void igs_m027_state::sdwx_gfx_decrypt()
{
int i;
unsigned rom_size = 0x80000;
UINT8 *src = (UINT8 *) (memregion("gfx1")->base());
dynamic_buffer result_data(rom_size);
for (i=0; i<rom_size; i++)
result_data[i] = src[BITSWAP24(i, 23,22,21,20,19,18,17,16,15,14,13,12,11,8,7,6,10,9,5,4,3,2,1,0)];
for (i=0; i<rom_size; i+=0x200)
{
memcpy(src+i+0x000,&result_data[i+0x000],0x80);
memcpy(src+i+0x080,&result_data[i+0x100],0x80);
memcpy(src+i+0x100,&result_data[i+0x080],0x80);
memcpy(src+i+0x180,&result_data[i+0x180],0x80);
}
}
void igs_m027_state::sdwx_gfx_decrypt()
{
int i;
unsigned rom_size = 0x80000;
uint8_t *src = (uint8_t *) (memregion("tilemaps")->base());
std::vector<uint8_t> result_data(rom_size);
for (i=0; i<rom_size; i++)
result_data[i] = src[bitswap<24>(i, 23,22,21,20,19,18,17,16,15,14,13,12,11,8,7,6,10,9,5,4,3,2,1,0)];
for (i=0; i<rom_size; i+=0x200)
{
memcpy(src+i+0x000,&result_data[i+0x000],0x80);
memcpy(src+i+0x080,&result_data[i+0x100],0x80);
memcpy(src+i+0x100,&result_data[i+0x080],0x80);
memcpy(src+i+0x180,&result_data[i+0x180],0x80);
}
}
int init_sip_local_align_plot(Tcl_Interp *interp,
int seq_id_h,
int seq_id_v,
int result_id,
char *raster_win,
int raster_id,
char *colour,
int line_width)
{
char *opts[7];
seq_result *result;
d_plot *data;
if (NULL == (opts[1] = (char *)xmalloc((strlen(colour)+1) *
sizeof(char))))
return -1;
if (NULL == (opts[3] = (char *)xmalloc(5 * sizeof(char))))
return -1;
if (NULL == (opts[5] = (char *)xmalloc(15 * sizeof(char))))
return -1;
opts[0] = "-fg";
strcpy(opts[1], colour);
opts[2] = "-linewidth";
sprintf(opts[3], "%d", line_width);
opts[4] = "-capstyle";
strcpy(opts[5], "round");
opts[6] = NULL;
result = result_data(result_id, GetSeqNum(seq_id_h));
data = result->data;
init_dot_plot(interp, seq_id_h, seq_id_v, result_id, "local", raster_win,
raster_id, opts, 6, LINE, data->dim);
xfree(opts[1]);
xfree(opts[3]);
xfree(opts[5]);
return 0;
}
int init_sip_similar_spans_plot(Tcl_Interp *interp,
int seq_id_h,
int seq_id_v,
int result_id,
char *raster_win,
int raster_id,
char *colour,
int line_width)
{
char *opts[5];
seq_result *result;
d_plot *data;
if (NULL == (opts[1] = (char *)xmalloc((strlen(colour)+1) *
sizeof(char))))
return -1;
if (NULL == (opts[3] = (char *)xmalloc(5 * sizeof(char))))
return -1;
opts[0] = "-fg";
strcpy(opts[1], colour);
opts[2] = "-linewidth";
sprintf(opts[3], "%d", line_width);
opts[4] = NULL;
result = result_data(result_id, GetSeqNum(seq_id_h));
data = result->data;
init_dot_plot(interp, seq_id_h, seq_id_v, result_id, "similar spans",
raster_win, raster_id, opts, 4, DOT, data->dim);
xfree(opts[1]);
xfree(opts[3]);
return 0;
}
/*
* plots the results of a search on the plot window of the contig selector
*/
void
PlotRepeats(GapIO *io,
mobj_repeat *repeat) {
int i;
char cmd[1024];
int pos1, pos2;
int x1, y1, x2, y2;
/* int max_x = 0; */
int sense1 = 1;
int sense2 = 1;
int inum;
char *colour = repeat->colour;
int width = repeat->linewidth;
char *tag_id = repeat->tagname;
obj_match new_match;
int cs_id;
obj_cs *cs;
cs_id = type_to_result(io, REG_TYPE_CONTIGSEL, 0);
cs = result_data(io, cs_id, 0);
for (i = 0; i < repeat->num_match; i++){
obj_match *match = (obj_match *)&repeat->match[i];
/* Check if shown */
if (match->flags & OBJ_FLAG_HIDDEN)
continue;
/* clip length of match if necessary */
new_match = *match;
DoClipping(io, &new_match);
/*
* printf("new pos1 %d pos2 %d length %d\n",
* new_match.pos1, new_match.pos2, new_match.length);
* printf("match pos1 %d pos2 %d length %d \n",
* match->pos1, match->pos2, match->length);
*/
pos1 = find_position_in_DB(io, abs(new_match.c1), new_match.pos1);
pos2 = find_position_in_DB(io, abs(new_match.c2), new_match.pos2);
/* convert contig code back to sense ie -ve contig number means
* match on opposite strand
*/
if (new_match.c1 < 0) {
sense1 = -1;
} else {
sense1 = 1;
}
if (new_match.c2 < 0) {
sense2 = -1;
} else {
sense2 = 1;
}
/*
* draw matches of same sense (+:+ or -:-) as p1,p2
* \
* p1+len, p2+len
* draw matches of different sense (+:- or -:+) as p1+len, p2
* /
* p1, p2+len
*/
x1 = pos1;
x2 = pos1 + new_match.length;
if (sense1 == sense2) {
y1 = pos2;
y2 = pos2 + new_match.length;
} else {
y1 = pos2 + new_match.length;
y2 = pos2;
}
/* need to plot in top half of screen therefore 'x' contig should be
* larger than the corresponding 'y' contig
*/
/*
printf("R:%d@%d,%d@%d(%d) C:%d@%d,%d@%d(%d)\n",
match->pos1, match->c1, match->pos2, match->c2, match->length,
new_match.pos1, new_match.c1,
new_match.pos2, new_match.c2, new_match.length);
printf("tag_id %s \n", tag_id);
*/
if (pos1 > pos2){
sprintf(cmd,"%s create line %d %d %d %d -width %d -capstyle round "
"-tags {num_%d num_%d %s S} -fill %s",
cs->window, x1, y1, x2, y2, width, abs(new_match.c1),
abs(new_match.c2), tag_id, colour);
} else {
sprintf(cmd,"%s create line %d %d %d %d -width %d -capstyle round "
"-tags \"num_%d num_%d %s S\" -fill %s",
cs->window, y1, x1, y2, x2, width, abs(new_match.c1),
abs(new_match.c2), tag_id, colour);
}
/* printf("cmd %s \n", cmd); */
if (TCL_ERROR == Tcl_Eval(GetInterp(), cmd))
printf("%s \n", GetInterpResult());
inum = atoi(GetInterpResult());
match->inum = inum;
HashInsert(csplot_hash, inum, match);
}
/* scale new matches */
scaleSingleCanvas(GetInterp(), cs->world, cs->canvas, cs->window, 'b',
tag_id);
}
void
update_contig_order(Tcl_Interp *interp,
GapIO *io,
int cs_id,
int *contig_array,
int num_contigs,
int cx)
{
GCardinal *order = ArrayBase(GCardinal, io->contig_order);
obj_cs *cs;
int i, j;
double wx, wy;
int left_position;
char cmd[1024];
int orig_pos = 0;
reg_buffer_start rs;
reg_buffer_end re;
reg_order ro;
cs = result_data(io, cs_id, 0);
CanvasToWorld(cs->canvas, cx, 0, &wx, &wy);
/*
* returns the nth contig to the left of the wx, NOT the contig number.
* If this is to the left of the first contig, returns 0.
*/
left_position = find_left_position(io, order, wx);
for (i = 0; i < NumContigs(io); i++) {
if (order[i] == contig_array[0]) {
orig_pos = i+1;
break;
}
}
/* convert index on order to index on contig num */
for (i = 0; i < num_contigs; i++) {
for (j = 0; j < NumContigs(io); j++) {
if (order[j] == contig_array[i])
break;
}
ReOrder(io, order, j, left_position);
if (j > left_position) {
left_position++;
orig_pos++;
}
}
ro.job = REG_ORDER;
ro.pos = left_position;
#ifdef HACK
/* HACK is there a better way of representing this - only need to
* replot once
*/
contig_notify(io, 1, (reg_data *)&ro);
#endif
/* Notify of the start of the flurry of updates */
rs.job = REG_BUFFER_START;
for (i = 0; i < num_contigs; i++) {
contig_notify(io, contig_array[i], (reg_data *)&rs);
}
ro.job = REG_ORDER;
ro.pos = left_position;
for (i = 0; i< num_contigs; i++)
contig_notify(io, contig_array[i], (reg_data *)&ro);
/* Notify the end of our updates */
re.job = REG_BUFFER_END;
for (i = 0; i < num_contigs; i++) {
contig_notify(io, contig_array[i], (reg_data *)&re);
}
/* draw larger separator tick to show where contig was moved from */
sprintf(cmd, "HighlightSeparator %s %d", cs->hori, orig_pos);
Tcl_Eval(interp, cmd);
}
void check_assembly_callback(GapIO *io, tg_rec contig, void *fdata,
reg_data *jdata) {
mobj_checkass *r = (mobj_checkass *)fdata;
obj_cs *cs;
int cs_id;
cs_id = type_to_result(io, REG_TYPE_CONTIGSEL, 0);
cs = result_data(io, cs_id);
switch (jdata->job) {
case REG_QUERY_NAME:
sprintf(jdata->name.line, "Check Assembly");
break;
case REG_JOIN_TO:
csmatch_join_to(io, contig, &jdata->join, (mobj_repeat *)r,
csplot_hash, cs->window);
break;
case REG_COMPLEMENT:
csmatch_complement(io, contig, (mobj_repeat *)r, csplot_hash,
cs->window);
break;
case REG_GET_OPS:
if (r->all_hidden)
jdata->get_ops.ops = "PLACEHOLDER\0PLACEHOLDER\0Information\0"
"PLACEHOLDER\0Hide all\0Reveal all\0Sort Matches\0"
"SEPARATOR\0Remove\0";
else
jdata->get_ops.ops = "Use for 'Next'\0Reset 'Next'\0Information\0"
"Configure\0Hide all\0Reveal all\0Sort Matches\0"
"SEPARATOR\0Remove\0";
break;
case REG_INVOKE_OP:
switch (jdata->invoke_op.op) {
case 0: /* Next */
Tcl_VarEval(GetInterp(), "CSLastUsed ", CPtr2Tcl(r), NULL);
break;
case 1: /* Reset Next */
csmatch_reset_next((mobj_repeat *)r);
break;
case 2: /* Information */
csmatch_info((mobj_repeat *)r, "Check Assembly");
break;
case 3: /* Configure */
csmatch_configure(io, cs->window, (mobj_repeat *)r);
break;
case 4: /* Hide all */
csmatch_hide(GetInterp(), cs->window, (mobj_repeat *)r,
csplot_hash);
break;
case 5: /* Reveal all */
csmatch_reveal(GetInterp(), cs->window, (mobj_repeat *)r,
csplot_hash);
break;
case 6: /* Sort */
qsort(r->match, r->num_match, sizeof(obj_checkass), sort_func);
csmatch_reset_hash(csplot_hash, (mobj_repeat *)r);
r->current = -1;
break;
case 7: /* Remove */
csmatch_remove(io, cs->window, (mobj_repeat *)r,
csplot_hash);
break;
}
break;
case REG_PARAMS:
jdata->params.string = r->params;
break;
case REG_NUMBER_CHANGE:
csmatch_renumber(io, contig, jdata->number.number,
(mobj_repeat *)r, csplot_hash, cs->window);
break;
case REG_ORDER:
csmatch_replot(io, (mobj_repeat *)r, csplot_hash, cs->window);
break;
case REG_QUIT:
csmatch_remove(io, cs->window, (mobj_repeat *)r, csplot_hash);
break;
case REG_DELETE:
csmatch_contig_delete(io, (mobj_repeat *)r, contig,
cs->window, csplot_hash);
break;
case REG_LENGTH:
csmatch_replot(io, (mobj_repeat *)r, csplot_hash, cs->window);
break;
}
}
/*
* Match callback.
* 'obj' is a match contained within the check assembly list.
*/
void *checkass_obj_func(int job, void *jdata, obj_checkass *obj,
mobj_checkass *ca) {
static char buf[80];
obj_cs *cs;
int cs_id;
cs_id = type_to_result(ca->io, REG_TYPE_CONTIGSEL, 0);
cs = result_data(ca->io, cs_id);
switch(job) {
case OBJ_LIST_OPERATIONS:
return "Information\0Hide\0Invoke contig editor *\0"
"SEPARATOR\0Remove\0";
case OBJ_INVOKE_OPERATION:
switch(*((int *)jdata)) {
case 0: /* Information */
vfuncgroup(1, "2D plot matches");
case -1: /* Information from results manager */
start_message();
vmessage("check_assembly match:\n");
vmessage(" From contig %s(#%"PRIrec") at %d\n",
get_contig_name(ca->io, ABS(obj->c1)),
io_clnbr(ca->io, ABS(obj->c1)), obj->pos1);
vmessage(" With contig %s(#%"PRIrec") at %d\n",
get_contig_name(ca->io, ABS(obj->c2)),
io_clnbr(ca->io, ABS(obj->c2)), obj->pos2);
vmessage(" Length %d, mismatch %2.2f%%\n\n",
obj->length, ((float)obj->score)/10000);
end_message(cs->window);
break;
case 1: /* Hide */
obj_hide(GetInterp(), cs->window, obj,
(mobj_repeat *)ca, csplot_hash);
break;
case -2: /* default */
case 2: /* Invoke contig editor */ {
tg_rec cnum, llino;
int pos;
obj->flags |= OBJ_FLAG_VISITED;
ca->current = obj - ca->match;
Tcl_VarEval(GetInterp(), "CSLastUsed ", CPtr2Tcl(ca), NULL);
cnum = abs(obj->c1);
llino = obj->read;
pos = obj->pos1 - io_relpos(ca->io, llino);
if (pos < 1)
pos = 1;
if (pos > ABS(io_length(ca->io, llino)))
pos = ABS(io_length(ca->io, llino));
// if ((id = editor_available(cnum, 1)) != -1) {
// move_editor(id, llino, pos);
// } else {
edit_contig(ca->io, cnum, llino, pos);
// }
break;
}
case 3: /* Remove */
obj_remove(GetInterp(), cs->window, obj,
(mobj_repeat *)ca, csplot_hash);
break;
}
break;
case OBJ_GET_BRIEF:
sprintf(buf,
"check_assembly: #%"PRIrec"@%d len %d, mis %2.2f%%",
obj->read, obj->pos1, obj->length, ((float)obj->score)/10000);
return buf;
}
return NULL;
}
void tst_QMessageAuthenticationCode::result_incremental_data()
{
result_data();
}
/*
* Match callback.
* 'obj' is a match contained within the 'repeat' list.
*/
void *repeat_obj_func(int job, void *jdata, obj_match *obj,
mobj_repeat *repeat) {
static char buf[80];
obj_cs *cs;
int cs_id;
cs_id = type_to_result(repeat->io, REG_TYPE_CONTIGSEL, 0);
cs = result_data(repeat->io, cs_id, 0);
switch(job) {
case OBJ_LIST_OPERATIONS:
if (io_rdonly(repeat->io) && ((obj->c1 > 0 && obj->c2 < 0) ||
(obj->c1 < 0 && obj->c2 > 0))) {
return "Information\0Hide\0IGNORE\0"
"IGNORE\0SEPARATOR\0Remove\0";
} else {
return "Information\0Hide\0Invoke join editor *\0"
"Invoke contig editors\0SEPARATOR\0Remove\0";
}
case OBJ_INVOKE_OPERATION:
switch(*((int *)jdata)) {
case 0: /* Information */
vfuncgroup(1, "2D plot matches");
case -1: /* Information from results manager */
start_message();
vmessage("Repeat match (%s)\n",
((obj->c1 > 0) == (obj->c2 > 0)) ? "direct" : "inverted");
vmessage(" From contig %s(#%d) at %d\n",
get_contig_name(repeat->io, ABS(obj->c1)),
io_clnbr(repeat->io, ABS(obj->c1)), obj->pos1);
vmessage(" With contig %s(#%d) at %d\n",
get_contig_name(repeat->io, ABS(obj->c2)),
io_clnbr(repeat->io, ABS(obj->c2)), obj->pos2);
vmessage(" Length %d\n\n", obj->length);
end_message(cs->window);
break;
case 1: /* Hide */
obj_hide(GetInterp(), cs->window, obj,
(mobj_repeat *)repeat, csplot_hash);
break;
case -2: /* default */
case 2: /* Invoke join editor */ {
int cnum[2], llino[2], pos[2];
obj->flags |= OBJ_FLAG_VISITED;
repeat->current = obj - repeat->match;
Tcl_VarEval(GetInterp(), "CSLastUsed ", CPtr2Tcl(repeat), NULL);
cnum[0] = ABS(obj->c1);
cnum[1] = ABS(obj->c2);
/* Complement a contig if needed */
if ((obj->c1 > 0) != (obj->c2 > 0)) {
if (cnum[0] == cnum[1]) {
verror(ERR_WARN, "join_editor",
"cannot display the same contig in two "
"different orientations");
break;
}
if (io_rdonly(repeat->io)) {
bell();
break;
}
if (io_clength(repeat->io, ABS(obj->c1)) <
io_clength(repeat->io, ABS(obj->c2))) {
if (-1 == complement_contig(repeat->io, ABS(obj->c1)))
if (-1 == complement_contig(repeat->io, ABS(obj->c2)))
return NULL;
} else {
if (-1 == complement_contig(repeat->io, ABS(obj->c2)))
if (-1 == complement_contig(repeat->io, ABS(obj->c1)))
return NULL;
}
}
/*
* NB: obj->pos1 now may not be the same value as when this
* function was entered, due to the complementing!
*/
pos[0] = obj->pos1;
pos[1] = obj->pos2;
llino[0] = io_clnbr(repeat->io, cnum[0]);
llino[1] = io_clnbr(repeat->io, cnum[1]);
join_contig(GetInterp(), repeat->io, cnum, llino, pos,
consensus_cutoff, quality_cutoff);
break;
}
case 3: /* Invoke contig editors */ {
int cnum, llino, pos;
cnum = ABS(obj->c1);
llino = io_clnbr(repeat->io, cnum);
pos = obj->pos1;
edit_contig(GetInterp(), repeat->io, cnum, llino, pos,
consensus_cutoff, quality_cutoff, 0, NULL);
cnum = ABS(obj->c2);
llino = io_clnbr(repeat->io, cnum);
pos = obj->pos2;
edit_contig(GetInterp(), repeat->io, cnum, llino, pos,
consensus_cutoff, quality_cutoff, 0, NULL);
break;
}
case 4: /* Remove */
obj_remove(GetInterp(), cs->window, obj,
(mobj_repeat *)repeat, csplot_hash);
break;
}
break;
case OBJ_GET_BRIEF:
sprintf(buf, "Repeat: %c#%d@%d with %c#%d@%d, len %d",
obj->c1 > 0 ? '+' : '-',
io_clnbr(repeat->io, ABS(obj->c1)), obj->pos1,
obj->c2 > 0 ? '+' : '-',
io_clnbr(repeat->io, ABS(obj->c2)), obj->pos2,
obj->length);
return buf;
}
return NULL;
}
int init_splice_search_plot(Tcl_Interp *interp,
char *raster_win,
int raster_id,
char *r_id,
int seq_id,
char *colours,
int line_width,
float tick_ht)
{
int seq_num;
int num_id;
Tcl_CmdInfo info;
Tk_Raster *raster;
RasterResult *raster_result;
cursor_t *cursor;
seq_result *nip_result = NULL;
seq_cursor_notify cn;
stick *data;
int i, cnt;
int retval = -1;
char **result_id = NULL;
char **colour = NULL;
seq_num = GetSeqNum(seq_id);
if (Tcl_SplitList(interp, colours, &num_id, &colour) != TCL_OK)
goto cleanup;
if (Tcl_SplitList(interp, r_id, &num_id, &result_id) != TCL_OK)
goto cleanup;
if (Tcl_GetCommandInfo(interp, raster_win, &info) == 0)
goto cleanup;
raster = (Tk_Raster*)info.clientData;
RasterInitPlotFunc(raster, SeqRasterPlotFunc);
raster_result = raster_id_to_result(raster_id);
cursor = find_raster_result_cursor(raster_result, seq_id, HORIZONTAL);
cnt = 0;
for (i = 0; i < num_id; i++) {
if (atoi(result_id[i]) > -1) {
nip_result = result_data(atoi(result_id[i]), seq_num);
} else {
cnt++;
}
}
/* no results were found */
if (cnt == num_id) {
retval = 0;
goto cleanup;
}
data = nip_result->data;
/* move cursor to start position if no cursor is yet present */
if (raster_result->cursor_array[cursor->id].prev_pos == -1
&& data->ap_array[0].dim.x0 > raster_result->cursor_array[cursor->id].prev_pos) {
cursor->abspos = data->ap_array[0].dim.x0;
}
for (i = 0; i < num_id; i++) {
if (-1 == NipSpliceSearchPlot(interp, atoi(result_id[i]),
seq_num, raster_win, colour[i],
line_width, tick_ht, i+1)) {
verror(ERR_FATAL,"nip splice search", "error in saving matches\n");
goto cleanup;
}
}
/*
* need to ensure done all the necessary plotting before adding the
* cursor
*/
Tcl_VarEval(interp, "update idletasks ", NULL);
cn.job = SEQ_CURSOR_NOTIFY;
cn.cursor = cursor;
cn.cursor->job = CURSOR_MOVE;
seq_notify(seq_num, (seq_reg_data *)&cn);
raster_result = raster_id_to_result(raster_id);
/* adding 3 results to a single raster */
AddResultToRaster(raster_result);
AddResultToRaster(raster_result);
AddResultToRaster(raster_result);
retval = 0;
cleanup:
if(result_id) Tcl_Free((char *)result_id);
if(colour) Tcl_Free((char *)colour);
return retval;
}
int NipSpliceSearchPlot(Tcl_Interp *interp,
int result_id,
int seq_num,
char *raster_win,
char *colour,
int line_width,
float tick_ht,
int frame)
{
Tcl_CmdInfo info;
Tk_Raster *raster;
char *opts[5];
out_raster *output;
config *configure_d;
config *configure_a;
int raster_id;
int superimpose = 1;
RasterResult *raster_result;
stick *data;
seq_result *nip_result;
/* no results were found */
if (result_id == -1)
return 0;
nip_result = result_data(result_id, seq_num);
data = nip_result->data;
if (NULL == (output = (out_raster *)xmalloc(sizeof(out_raster))))
return -1;
if (NULL == (opts[1] = (char *)xmalloc(100 * sizeof(char))))
return -1;
if (NULL == (opts[3] = (char *)xmalloc(5 * sizeof(char))))
return -1;
if (NULL == (output->configure = (config **)xmalloc(2*sizeof(config*))))
return -1;
if (NULL == (configure_a = (config *)xmalloc(sizeof(config))))
return -1;
if (NULL == (configure_d = (config *)xmalloc(sizeof(config))))
return -1;
configure_a->position = 0.0;
configure_a->x_direction = '+';
configure_a->y_direction = '-';
configure_a->height = tick_ht;
configure_a->zoom = 1;
configure_a->scroll = 0;
configure_d->position = 0.0;
configure_d->x_direction = '+';
configure_d->y_direction = '+';
configure_d->height = tick_ht;
configure_d->zoom = 1;
configure_d->scroll = 0;
if (Tcl_GetCommandInfo(interp, raster_win, &info) == 0)
return -1;
raster = (Tk_Raster*)info.clientData;
RasterInitPlotFunc(raster, SeqRasterPlotFunc);
strcpy(output->raster_win, raster_win);
output->interp = interp;
output->hidden = 0;
/* need to check if superimposing result on another plot */
Tcl_VarEval(interp, "GetRasterId ", output->raster_win, NULL);
raster_id = atoi(Tcl_GetStringResult(interp));
raster_result = raster_id_to_result(raster_id);
if (raster_result->num_results == 0) {
superimpose = 0;
}
if (!superimpose) {
RasterSetWorldScroll(raster, (double)data->ap_array[0].dim.x0,
data->ap_array[0].dim.y0,
(double)data->ap_array[0].dim.x1,
data->ap_array[0].dim.y1);
SeqAddRasterToWindow(interp, raster_win, nip_result->graph);
}
opts[0] = "-fg";
strcpy(opts[1], colour);
opts[2] = "-linewidth";
sprintf(opts[3], "%d", line_width);
opts[4] = NULL;
output->env_index = CreateDrawEnviron(interp, raster, 4, opts);
nip_result->output = (void *)output;
output->scroll = 'x';
output->configure[0] = configure_d;
output->configure[1] = configure_a;
output->sf_m = 1.0;
output->sf_c = 0.0;
if (superimpose) {
SeqSuperimposeResult(interp, output->raster_win, result_id,
data->ap_array[0].dim.x0,
data->ap_array[0].dim.y0,
data->ap_array[0].dim.x1,
data->ap_array[0].dim.y1);
}
ReplotAllCurrentZoom(interp, raster_win);
xfree(opts[1]);
xfree(opts[3]);
return 0;
}
/*
* functions to act upon matches generated using TAGs
*/
void *find_oligo_obj_func1(int job,
void *jdata,
obj_match *obj,
mobj_find_oligo *find_oligo)
{
static char buf[80];
obj_cs *cs;
int cs_id;
cs_id = type_to_result(find_oligo->io, REG_TYPE_CONTIGSEL, 0);
cs = result_data(find_oligo->io, cs_id);
switch(job) {
case OBJ_LIST_OPERATIONS:
return "Information\0Hide\0Invoke join editor *\0"
"Invoke contig editors\0SEPARATOR\0Remove\0";
case OBJ_INVOKE_OPERATION:
switch(*((int *)jdata)) {
case 0: /* Information */
vfuncgroup(1, "2D plot matches");
case -1: /* Information from results manager */
start_message();
vmessage("Sequence search:\n");
vmessage(" From contig %s(#%"PRIrec") at %d\n",
get_contig_name(find_oligo->io, ABS(obj->c1)),
io_clnbr(find_oligo->io, ABS(obj->c1)), obj->pos1);
vmessage(" With contig %s(#%"PRIrec") at %d\n",
get_contig_name(find_oligo->io, ABS(obj->c2)),
io_clnbr(find_oligo->io, ABS(obj->c2)), obj->pos2);
vmessage(" Length %d, match %2.2f%%\n\n",
obj->length,
(float)obj->score / obj->length * 100.0 );
end_message(cs->window);
break;
case 1: /* Hide */
obj_hide(GetInterp(), cs->window, obj,
(mobj_find_oligo *)find_oligo, csplot_hash);
break;
case -2: /* default */
case 2: /* Invoke join editor */ {
tg_rec cnum[2], llino[2];
int pos[2];
obj->flags |= OBJ_FLAG_VISITED;
find_oligo->current = obj - find_oligo->match;
Tcl_VarEval(GetInterp(), "CSLastUsed ", CPtr2Tcl(find_oligo), NULL);
cnum[0] = ABS(obj->c1);
cnum[1] = ABS(obj->c2);
/* Complement a contig if needed */
if ((obj->c1 > 0) != (obj->c2 > 0)) {
if (cnum[0] == cnum[1]) {
verror(ERR_WARN, "join_editor",
"cannot display the same contig in two "
"different orientations");
break;
}
if (find_oligo->io->read_only) {
bell();
break;
}
if (io_clength(find_oligo->io, ABS(obj->c1)) <
io_clength(find_oligo->io, ABS(obj->c2))) {
if (-1 == complement_contig(find_oligo->io, ABS(obj->c1)))
if (-1 == complement_contig(find_oligo->io,
ABS(obj->c2)))
return NULL;
} else {
if (-1 == complement_contig(find_oligo->io, ABS(obj->c2)))
if (-1 == complement_contig(find_oligo->io,
ABS(obj->c1)))
return NULL;
}
}
/*
* NB: obj->pos1 now may not be the same value as when this
* function was entered, due to the complementing!
*/
pos[0] = obj->pos1;
pos[1] = obj->pos2;
llino[0] = io_clnbr(find_oligo->io, cnum[0]);
llino[1] = io_clnbr(find_oligo->io, cnum[1]);
join_contig(find_oligo->io, cnum, llino, pos);
break;
}
case 3: /* Invoke contig editors */ {
tg_rec cnum, llino;
int pos;
cnum = ABS(obj->c1);
llino = io_clnbr(find_oligo->io, cnum);
pos = obj->pos1;
edit_contig(find_oligo->io, cnum, llino, pos);
cnum = ABS(obj->c2);
llino = io_clnbr(find_oligo->io, cnum);
pos = obj->pos2;
edit_contig(find_oligo->io, cnum, llino, pos);
break;
}
case 4: /* Remove */
obj_remove(GetInterp(), cs->window, obj,
(mobj_find_oligo *)find_oligo, csplot_hash);
break;
}
break;
case OBJ_GET_BRIEF:
sprintf(buf,
"Oligo: %c#%"PRIrec"@%d with %c#%"PRIrec"@%d, "
"len %d, match %2.2f%%",
obj->c1 > 0 ? '+' : '-',
io_clnbr(find_oligo->io, ABS(obj->c1)), obj->pos1,
obj->c2 > 0 ? '+' : '-',
io_clnbr(find_oligo->io, ABS(obj->c2)), obj->pos2,
obj->length, (float)obj->score / obj->length * 100.0);
return buf;
}
return NULL;
}
/*
* functions to act upon matches generated using SEQUENCE
*/
void *find_oligo_obj_func2(int job,
void *jdata,
obj_match *obj,
mobj_find_oligo *find_oligo)
{
static char buf[80];
obj_cs *cs;
int cs_id;
cs_id = type_to_result(find_oligo->io, REG_TYPE_CONTIGSEL, 0);
cs = result_data(find_oligo->io, cs_id);
switch(job) {
case OBJ_LIST_OPERATIONS:
return "Information\0Hide\0Invoke contig editor *\0"
"SEPARATOR\0Remove\0";
case OBJ_INVOKE_OPERATION:
switch(*((int *)jdata)) {
case 0: /* Information */
vfuncgroup(1, "2D plot matches");
case -1: /* Information from results manager */
start_message();
vmessage("Sequence search\n");
vmessage(" Contig %s(#%"PRIrec") at %d\n",
get_contig_name(find_oligo->io, ABS(obj->c1)),
io_clnbr(find_oligo->io, ABS(obj->c1)), obj->pos1);
vmessage(" Length %d, match %2.2f%%\n\n",
obj->length, (float)obj->score / obj->length * 100.0 );
end_message(cs->window);
break;
case 1: /* Hide */
obj_hide(GetInterp(), cs->window, obj,
(mobj_find_oligo *)find_oligo, csplot_hash);
break;
case -2: /* default */
case 2: /* Invoke contig editor */ {
tg_rec cnum, llino;
int pos;
obj->flags |= OBJ_FLAG_VISITED;
find_oligo->current = (int)(obj - find_oligo->match);
cnum = ABS(obj->c1);
llino = 0;
pos = obj->pos1;
/* FIXME
if ((id = editor_available(cnum, 1)) == -1) {
edit_contig(GetInterp(), find_oligo->io, cnum, llino, pos,
consensus_cutoff, quality_cutoff, 0, NULL);
}
if ((id = editor_available(cnum, 1)) != -1) {
move_editor(id, llino, pos);
editor_select_region(id, llino, pos, obj->length);
}
*/
edit_contig(find_oligo->io, cnum, llino, pos);
break;
}
case 3: /* Remove */
obj_remove(GetInterp(), cs->window, obj,
(mobj_find_oligo *)find_oligo, csplot_hash);
break;
}
break;
case OBJ_GET_BRIEF:
sprintf(buf,
"Oligo: %c#%"PRIrec"@%d with %c#%"PRIrec"@%d, "
"len %d, match %2.2f%%",
obj->c1 > 0 ? '+' : '-',
io_clnbr(find_oligo->io, ABS(obj->c1)), obj->pos1,
obj->c2 > 0 ? '+' : '-',
io_clnbr(find_oligo->io, ABS(obj->c2)), obj->pos2,
obj->length, (float)obj->score / obj->length * 100.0);
return buf;
}
return NULL;
}
