void ed_nip_renz_info(int seq_num,
ed_renz_res *data,
int start,
int print_opt)
{
int seq_len;
char *seq;
int sequence_type;
seq = GetEdenSeq(seq_num);
seq_len = GetEdenLength(seq_num);
/*sequence_type = GetSequenceStructure(seq_num);*/
sequence_type = GetEdenType(seq_num);
vfuncheader("Restriction enzymes result list");
vmessage("Sequence %s\n", GetEdenName(seq_num));
vmessage("Number of enzymes = %d\n", data->num_enzymes);
vmessage("Number of matches = %d\n", data->num_match);
if (print_opt == 0) {
start_message();
EdPrintEnzymeByEnzyme(data->r_enzyme, data->match, data->num_match,
data->num_enzymes, seq, seq_len,
sequence_type, start);
end_message(data->re_win);
} else {
start_message();
EdOrderOnPosition(data->r_enzyme, data->match, data->num_match,
seq, seq_len, sequence_type, start);
end_message(data->re_win);
}
}
void ShutdownService::_sendShutdownRequestToService(const char * serviceName)
{
MessageQueueService* _mqs = static_cast<MessageQueueService*>(_controller);
Array<Uint32> _services;
Uint32 _queueId;
_mqs->find_services(String(serviceName), 0, 0, &_services);
if (_services.size() == 0 )
{
// service not found, just return
return;
}
_queueId = _services[0];
// send a Stop (this is a legacy message that in some of the MQS does termination
// of its internal stuff. Then follow it with a Stop (to open up its incoming queue),
// and then with a AsyncIoctl::IO_CLOSE which closes the incoming queue.
// All of these messages MUST be sequential. Do not use SendForget or SendAsync as those
// are asynchronous and their receival is guaranteed to be undeterministic and possibly
// out of sequence (which is something we do not want).
CimServiceStop stop_message (_mqs->get_next_xid(),
NULL,
_queueId,
_controller->getQueueId(),
true);
AutoPtr <AsyncReply> StopAsyncReply
(_controller->ClientSendWait ( *_client_handle, _queueId, &stop_message));
CimServiceStart start_message (_mqs->get_next_xid(),
NULL,
_queueId,
_controller->getQueueId(),
true);
AutoPtr <AsyncReply> StartAsyncReply
(_controller->ClientSendWait ( *_client_handle, _queueId, &start_message));
AsyncIoctl close_request (_mqs->get_next_xid(),
NULL,
_queueId,
_controller->getQueueId(),
false,
AsyncIoctl::IO_CLOSE,
0,
0);
AutoPtr <AsyncReply> CloseAsyncReply
(_controller->ClientSendWait ( *_client_handle, _queueId, &close_request));
return;
}
void ShutdownService::_sendShutdownRequestToService(const char* serviceName)
{
MessageQueueService* _mqs = static_cast<MessageQueueService*>(_controller);
MessageQueue *queue = MessageQueue::lookup(serviceName);
Uint32 _queueId;
if (queue)
{
_queueId = queue->getQueueId();
}
else
{
// service not found, just return
return;
}
// send a Stop (this is a legacy message that in some of the MQS does
// termination of its internal stuff. Then follow it with a Stop (to
// open up its incoming queue), and then with a AsyncIoClose
// which closes the incoming queue.
// All of these messages MUST be sequential. Do not use SendForget or
// SendAsync as those are asynchronous and their receipt is guaranteed
// to be undeterministic and possibly out of sequence (which is something
// we do not want).
CimServiceStop stop_message(
NULL,
_queueId,
_controller->getQueueId(),
true);
AutoPtr<AsyncReply> StopAsyncReply(
_controller->ClientSendWait(_queueId, &stop_message));
CimServiceStart start_message(
NULL,
_queueId,
_controller->getQueueId(),
true);
AutoPtr <AsyncReply> StartAsyncReply(
_controller->ClientSendWait(_queueId, &start_message));
AsyncIoClose close_request(
NULL,
_queueId,
_controller->getQueueId(),
false);
AutoPtr <AsyncReply> CloseAsyncReply(
_controller->ClientSendWait(_queueId, &close_request));
}
/*
* 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;
}
/*
* 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;
}
/*
* 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;
}
