You should have received a copy of the GNU General Public License
along with this program.  If not, see <http://www.gnu.org/licenses/>.

Contact the author by mkorpar@gmail.com.
*/
#ifndef __SW_SHARP_GPU_MODULEH__
#define __SW_SHARP_GPU_MODULEH__

#include "alignment.h"
#include "chain.h"
#include "scorer.h"
#include "thread.h"

#ifdef __cplusplus 
extern "C" {
#endif

//******************************************************************************
// SINGLE ALIGNMENT

extern void hwEndDataGpu(int* queryEnd, int* targetEnd, int* outScore, 
    Chain* query, Chain* target, Scorer* scorer, int score, int card, 
    Thread* thread);
    
extern void nwFindScoreGpu(int* queryStart, int* targetStart, Chain* query, 
    Chain* target, Scorer* scorer, int score, int card, Thread* thread);

extern void nwLinearDataGpu(int** scores, int** affines, Chain* query, 
    int queryFrontGap, Chain* target, int targetFrontGap, Scorer* scorer, 
    int pLeft, int pRight, int card, Thread* thread);

extern void ovEndDataGpu(int* queryEnd, int* targetEnd, int* outScore, 
    Chain* query, Chain* target, Scorer* scorer, int score, int card, 
    Thread* thread);

extern void ovFindScoreGpu(int* queryStart, int* targetStart, Chain* query, 
    Chain* target, Scorer* scorer, int score, int card, Thread* thread);

extern void swEndDataGpu(int* queryEnd, int* targetEnd, int* outScore, 
    int** scores, int** affines, Chain* query, Chain* target, Scorer* scorer, 
    int score, int card, Thread* thread);

//******************************************************************************

//******************************************************************************
// DATABASE ALIGNMENT

typedef struct ChainDatabaseGpu ChainDatabaseGpu;

extern ChainDatabaseGpu* chainDatabaseGpuCreate(Chain** database, int databaseLen, 
    int* cards, int cardsLen);

extern void chainDatabaseGpuDelete(ChainDatabaseGpu* chainDatabaseGpu);

extern void scoreDatabaseGpu(int** scores, int type, Chain* query, 
    ChainDatabaseGpu* chainDatabaseGpu, Scorer* scorer, int* indexes, 
    int indexesLen, int* cards, int cardsLen, Thread* thread);

extern void scoreDatabasesGpu(int** scores, int type, Chain** queries, 
    int queriesLen, ChainDatabaseGpu* chainDatabaseGpu, Scorer* scorer, 
    int* indexes, int indexesLen, int* cards, int cardsLen, Thread* thread);
    
//******************************************************************************

#ifdef __cplusplus 
}
#endif
#endif // __SW_SHARP_GPU_MODULEH__