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/*
* This file is part of zAlign.
*
* zAlign 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.
*
* zAlign 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 zAlign. If not, see <http://www.gnu.org/licenses/>.
*/
/* Header file inclusions */
#include "zalign.h"
/* Function definitions */
/*
* zalign_stage1() is the first stage the 'zalign' executable, analogous to the
* second stage of 'mpialign'. It finds the best alignment scores of the
* inverted input sequences 's' and 't' using a blocked aligner algorithm, then
* iterates over the obtained list of alignments executing zalign_stage2().
*/
void zalign_stage1 (sequence_t s, sequence_t t, score_t scores) {
alignbounds_t bounds;
blkalign_t blkaligner;
sequence_t rs,
rt;
/* show introductory information for zalign_stage1() */
/* TODO: show a progress meter on this stage */
printf ("Stage 1: Find best scores\n");
printf ("-------------------------\n\n\n");
/* invert input sequences */
rs = sequence_invert (s);
rt = sequence_invert (t);
/* initialize blocked aligner and align inverted sequences */
blkaligner = blkalign_new (BLKALIGN_STD, rs, rt, scores, NULL, 0, 0);
blkalign_align (blkaligner);
/* store pointer to alignment array's first element */
bounds = blkaligner->strat->alignarray->alignments;
/* show introductory information for zalign_stage2() */
printf ("Stage 2: Obtain alignments\n");
printf ("--------------------------\n\n");
/* iterate through each alignment array element, executing zalign_stage2() */
do {
zalign_stage2 (bounds, s, t, scores);
bounds = bounds->next;
} while (bounds != NULL);
/* housekeeping... */
blkalign_free (blkaligner);
free (rt);
free (rs);
}
/*
* zalign_stage2() is the second stage the 'zalign' executable, analogous to the
* fourth stage of 'mpialign'. It finds and prints an alignment of 's' and 't'
* sequences, given by the 'bounds' parameter. No value is returned.
*/
void zalign_stage2 (alignbounds_t bounds, sequence_t s, sequence_t t, score_t scores) {
alignment_t alignment;
sequence_t ss,
st;
size_t slen,
tlen;
/* calculate sequence sizes */
slen = strlen (s);
tlen = strlen (t);
/* obtain subsequences to be aligned */
ss = sequence_subseq (s, slen - bounds->s_end + 1, slen);
st = sequence_subseq (t, tlen - bounds->t_end + 1, tlen);
/* initialize linear fickett aligner, set parameters and align subsequences */
LinearFickettAligner aligner (ss, st, scores, bounds->score);
aligner.setK (-bounds->vdiv);
aligner.setL (-bounds->hdiv);
aligner.setSDisplacement (slen - bounds->s_end);
aligner.setTDisplacement (tlen - bounds->t_end);
aligner.align ();
/* print obtained alignment to screen */
alignment = aligner.getAlignment (0);
SET_DISPLACEMENT (alignment->s_start, alignment->s_end,
(slen - bounds->s_end));
SET_DISPLACEMENT (alignment->t_start, alignment->t_end,
(tlen - bounds->t_end));
alignment_display (alignment, s, t);
/* housekeeping... */
alignment_free (alignment);
free (st);
free (ss);
}
/*
* zalign entrypoint
*/
int main(int argc, char *argv[]) {
sequence_t s,
t;
st_options options = {"", "", 1, 1, 1, NULL};
/* parse commandline options, exiting on error */
if (opt_parse (argc, argv, ZALIGN_RANK, &options))
return EXIT;
/* read sequences from filesystem */
s = fasta_read (options.sfile);
t = fasta_read (options.tfile);
/* print some informational stuff before we begin */
printf ("\nAlignment configuration\n");
printf ("-----------------------\n\n");
printf (" # File parameters\n\n");
printf (" S sequence: %u characters\n", strlen(s));
printf (" Filename: %s\n\n", options.sfile);
printf (" T sequence: %u characters\n", strlen(t));
printf (" Filename: %s\n\n", options.tfile);
printf (" # Scoring parameters\n\n");
printf (" Match: %3d\n", options.scores->match);
printf (" Mismatch: %3d\n", options.scores->mismatch);
printf (" Gap Opening: %3d\n", options.scores->gap_open);
printf (" Gap Extension:%3d\n\n\n", options.scores->gap_extension);
/* execute first stage of alignment -- it'll call second stage later on */
zalign_stage1 (s, t, options.scores);
/* housekeeping... */
free (s);
free (t);
score_free (options.scores);
return SUCCESS;
}
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