void
Transient::execute()
{
preExecute();
// NOTE: if you remove this line, you will see a subset of tests failing. Those tests might have a wrong answer and might need to be regolded.
// The reason is that we actually move the solution back in time before we actually start solving (which I think is wrong). So this call here
// is to maintain backward compatibility and so that MOOSE is giving the same answer. However, we might remove this call and regold the test
// in the future eventually.
if (!_app.isRecovering())
_problem.copyOldSolutions();
// Start time loop...
while (true)
{
if (_first != true)
incrementStepOrReject();
_first = false;
if (!keepGoing())
break;
computeDT();
takeStep();
endStep();
_steps_taken++;
}
postExecute();
}
int main(int argc, char* argv[])
{
int argi;
char* dumpFile = NULL;
unsigned flags = 0;
char* database, *accPrefix;
struct gbIndex* index;
struct stepInfo runInfo;
gbVerbInit(0);
optionInit(&argc, argv, optionSpecs);
if (argc < 2)
usage();
if (optionExists("processed"))
flags |= DO_PROCESSED;
if (optionExists("aligned"))
flags |= DO_PROCESSED|DO_ALIGNED;
if (optionExists("mrna"))
flags |= DO_MRNA;
if (optionExists("est"))
flags |= DO_EST;
dumpFile = optionVal("dump", NULL);
database = optionVal("db", NULL);
accPrefix = optionVal("accPrefix", NULL);
if ((flags & DO_ALIGNED) && (database == NULL))
errAbort("must specify -db with -aligned");
if (!(flags & (DO_MRNA|DO_EST)))
errAbort("must specify at least one of -mrna or -est");
if (!(flags & (DO_ALIGNED|DO_PROCESSED)))
errAbort("must specify at least one of -processed or -aligned");
index = gbIndexNew(database, NULL);
runInfo = beginStep(index, NULL, "loading index files");
for (argi = 1; argi < argc; argi++)
testRelLoad(index, gbIndexMustFindRelease(index, argv[argi]),
database, flags, accPrefix);
if (dumpFile != NULL)
{
FILE* dumpOut = mustOpen(dumpFile, "w");
gbIndexDump(index, dumpOut);
if (fclose(dumpOut) != 0)
errnoAbort("close of dumpfile");
}
endStep(index, &runInfo);
gbIndexFree(&index);
return 0;
}
void
AdaptiveTransient::execute()
{
preExecute();
// Start time loop...
while (keepGoing())
{
takeStep();
if (lastSolveConverged())
endStep();
}
postExecute();
}
ControlWindows::ControlWindows()
{
m_ui = new Ui::ControlWindows;
m_ui->setupUi(this);
m_timer.setSingleShot(false);
m_clock.setSingleShot(false);
m_clock.setInterval(2000);
connect( m_ui->start, SIGNAL( clicked(bool) ), this, SLOT( start() ));
connect( &m_timer, SIGNAL( timeout() ), this, SLOT( endStep()) );
connect( this, SIGNAL( endOfSet() ), this, SLOT(Save()) );
}
static void testLoad(struct gbSelect* select, unsigned flags)
/* do load testing of part of a release */
{
char desc[512];
struct stepInfo info;
select->type = (flags & DO_MRNA) ? GB_MRNA : GB_EST;
safef(desc, sizeof(desc), "%s %s",
((flags & DO_PROCESSED) ? "processed" : "aligned"),
gbSelectDesc(select));
info = beginStep(select->release->index, select->release, desc);
if (flags & DO_PROCESSED)
gbReleaseLoadProcessed(select);
else
{
select->orgCats = GB_NATIVE|GB_XENO;
gbReleaseLoadAligned(select);
}
endStep(select->release->index, &info);
select->type = 0;
}
