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#include <tk.h>
#include "IO1.h"
#include "io_handle.h"
#include "complement.h"
#include "gap_cli_arg.h"
#include "io-reg.h"
#include "misc.h"
#include "tcl_utils.h"
#include "fort.h"
#include "tagUtils.h"
#include "list_proc.h"
#include "dna_utils.h"
typedef struct {
int position;
int rnum;
} read_details;
static int rd_sort_func(const void *p1, const void *p2) {
return ((const read_details *)p1)->position
- ((const read_details *)p2)->position;
}
/*
* Complements a contig. This is a C rewrite of the old CMPLMT fortran
* function.
*
* Initially we resort the sequence coordinates so that they are sorted
* decrementally by their end coordinates. Then we effectively complement
* those coordinates. This gets written back to the reading
* structures/contig left/right ends.
*
* Secondly we reverse/complement the sequences themselves.
*
* Finally we update the tags on the consensus.
*
* Returns 0 for success, -1 for failure
*/
int complement_contig(GapIO *io, int contig) {
read_details *rd = NULL;
int rnum, clen = io_clength(io, contig);
int count, i, err = 0;
GContigs c;
reg_complement rc;
if (contig_lock_write(io, contig) == -1) {
verror(ERR_WARN, "complement_contig", "Contig is busy");
return -1;
}
/* Fill our read_details array with sequence numbers and lengths */
for (count = 0, rnum = io_clnbr(io, contig);
rnum;
rnum = io_rnbr(io, rnum))
count++;
if (NULL == (rd = (read_details *)malloc(sizeof(*rd) * count)))
return -1;
for (count = 0, rnum = io_clnbr(io, contig);
rnum;
rnum = io_rnbr(io, rnum), count++) {
rd[count].rnum = rnum;
rd[count].position = io_relpos(io, rnum)+ABS(io_length(io, rnum))-1;
}
/*
* Sort incrementally.
* This list is mostly sorted already, so maybe a bubble sort
* would be preferable.
*/
qsort(rd, count, sizeof(*rd), rd_sort_func);
/*
* Reproduce the contig linked list from the sorted array.
*/
io_crnbr(io, contig) = rd[0].rnum;
for (i = 0; i < count; i++) {
io_rnbr(io, rd[i].rnum) = i > 0 ? rd[i-1].rnum : 0;
io_lnbr(io, rd[i].rnum) = i < count-1 ? rd[i+1].rnum : 0;
io_relpos(io, rd[i].rnum) = clen+1-rd[i].position;
io_length(io, rd[i].rnum) = -io_length(io, rd[i].rnum);
}
io_clnbr(io, contig) = rd[count-1].rnum;
/*
* Update the GReadings and GContigs structures.
* The r.start, r.end and r.length will be updated later by the
* call to io_complement_seq().
*/
for (i = 0; i < count; i++) {
GReadings r;
rnum = rd[i].rnum;
gel_read(io, rnum, r);
r.left = io_lnbr(io, rnum);
r.right = io_rnbr(io, rnum);
r.position = io_relpos(io, rnum);
r.sense ^= 1;
gel_write(io, rnum, r);
}
contig_read(io, contig, c);
c.left = io_clnbr(io, contig);
c.right = io_crnbr(io, contig);
contig_write(io, contig, c);
/* Complement the sequence data */
for (i = 0; i < count; i++) {
int length, start, end;
char *seq = NULL;
int1 *conf = NULL;
int2 *opos = NULL;
if (0 != io_aread_seq(io, rd[i].rnum,
&length, &start, &end,
&seq, &conf, &opos, 0)) {
err = 1;
continue;
}
io_complement_seq(&length, &start, &end, seq, conf, opos);
io_write_seq(io, rd[i].rnum, &length, &start, &end, seq, conf, opos);
if (seq) xfree(seq);
if (conf) xfree(conf);
if (opos) xfree(opos);
}
xfree(rd);
/* Complement the contig tags */
complement_contig_tags(io, contig);
flush2t(io);
/*
* Notify complement - this should be done in CMPLMT really, as should
* the busy checks etc.
*/
rc.job = REG_COMPLEMENT;
contig_notify(io, contig, (reg_data *)&rc);
return err;
}
/*
* Tk interface to complement_contig
*/
typedef struct {
GapIO *io;
char *contigs;
} com_args;
int tk_complement_contig(ClientData clientData,
Tcl_Interp *interp,
int argc,
char *argv[]) {
com_args args;
int num_contigs;
contig_list_t *contig_array = NULL;
int *contigs;
int err = 0, i;
cli_args a[] = {
{"-io", ARG_IO, 1, NULL, offsetof(com_args, io)},
{"-contigs", ARG_STR,1, NULL, offsetof(com_args, contigs)},
{NULL, 0, 0, NULL, 0}
};
vfuncheader("complement contig");
if (-1 == gap_parse_args(a, &args, argc, argv))
return TCL_ERROR;
/* create contig name array */
active_list_contigs(args.io, args.contigs, &num_contigs, &contig_array);
if (num_contigs == 0) {
xfree(contig_array);
return TCL_OK;
}
contigs = to_contigs_only(num_contigs, contig_array);
xfree(contig_array);
for (i = 0; i < num_contigs; i++)
if (-1 == complement_contig(args.io, contigs[i]))
err |= 1;
xfree(contigs);
if (err)
Tcl_SetResult(interp, "1", TCL_STATIC);
else
Tcl_SetResult(interp, "0", TCL_STATIC);
return TCL_OK;
}
f_proc_ret cmplmt_(f_int *RELPG, f_int *LNGTHG, f_int *LNBR, f_int *RNBR,
f_int *NGELS, f_int *NCONTS, f_int *LINCON, f_int *LLINO,
char *GEL, f_int *IDBSIZ, f_int *IDEVR, f_int *MAXGEL,
f_implicit gel_l) {
GapIO *io;
int contig;
if ( (io = io_handle(IDEVR)) == NULL) f_proc_return();
contig = io_dbsize(io) - *LINCON;
complement_contig(io, contig);
f_proc_return();
}
f_proc_ret sqcom_(char *SEQ, f_int *IDIM, f_implicit gel_l) {
complement_dna(SEQ, *IDIM);
f_proc_return();
}
f_proc_ret sqrev_(char *SEQ, f_int *IDIM, f_implicit gel_l) {
reverse_dna(SEQ, *IDIM);
f_proc_return();
}
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