25 lines
1.3 KiB
C
Executable File
25 lines
1.3 KiB
C
Executable File
/*
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* sse_banded_LCS_alignment.h
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*
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* Created on: november 29, 2012
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* Author: mercier
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*/
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#ifndef SSE_BANDED_LCS_ALIGNMENT_H_
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#define SSE_BANDED_LCS_ALIGNMENT_H_
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#include <stdint.h>
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double sse_banded_lcs_align(int16_t* seq1, int16_t* seq2, int l1, int l2, BOOL normalize, int reference, BOOL lcsmode, int16_t* address, int LCSmin);
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int calculateSizeToAllocate(int maxLen, int minLen, int LCSmin);
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void calculateThresholdFromErrorNumber(int error, int length, double* threshold);
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void iniSeq(int16_t* seq, int size, int16_t iniValue);
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void putSeqInSeq(int16_t* seq, char* s, int l, BOOL reverse);
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double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, BOOL normalize, int reference, BOOL lcsmode, int16_t** address, int* buffer_size, int16_t** iseq1,
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int16_t** iseq2, int* buffer_sizeS);
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int prepareTablesForSumathings(int lmax, int lmin, double threshold, BOOL normalize, int reference, BOOL lcsmode,
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int16_t** address, int16_t** iseq1, int16_t** iseq2);
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double alignForSumathings(char* seq1, int16_t* iseq1, char* seq2, int16_t* iseq2, int l1, int l2, BOOL normalize,
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int reference, BOOL lcsmode, int16_t* address, int sizeForSeqs, int LCSmin);
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int calculateLCSmin(int l1, int l2, double threshold, BOOL normalize, int reference, BOOL lcsmode);
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#endif
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