Eric Coissac
d298385685
Former-commit-id: 202296404e6a70f8ae96db99faffb456104c57e9 Former-commit-id: 118417735d2055683607df9809c9b721cc1b1bab
68 lines
2.7 KiB
C
68 lines
2.7 KiB
C
/*
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Copyright (C) 2006 G achaz, F boyer, E rocha, A viari and E coissac.
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This program is free software; you can redistribute it and/or
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modify it under the terms of the GNU Lesser General Public License
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as published by the Free Software Foundation; either version 2.1
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of the License, or (at your option) any later version.
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This program is distributed in the hope that it will be useful,
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but WITHOUT ANY WARRANTY; without even the implied warranty of
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MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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GNU Lesser General Public License for more details.
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You should have received a copy of the GNU Lesser General Public License
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along with this program; if not, write to the Free Software
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Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA.
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for more information, please contact guillaume achaz <achaz@abi.snv.jussieu.fr>
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*/
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#ifndef _ALIGN_H_
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#define _ALIGN_H_
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/*
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Macros to turn any char from A-Z to a symb 0-26 (for S&W scoring matrix)
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*/
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#define CHAR2SYMB( A ) ( (A) - 65 )
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#define SYMB2CHAR( i ) ( (i) + 65 )
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#define Match(A,B) pScoring->matrix[ CHAR2SYMB(seq1[ (A)-1 ]) ][ CHAR2SYMB(seq2[ (B)-1 ]) ]
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/*
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The Seed2Repeat part
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*/
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Repeats align_seeds(AllSeeds_type *AllSeeds, char *sequence, float Xg, float gap_open, float gap_ext,\
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char matrix_type, int16_t Lmin, int8_t opt_dir, int8_t opt_inv, int8_t opt_overlap, float merge_repeats);
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Repeats align_seeds_2seq(AllSeeds_type *AllSeeds, char *seq1, char *seq2, float Xg, float gap_open, float gap_ext, char matrix_type,\
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int16_t Lmin, int8_t opt_dir, int8_t opt_inv, float merge_repeats);
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Rep alignd(int32_t pos1, int32_t pos2, int32_t len, char *sequence, int32_t sizeseq,
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float Xg, SCORING *pScoring, RESULTS *pResults , int8_t opt_overlap);
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Rep aligni(int32_t pos1, int32_t pos2, int32_t len, char *sequence, char *invsequence, int32_t sizeseq,\
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float Xg, SCORING *pScoring, RESULTS *pResults );
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Rep alignd_2seq(int32_t pos1, int32_t pos2, int32_t len, char *seq1, char *seq2, \
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int32_t size1, int32_t size2, float Xg, SCORING *pScoring, RESULTS *pResults );
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Rep aligni_2seq(int32_t pos1, int32_t pos2, int32_t len, char *seq1, char *invseq2, \
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int32_t size1, int32_t size2, float Xg, SCORING *pScoring, RESULTS *pResults );
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/*
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The alignemnt itself
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*/
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void align_blast2like(char *seq1, char *seq2, float Xg, SCORING *pScoring,\
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RESULTS *pResults, char direction, int32_t max_row, int32_t max_col, int32_t diff_max);
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void log_matrix(char *sequence, float gap_open, float gap_ext, SCORING *pScoring );
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void identity_matrix(char *sequence, float gap_open, float gap_ext, SCORING *pScoring);
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#endif /*_ALIGN_H_*/
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