void EnzymesSelectorWidget::loadFile(const QString& url) {
TaskStateInfo ti;
QList<SEnzymeData> enzymes;
if (!QFileInfo(url).exists()) {
ti.setError( tr("File not exists: %1").arg(url) );
} else {
GTIMER(c1,t1,"FindEnzymesDialog::loadFile [EnzymesIO::readEnzymes]");
enzymes = EnzymesIO::readEnzymes(url, ti);
}
if (ti.hasError()) {
if (isVisible()) {
QMessageBox::critical(NULL, tr("Error"), ti.getError());
} else {
ioLog.error(ti.getError());
}
return;
}
if (!enzymes.isEmpty()) {
if (AppContext::getSettings()->getValue(EnzymeSettings::DATA_FILE_KEY).toString() != url) {
lastSelection.clear();
}
AppContext::getSettings()->setValue(EnzymeSettings::DATA_FILE_KEY, url);
}
setEnzymesList(enzymes);
}
void EnzymesSelectorWidget::saveFile(const QString& url) {
TaskStateInfo ti;
QString source = AppContext::getSettings()->getValue(EnzymeSettings::DATA_FILE_KEY).toString();
GTIMER(c1,t1,"FindEnzymesDialog::saveFile [EnzymesIO::writeEnzymes]");
QSet<QString> enzymes;
for(int i=0, n = tree->topLevelItemCount(); i<n; i++){
EnzymeGroupTreeItem* gi = static_cast<EnzymeGroupTreeItem*>(tree->topLevelItem(i));
for (int j=0, m = gi->childCount(); j < m; j++) {
EnzymeTreeItem* item = static_cast<EnzymeTreeItem*>(gi->child(j));
if (item->checkState(0) == Qt::Checked) {
enzymes.insert(item->enzyme->id);
}
}
}
EnzymesIO::writeEnzymes(url, source, enzymes, ti);
if (ti.hasError()) {
if (isVisible()) {
QMessageBox::critical(NULL, tr("Error"), ti.getError());
} else {
uiLog.error(ti.getError());
}
return;
}
if (QMessageBox::question(this, tr("New enzymes database has been saved."),
tr("Do you want to work with new database?"), QMessageBox::Yes | QMessageBox::No) == QMessageBox::Yes) {
loadFile(url);
}
}
void EnzymesSelectorWidget::setEnzymesList(const QList<SEnzymeData>& enzymes) {
tree->setSortingEnabled(false);
tree->disconnect(this);
tree->clear();
totalEnzymes = 0;
GTIMER(c2,t2,"FindEnzymesDialog::loadFile [refill data tree]");
enzymesFilterEdit->clear();
foreach (const SEnzymeData& enz, enzymes) {
EnzymeTreeItem* item = new EnzymeTreeItem(enz);
if (lastSelection.contains(enz->id)) {
item->setCheckState(0, Qt::Checked);
}
totalEnzymes++;
EnzymeGroupTreeItem* gi = findGroupItem(enz->id.isEmpty() ? QString(" ") : enz->id.left(1), true);
gi->addChild(item);
}
void ReadShortReadsSubTask::run() {
stateInfo.setProgress(0);
GTIMER(cvar, tvar, "ReadSubTask");
GenomeAlignerTask *parent = static_cast<GenomeAlignerTask*>(getParentTask());
if (!alignContext.bestMode) {
parent->pWriteTask->flush();
}
alignContext.cleanVectors();
dataBunch = new DataBunch();
if (isCanceled()) {
readingFinishedWakeAll();
return;
}
qint64 m = freeMemorySize;
taskLog.details(QString("Memory size is %1").arg(m));
bool alignReversed = settings.getCustomValue(GenomeAlignerTask::OPTION_ALIGN_REVERSED, true).toBool();
int qualityThreshold = settings.getCustomValue(GenomeAlignerTask::OPTION_QUAL_THRESHOLD, 0).toInt();
DNATranslation* transl = AppContext::getDNATranslationRegistry()->
lookupTranslation(BaseDNATranslationIds::NUCL_DNA_DEFAULT_COMPLEMENT);
alignContext.isReadingStarted = true;
bunchSize = 0;
int readNum = 0;
while(!seqReader->isEnd()) {
if (isCanceled()) {
readingFinishedWakeAll();
return;
}
SearchQuery *query = seqReader->read();
if (NULL == query) {
if (!seqReader->isEnd()) {
setError("Short-reads object type must be a sequence, but not a multiple alignment");
readingFinishedWakeAll();
return;
}
break;
}
++bunchSize;
if (!checkDnaQuality(query, qualityThreshold)) {
continue;
}
updateMinMaxReadLengths(alignContext, query->length());
int W = 0, q = 0;
int CMAX = alignContext.nMismatches;
if (!add(CMAX, W, q, readNum, query, parent)) {
delete query;
continue;
}
m -= query->memoryHint();
if (alignReversed) {
SearchQuery *rQu = createRevComplQuery(query, transl);
if (rQu) {
add(CMAX, W, q, readNum, rQu, parent);
m -= rQu->memoryHint();
}
}
qint64 alignContextMemoryHint = dataBunch->memoryHint();
if (m <= alignContextMemoryHint + prevMemoryHint) {
break;
}
SAFE_POINT(NULL != dataBunch, "No dataBunch",);
if (dataBunch->bitValuesV.size() > DROP_BUNCH_DATA_SIZE) {
dropToAlignContext();
readNum = 0;
alignContext.readShortReadsWait.wakeOne();
}
}
dropToAlignContext();
readingFinishedWakeAll();
}
