117 lines
6.3 KiB
C
Executable File
117 lines
6.3 KiB
C
Executable File
/****************************************************************************
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* LCS alignment of two sequences header file *
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****************************************************************************/
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/**
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* @file sse_banded_LCS_alignment.h
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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* @date November 7th 2012
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* @brief header file for the functions handling the alignment of two sequences to compute their Longest Common Sequence.
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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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#include <stdbool.h>
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#include "obiblob.h"
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/**
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* @brief Macros for reference lengths to use when aligning.
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*
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* @since 2012
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* @author Eric Coissac (eric.coissac@metabarcoding.org)
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*/
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#define ALILEN (0)
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#define MAXLEN (1)
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#define MINLEN (2)
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/**
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* @brief Function calculating the minimum length of the Longest Common Subsequence between two sequences to be above a chosen score threshold.
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*
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* @warning The first argument (lmax) must correspond to length of the longest sequence.
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*
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* @param lmax The length of the longest sequence to align.
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* @param lmin The length of the shortest sequence to align.
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* @param threshold Score threshold. If the score is normalized and expressed in similarity, it is an identity, e.g. 0.95
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* for an identity of 95%. If the score is normalized and expressed in distance, it is (1.0 - identity),
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* e.g. 0.05 for an identity of 95%. If the score is not normalized and expressed in similarity, it is
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* the length of the Longest Common Subsequence. If the score is not normalized and expressed in distance,
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* it is (reference length - LCS length). Only sequence pairs with a similarity above the threshold are printed.
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* @param normalize Whether the score should be normalized with the reference sequence length.
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* @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length. // TODO
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* @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
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*
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* @returns The minimum length of the Longest Common Subsequence between two sequences to be above the chosen score threshold.
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*
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* @since 2012
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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int calculateLCSmin(int lmax, int lmin, double threshold, bool normalize, int reference, bool similarity_mode);
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/**
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* @brief Function aligning two sequences.
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*
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* The alignment algorithm is a banded global alignment algorithm, a modified version of the classical Needleman and Wunsch algorithm,
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* and uses indices based on the length of the Longest Common Subsequence between the two sequences.
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*
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* Note: the sequences do not need to be ordered (e.g. with the longest sequence as first argument).
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*
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* @param seq1 A pointer on the character string corresponding to the first sequence.
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* @param seq2 A pointer on the character string corresponding to the second sequence.
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* @param threshold Score threshold. If the score is normalized and expressed in similarity, it is an identity, e.g. 0.95
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* for an identity of 95%. If the score is normalized and expressed in distance, it is (1.0 - identity),
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* e.g. 0.05 for an identity of 95%. If the score is not normalized and expressed in similarity, it is
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* the length of the Longest Common Subsequence. If the score is not normalized and expressed in distance,
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* it is (reference length - LCS length). Only sequence pairs with a similarity above the threshold are printed.
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* @param normalize Whether the score should be normalized with the reference sequence length.
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* @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length. // TODO
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* @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
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* @param lcs_length A pointer on the int where the LCS length will be stored.
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* @param ali_length A pointer on the int where the alignment length will be stored.
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*
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* @returns The alignment score (normalized according to the parameters).
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*
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* @since 2012
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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double generic_sse_banded_lcs_align(char* seq1, char* seq2, double threshold, bool normalize, int reference, bool similarity_mode, int* lcs_length, int* ali_length);
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/**
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* @brief Function aligning two sequences encoded in obiblobs.
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*
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* The alignment algorithm is a banded global alignment algorithm, a modified version of the classical Needleman and Wunsch algorithm,
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* and uses indices based on the length of the Longest Common Subsequence between the two sequences.
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*
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* Note: the obiblobs do not need to be ordered (e.g. with the obiblob containing the longest sequence as first argument).
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*
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* @param seq1 A pointer on the blob containing the first sequence.
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* @param seq2 A pointer on the blob containing the second sequence.
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* @param threshold Score threshold. If the score is normalized and expressed in similarity, it is an identity, e.g. 0.95
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* for an identity of 95%. If the score is normalized and expressed in distance, it is (1.0 - identity),
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* e.g. 0.05 for an identity of 95%. If the score is not normalized and expressed in similarity, it is
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* the length of the Longest Common Subsequence. If the score is not normalized and expressed in distance,
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* it is (reference length - LCS length). Only sequence pairs with a similarity above the threshold are printed.
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* @param normalize Whether the score should be normalized with the reference sequence length.
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* @param reference The reference length. 0: The alignment length; 1: The longest sequence's length; 2: The shortest sequence's length. // TODO
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* @param similarity_mode Whether the score should be expressed in similarity (true) or distance (false).
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* @param lcs_length A pointer on the int where the LCS length will be stored.
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* @param ali_length A pointer on the int where the alignment length will be stored.
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*
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* @returns The alignment score (normalized according to the parameters).
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*
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* @since December 2016
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* @author Celine Mercier (celine.mercier@metabarcoding.org)
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*/
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double obiblob_sse_banded_lcs_align(Obi_blob_p seq1, Obi_blob_p seq2, double threshold, bool normalize, int reference, bool similarity_mode, int* lcs_length, int* ali_length);
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#endif
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