RFDiagonalAlgorithmWK::RFDiagonalAlgorithmWK(RFResultsListener* rl, const char* seqX, int sizeX, const char* seqY, int sizeY,
DNAAlphabetType seqType, int w, int k)
: RFAlgorithmBase(rl, seqX, sizeX, seqY, sizeY, seqType, w, k)
{
setMaxParallelSubtasks(MAX_PARALLEL_SUBTASKS_AUTO);
START_DIAG = SIZE_X - WINDOW_SIZE;
END_DIAG = reflective ? 1 : -int(SIZE_Y - WINDOW_SIZE);
}
void HMMCalibrateParallelTask::prepare() {
TaskLocalData::createHMMContext(getTaskId(), false);
initTask = new HMMCreateWPoolTask(this);
addSubTask(initTask);
for(int i=0;i < settings.nThreads;i++){
addSubTask(new HMMCalibrateParallelSubTask(this));
}
setMaxParallelSubtasks(1);
}
void GenomeAlignerFindTask::prepare() {
alignerTaskCount = alignContext->openCL ? 1 : AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount();
if (alignContext->openCL) {
Task *subTask = new ShortReadAlignerOpenCL(0, index, alignContext, writeTask);
subTask->setSubtaskProgressWeight(1.0f);
addSubTask(subTask);
} else {
setMaxParallelSubtasks(alignerTaskCount);
for (int i = 0; i < alignerTaskCount; i++) {
Task *subTask = new ShortReadAlignerCPU(i, index, alignContext, writeTask);
subTask->setSubtaskProgressWeight(1.0f / alignerTaskCount);
addSubTask(subTask);
}
}
}
MuscleTask::MuscleTask(const MultipleSequenceAlignment &ma, const MuscleTaskSettings& _config)
: Task(tr("MUSCLE alignment"), TaskFlags_FOSCOE | TaskFlag_MinimizeSubtaskErrorText),
config(_config),
inputMA(ma->getExplicitCopy())
{
GCOUNTER( cvar, tvar, "MuscleTask" );
config.nThreads = (config.nThreads == 0 ? AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount() : config.nThreads);
SAFE_POINT_EXT(config.nThreads > 0,
setError("Incorrect number of max parallel subtasks"), );
setMaxParallelSubtasks(config.nThreads);
algoLog.info(tr("MUSCLE alignment started"));
ctx = new MuscleContext(config.nThreads);
ctx->params.g_bStable = config.stableMode;
ctx->params.g_uMaxIters = config.maxIterations;
ctx->params.g_ulMaxSecs = config.maxSecs;
parallelSubTask = NULL;
//todo: make more precise estimation, use config.op mode
int aliLen = ma->getLength();
int nSeq = ma->getNumRows();
int memUseMB = qint64(aliLen) * qint64(nSeq) * 200 / (1024 * 1024); //200x per char in alignment
TaskResourceUsage tru(RESOURCE_MEMORY, memUseMB);
QString inputAlName = inputMA->getName();
resultMA->setName(inputAlName);
resultSubMA->setName(inputAlName);
inputSubMA = inputMA->getExplicitCopy();
if (config.alignRegion && config.regionToAlign.length != inputMA->getLength()) {
SAFE_POINT_EXT(config.regionToAlign.length > 0,
setError(tr("Incorrect region to align")), );
inputSubMA = inputMA->mid(config.regionToAlign.startPos, config.regionToAlign.length);
CHECK_EXT(inputSubMA != MultipleSequenceAlignment(), setError(tr("Stopping MUSCLE task, because of error in MultipleSequenceAlignment::mid function")), );
}
QList<Task*> HMMCalibrateParallelTask::onSubTaskFinished(Task* subTask) {
if (subTask == initTask) {
setMaxParallelSubtasks(settings.nThreads);
}
return QList<Task*>();
}
