char MaIterator::operator *() {
SAFE_POINT(isInRange(position), "Out of boundaries", U2Msa::INVALID_CHAR);
const QPoint maPoint = getMaPoint();
SAFE_POINT(0 <= maPoint.x() && maPoint.x() < ma->getLength() &&
0 <= maPoint.y() && maPoint.y() < ma->getNumRows(), "Out of boundaries", U2Msa::INVALID_CHAR);
return ma->charAt(maPoint.y(), maPoint.x());
}
QWidget * PcrOptionsPanelSavableTab::getPrimerEditWidgetById(const QString &childId) const {
const QStringList ids = childId.split(WIDGET_ID_SEPARATOR);
SAFE_POINT(2 == ids.size(), "Invalid widget ID", NULL);
QWidget *primerGroup = wrappedWidget->findChild<QWidget *>(ids.first());
SAFE_POINT(NULL != primerGroup, "Invalid parent widget", NULL);
return primerGroup->findChild<QWidget *>(ids.last());
}
inline bool ReadShortReadsSubTask::add(int &CMAX, int &W, int &q, int &readNum, SearchQuery *query, GenomeAlignerTask *parent) {
SAFE_POINT(NULL != dataBunch, "No dataBunch", false);
SAFE_POINT(NULL != query, "No query", false);
W = query->length();
if (!alignContext.absMismatches) {
CMAX = (W * alignContext.ptMismatches) / MAX_PERCENTAGE;
}
q = W / (CMAX + 1);
CHECK_EXT(0 != q,, false);
const char* querySeq = query->constData();
SAFE_POINT(NULL != querySeq, "No querySeq", false);
int win = query->length() < GenomeAlignerTask::MIN_SHORT_READ_LENGTH ?
GenomeAlignerTask::calculateWindowSize(alignContext.absMismatches,
alignContext.nMismatches, alignContext.ptMismatches, query->length(), query->length()) :
GenomeAlignerTask::calculateWindowSize(alignContext.absMismatches,
alignContext.nMismatches, alignContext.ptMismatches, alignContext.minReadLength, alignContext.maxReadLength);
for (int i = 0; i < W - q + 1; i+=q) {
const char *seq = querySeq + i;
BMType bv = parent->index->getBitValue(seq, qMin(GenomeAlignerIndex::charsInMask, W - i));
dataBunch->bitValuesV.append(bv);
dataBunch->readNumbersV.append(readNum);
dataBunch->positionsAtReadV.append(i);
dataBunch->windowSizes.append(win);
}
readNum++;
dataBunch->queries.append(query);
return true;
}
bool ActorCfgFilterProxyModel::filterAcceptsRow(int sourceRow, const QModelIndex & /*sourceParent*/) const {
ActorCfgModel *srcModel = qobject_cast<ActorCfgModel *>(sourceModel());
SAFE_POINT(NULL != srcModel, "Invalid actor configuration model", true);
Attribute *attr = srcModel->getAttributeByRow(sourceRow);
SAFE_POINT(NULL != attr, "Invalid actor attribute", true);
return srcModel->isVisible(attr);
}
GUITests GUITestService::postActions() {
UGUITestBase* tb = AppContext::getGUITestBase();
SAFE_POINT(NULL != tb,"",GUITests());
GUITests additionalChecks = tb->takeTests(UGUITestBase::PostAdditionalActions);
SAFE_POINT(additionalChecks.size()>0,"",GUITests());
return additionalChecks;
}
QWidget* RefSeqCommonWidgetFactory::createWidget(GObjectView *objView) {
SAFE_POINT(NULL != objView, QString("NULL object view!"), NULL);
MSAEditor* msa = qobject_cast<MSAEditor*>(objView);
SAFE_POINT(NULL != msa, QString("Not MSAEditor!"), NULL);
RefSeqCommonWidget *widget = new RefSeqCommonWidget(msa);
return widget;
}
bool TestDbiProvider::init(const QString& dbiFileName, bool _useConnectionPool){
if(initialized){
close();
initialized = false;
}
TestRunnerSettings* trs = AppContext::getAppSettings()->getTestRunnerSettings();
QString originalFile = trs->getVar("COMMON_DATA_DIR") + "/" + dbiFileName;
QString tmpFile = QDir::temp().absoluteFilePath(QFileInfo(originalFile).fileName());
if(QFile::exists(tmpFile)) {
QFile::remove(tmpFile);
}
bool _create = false;
if (QFile::exists(originalFile)) {
SAFE_POINT(QFile::copy(originalFile, tmpFile), "db file not copied", false);
}else{
_create = true;
}
dbUrl = tmpFile;
useConnectionPool = _useConnectionPool;
U2DbiFactory *factory = AppContext::getDbiRegistry()->getDbiFactoryById(SQLITE_DBI_ID);
SAFE_POINT(factory!=NULL, "No dbi factory", false);
U2OpStatusImpl opStatus;
if(useConnectionPool){
U2DbiRef ref;
ref.dbiFactoryId = factory->getId();
ref.dbiId = dbUrl;
dbi = AppContext::getDbiRegistry()->getGlobalDbiPool()->openDbi(ref, _create, opStatus);
CHECK_OP(opStatus, false);
}else{
dbi = factory->createDbi();
SAFE_POINT(NULL != dbi, "dbi not created", false);
QHash<QString, QString> properties;
if(_create){
properties[U2DbiOptions::U2_DBI_OPTION_CREATE] = U2DbiOptions::U2_DBI_VALUE_ON;
}
properties["url"] = dbUrl;
QVariantMap persistentData;
dbi->init(properties, persistentData, opStatus);
SAFE_POINT_OP(opStatus, false);
}
U2ObjectDbi* objDbi = dbi->getObjectDbi();
SAFE_POINT(NULL != objDbi, "object dbi not loaded", false);
initialized = true;
return true;
}
QWidget* AssemblyNavigationWidgetFactory::createWidget(GObjectView* objView) {
SAFE_POINT(NULL != objView,
QString("Internal error: unable to create widget for group '%1', object view is NULL.").arg(GROUP_ID),
NULL);
AssemblyBrowser* assemblyBrowser = qobject_cast<AssemblyBrowser*>(objView);
SAFE_POINT(NULL != assemblyBrowser,
QString("Internal error: unable to cast object view to Assembly Browser for group '%1'.").arg(GROUP_ID),
NULL);
AssemblyNavigationWidget* widget = new AssemblyNavigationWidget(assemblyBrowser, assemblyBrowser->getMainWidget());
return widget;
}
QWidget * MSAExportConsensusFactoryTab::createWidget(GObjectView* objView) {
SAFE_POINT(NULL != objView,
QString("Internal error: unable to create widget for group '%1', object view is NULL.").arg(GROUP_ID),
NULL);
MSAEditor* msa = qobject_cast<MSAEditor*>(objView);
SAFE_POINT(NULL != msa,
QString("Internal error: unable to cast object view to MSAEditor for group '%1'.").arg(GROUP_ID),
NULL);
MSAExportConsensusTab *widget = new MSAExportConsensusTab(msa);
return widget;
}
QWidget * SeqStatisticsWidgetFactory::createWidget(GObjectView* objView) {
SAFE_POINT(NULL != objView,
QString("Internal error: unable to create widget for group '%1', object view is NULL.").arg(GROUP_ID),
NULL);
MSAEditor* msa = qobject_cast<MSAEditor*>(objView);
SAFE_POINT(NULL != msa,
QString("Internal error: unable to cast object view to MSAEditor for group '%1'.").arg(GROUP_ID),
NULL);
SeqStatisticsWidget *SeqStatisticsWidgetWidget = new SeqStatisticsWidget(msa);
return SeqStatisticsWidgetWidget;
}
QWidget * FindPatternWidgetFactory::createWidget(GObjectView* objView) {
SAFE_POINT(NULL != objView,
QString("Internal error: unable to create widget for group '%1', object view is NULL.").arg(GROUP_ID),
NULL);
AnnotatedDNAView* annotatedDnaView = qobject_cast<AnnotatedDNAView*>(objView);
SAFE_POINT(NULL != annotatedDnaView,
QString("Internal error: unable to cast object view to AnnotatedDNAView for group '%1'.").arg(GROUP_ID),
NULL);
FindPatternWidget* widget = new FindPatternWidget(annotatedDnaView);
widget->setObjectName("FindPatternWidget");
return widget;
}
QWidget* MSATreeOptionsWidgetFactory::createWidget(GObjectView* objView) {
SAFE_POINT(NULL != objView,
QString("Internal error: unable to create widget for group '%1', object view is NULL.").arg(GROUP_ID),
NULL);
MSAEditor* msa = qobject_cast<MSAEditor*>(objView);
SAFE_POINT(NULL != msa,
QString("Internal error: unable to cast object view to MSAEditor for group '%1'.").arg(GROUP_ID),
NULL);
SAFE_POINT(NULL != viewSettings, "Invalid tree view settings", NULL);
TreeOptionsWidget *treeOpWidget = new TreeOptionsWidget(msa, *viewSettings);
connect(treeOpWidget, SIGNAL(saveViewSettings(const TreeOpWidgetViewSettings&)), SLOT(sl_onWidgetViewSaved(const TreeOpWidgetViewSettings&)));
return treeOpWidget;
}
GroupOptionsWidget* OptionsPanelWidget::createOptionsWidget(const QString& groupId,
const QString& title,
const QString& documentationPage,
QWidget* _widget, QList<QWidget*> commonWidgets)
{
SAFE_POINT(NULL != _widget, "NULL main widget!", NULL);
QWidget *innerWidgets = new QWidget;
QVBoxLayout *layout = new QVBoxLayout;
layout->setContentsMargins(0, 0, 0, 0);
layout->setMargin(0);
foreach (QWidget *commonWidget, commonWidgets) {
SAFE_POINT(NULL != commonWidget, "NULL common widget!", NULL);
layout->addWidget(commonWidget);
}
qint64 MultipleSequenceAlignmentRowData::getCoreLength() const {
int coreStart = getCoreStart();
int coreEnd = getCoreEnd();
int length = coreEnd - coreStart;
SAFE_POINT(length >= 0, QString("Internal error in MultipleSequenceAlignmentRowData: coreEnd is %1, coreStart is %2!").arg(coreEnd).arg(coreStart), length);
return length;
}
GObjectType U2ObjectTypeUtils::toGObjectType( const U2DataType &dbType ) {
GObjectType result = GObjectTypes::UNKNOWN;
if ( U2Type::Sequence == dbType ) {
result = GObjectTypes::SEQUENCE;
} else if ( U2Type::AnnotationTable == dbType ) {
result = GObjectTypes::ANNOTATION_TABLE;
} else if ( U2Type::PhyTree == dbType ) {
result = GObjectTypes::PHYLOGENETIC_TREE;
} else if ( U2Type::Chromatogram == dbType ) {
result = GObjectTypes::CHROMATOGRAM;
} else if ( U2Type::BioStruct3D == dbType ) {
result = GObjectTypes::BIOSTRUCTURE_3D;
} else if ( U2Type::Assembly == dbType ) {
result = GObjectTypes::ASSEMBLY;
} else if ( U2Type::Mca == dbType ) {
result = GObjectTypes::MULTIPLE_CHROMATOGRAM_ALIGNMENT;
} else if ( U2Type::Msa == dbType ) {
result = GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT;
} else if ( U2Type::VariantTrack == dbType ) {
result = GObjectTypes::VARIANT_TRACK;
} else if ( U2Type::Text == dbType ) {
result = GObjectTypes::TEXT;
}
SAFE_POINT( GObjectTypes::UNKNOWN != result, "Unsupported object relation type detected!",
result );
return result;
}
U2DataType U2ObjectTypeUtils::toDataType( const GObjectType &gType ) {
U2DataType result = U2Type::Unknown;
if ( GObjectTypes::SEQUENCE == gType ) {
result = U2Type::Sequence;
} else if ( GObjectTypes::ANNOTATION_TABLE == gType ) {
result = U2Type::AnnotationTable;
} else if ( GObjectTypes::PHYLOGENETIC_TREE == gType ) {
result = U2Type::PhyTree;
} else if ( GObjectTypes::CHROMATOGRAM == gType ) {
result = U2Type::Chromatogram;
} else if ( GObjectTypes::BIOSTRUCTURE_3D == gType ) {
result = U2Type::BioStruct3D;
} else if ( GObjectTypes::ASSEMBLY == gType ) {
result = U2Type::Assembly;
} else if ( GObjectTypes::MULTIPLE_CHROMATOGRAM_ALIGNMENT == gType ) {
result = U2Type::Mca;
} else if ( GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT == gType ) {
result = U2Type::Msa;
} else if ( GObjectTypes::VARIANT_TRACK == gType ) {
result = U2Type::VariantTrack;
} else if ( GObjectTypes::TEXT == gType ) {
result = U2Type::Text;
}
SAFE_POINT( U2Type::Unknown != result, "Unsupported object relation type detected!",
result );
return result;
}
Task * TextReader::processFile(const QString &url) {
IOAdapterFactory *iof = AppContext::getIOAdapterRegistry()->getIOAdapterFactoryById(IOAdapterUtils::url2io(url));
io = iof->createIOAdapter();
if(!io->open(url,IOAdapterMode_Read)) {
return new FailTask(tr("Can't load file %1").arg(url));
}
if(actor->getParameter(BaseAttributes::READ_BY_LINES_ATTRIBUTE().getId())->getAttributeValue<bool>(context) == false) {
QByteArray buf;
int read = 0;
int offs = 0;
buf.resize(READ_BLOCK_SIZE);
buf.fill(0);
do {
read = io->readBlock(buf.data() + offs, READ_BLOCK_SIZE);
if (read == -1) {
return new FailTask(tr("Can't load file %1. %2").arg(url).arg(io->errorString()));
}
if (read != READ_BLOCK_SIZE) {
SAFE_POINT(read < READ_BLOCK_SIZE, "Error while reading file", NULL);
buf.resize(buf.size() - READ_BLOCK_SIZE + read);
break;
}
offs += read;
buf.resize(offs + READ_BLOCK_SIZE);
} while(read == READ_BLOCK_SIZE);
sendMessage(buf);
io->close();
} else {
processNextLine();
}
return NULL;
}
Document* DatabaseConnectionFormat::loadDocument(IOAdapter* io, const U2DbiRef&, const QVariantMap& hints, U2OpStatus& os) {
DatabaseConnectionAdapter* databaseConnectionAdapter = qobject_cast<DatabaseConnectionAdapter*>(io);
SAFE_POINT(NULL != databaseConnectionAdapter, QString("Can't use current IOAdapter: %1").arg(io->getAdapterName()), NULL);
U2Dbi* dbi = databaseConnectionAdapter->getConnection().dbi;
SAFE_POINT(NULL != dbi, "NULL dbi", NULL);
QList<GObject*> objects = getObjects(dbi, os);
CHECK_OP_EXT(os, qDeleteAll(objects), NULL);
const QString modLockDesc = dbi->getFeatures().contains(U2DbiFeature_GlobalReadOnly)
? DocumentFormat::tr("You have no permissions to modify the content of this database")
: QString();
Document* resultDocument = new Document(this, io->getFactory(), io->getURL(), dbi->getDbiRef(), objects, hints, modLockDesc);
resultDocument->setDocumentOwnsDbiResources(false);
return resultDocument;
}
QWidget * InSilicoPcrOPWidgetFactory::createWidget(GObjectView *objView) {
AnnotatedDNAView *annotatedDnaView = qobject_cast<AnnotatedDNAView*>(objView);
SAFE_POINT(NULL != annotatedDnaView, L10N::nullPointerError("AnnotatedDNAView"), NULL);
InSilicoPcrOptionPanelWidget *opWidget = new InSilicoPcrOptionPanelWidget(annotatedDnaView);
opWidget->setObjectName("InSilicoPcrOptionPanelWidget");
return opWidget;
}
Task* PFMatrixBuildWorker::tick() {
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
if (inputMessage.isEmpty()) {
output->transit();
return NULL;
}
mtype = PFMatrixWorkerFactory::FREQUENCY_MATRIX_MODEL_TYPE();
QVariantMap data = inputMessage.getData().toMap();
cfg.type = actor->getParameter(TYPE_ATTR)->getAttributeValue<bool>(context) ? PM_DINUCLEOTIDE : PM_MONONUCLEOTIDE;
QVariantMap qm = inputMessage.getData().toMap();
SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<MAlignmentObject> msaObj(StorageUtils::getMsaObject(context->getDataStorage(), msaId));
SAFE_POINT(!msaObj.isNull(), "NULL MSA Object!", NULL);
const MAlignment &msa = msaObj->getMAlignment();
Task* t = new PFMatrixBuildTask(cfg, msa);
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
return t;
} else if (input->isEnded()) {
setDone();
output->setEnded();
}
return NULL;
}
FSItem * FSItem::child(int pos) const {
SAFE_POINT(isDir(), "Files can not have children", NULL);
if (pos >= items.size() || pos < 0) {
return NULL;
}
return items[pos];
}
Task * CufflinksWorker::tick() {
if (false == settingsAreCorrect) {
return NULL;
}
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
SAFE_POINT(!inputMessage.isEmpty(), "Internal error: message can't be NULL!", NULL);
QVariantMap data = inputMessage.getData().toMap();
if (settings.fromFile) {
settings.url = data[BaseSlots::URL_SLOT().getId()].toString();
} else {
settings.assemblyId = data[BaseSlots::ASSEMBLY_SLOT().getId()].value<SharedDbiDataHandler>();
}
// Create the task
CufflinksSupportTask* cufflinksSupportTask = new CufflinksSupportTask(settings);
cufflinksSupportTask->addListeners(createLogListeners());
connect(cufflinksSupportTask, SIGNAL(si_stateChanged()), SLOT(sl_cufflinksTaskFinished()));
return cufflinksSupportTask;
}
else if (input->isEnded()) {
setDone();
output->setEnded();
}
return NULL;
}
bool str2DataType(const QString &str, U2DataType &res) {
bool conversionOk = false;
// hope that "U2DataType" typedef won't change
SAFE_POINT(sizeof(U2DataType) == sizeof(qint16), "Unexpected data type detected", false);
res = str.toUShort(&conversionOk);
return conversionOk;
}
QString AnnotHighlightTree::getFirstItemAnnotName()
{
QTreeWidgetItem* firstItem = topLevelItem(0);
SAFE_POINT(0 != firstItem, "There is no first item in the tree!", QString());
QString annotName = firstItem->text(COL_NUM_ANNOT_NAME);
return annotName;
}
QString SiteconWritePrompter::composeRichDoc() {
IntegralBusPort *input = qobject_cast<IntegralBusPort*>(target->getPort(SITECON_IN_PORT_ID));
SAFE_POINT(NULL != input, "NULL input port", "");
QString from = getProducersOrUnset(SITECON_IN_PORT_ID, SiteconWorkerFactory::SITECON_SLOT.getId());
QString url = getScreenedURL(input, BaseAttributes::URL_OUT_ATTRIBUTE().getId(), BaseSlots::URL_SLOT().getId());
url = getHyperlink(BaseAttributes::URL_OUT_ATTRIBUTE().getId(), url);
return tr("Save the profile(s) from <u>%1</u> to %2.").arg(from).arg(url);
}
U2Msa MAlignmentExporter::getAlignmentObject(const U2DbiRef &dbiRef, const U2DataId &msaId, U2OpStatus &os) const {
SAFE_POINT(!con.isOpen(), OPENED_DBI_CONNECTION_ERROR, U2Msa());
con.open(dbiRef, false, os);
U2Msa msa = exportAlignmentObject(msaId, os);
CHECK_OP(os, U2Msa());
return msa;
}
QList<Task*> DNASequenceGeneratorTask::onGenerateTaskFinished( ) {
QList<Task *> resultTasks;
SAFE_POINT( generateTask->isFinished( ) && !generateTask->getStateInfo( ).isCoR( ),
"Invalid task encountered", resultTasks );
IOAdapterFactory *iof = AppContext::getIOAdapterRegistry( )->getIOAdapterFactoryById(
IOAdapterUtils::url2io( cfg.getOutUrlString( ) ) );
if (cfg.saveDoc) {
DocumentFormat *format = AppContext::getDocumentFormatRegistry()->getFormatById(cfg.getDocumentFormatId());
Document* doc = format->createNewLoadedDocument(iof, cfg.getOutUrlString(), stateInfo);
CHECK_OP( stateInfo, resultTasks );
const QSet<QString> &supportedFormats = format->getSupportedObjectTypes( );
const bool isSequenceFormat = supportedFormats.contains( GObjectTypes::SEQUENCE );
if ( isSequenceFormat) {
addSequencesToSeqDoc( doc );
} else { // consider alignment format
SAFE_POINT( supportedFormats.contains( GObjectTypes::MULTIPLE_SEQUENCE_ALIGNMENT ),
"Unexpected format encountered", resultTasks );
addSequencesToMsaDoc( doc );
}
saveTask = new SaveDocumentTask(doc, SaveDoc_Overwrite);
resultTasks << saveTask;
} else { // TODO: avoid high memory consumption here
const DNAAlphabet *alp = cfg.getAlphabet( );
SAFE_POINT( NULL != alp, "Generated sequence has invalid alphabet", resultTasks );
const U2DbiRef dbiRef = generateTask->getDbiRef( );
const QString baseSeqName = cfg.getSequenceName( );
QList<U2Sequence> seqs = generateTask->getResults( );
for ( int sequenceNum = 0, totalSeqCount = seqs.size( ); sequenceNum < totalSeqCount;
++sequenceNum )
{
const QString seqName = ( 1 < totalSeqCount )
? ( baseSeqName + " " + QString::number( sequenceNum + 1 ) ) : baseSeqName;
DbiConnection con( dbiRef, stateInfo );
CHECK_OP( stateInfo, resultTasks );
const QByteArray seqContent = con.dbi->getSequenceDbi( )->getSequenceData(
seqs[sequenceNum].id, U2_REGION_MAX, stateInfo );
results << DNASequence( seqName, seqContent, alp );
}
}
return resultTasks;
}
bool DnaAssemblyAlgorithmMainWidget::requiredToolsAreOk() const {
QStringList missedExtTools;
ExternalToolRegistry *extToolRegistry = AppContext::getExternalToolRegistry();
SAFE_POINT(NULL != extToolRegistry, L10N::nullPointerError("External tool subsystem"), false);
foreach (const QString &toolName, requiredExtToolNames) {
ExternalTool *tool = extToolRegistry->getByName(toolName);
if (NULL == tool || tool->getPath().isEmpty()) {
missedExtTools.append(toolName);
}
}
bool GTUtilsCv::cvBtn::isChecked(HI::GUITestOpStatus &os, ADVSingleSequenceWidget *seqWidget) {
QAbstractButton *cvButton = getCvButton(os, seqWidget, true /* CV button must exist */ );
CHECK_OP_SET_ERR_RESULT(os, "Error getting CV button!", false);
SAFE_POINT(NULL != cvButton, "cvButton is NULL!", false);
CHECK_SET_ERR_RESULT(cvButton->isCheckable(), "CV button is not checkable!", false);
return cvButton->isChecked();
}
bool OPWidgetFactory::passFiltration( OPFactoryFilterVisitorInterface* filter ){
//by default checks type only
bool res = false;
SAFE_POINT(filter != NULL, "OPWidgetFactory::passFiltration. Filter is null", res);
res = filter->typePass(getObjectViewType());
return res;
}