/*******************************************
* WorkflowRunFromCMDLineBase
*******************************************/
WorkflowRunFromCMDLineBase::WorkflowRunFromCMDLineBase()
: Task(tr("Workflow run from cmdline"), TaskFlag_None),
schema(NULL),
optionsStartAt(-1),
loadTask(NULL),
workflowRunTask(NULL)
{
GCOUNTER(cvar,tvar,"workflow_run_from_cmdline");
CMDLineRegistry * cmdLineRegistry = AppContext::getCMDLineRegistry();
// try to process schema without 'task' option (it can only be the first one)
QStringList pureValues = CMDLineRegistryUtils::getPureValues();
if( !pureValues.isEmpty() ) {
QString schemaName = pureValues.first();
processLoadSchemaTask( schemaName, 1 ); // because after program name
}
if( loadTask != NULL ) {
addSubTask( loadTask );
return;
}
// process schema with 'task' option
int taskOptionIdx = CMDLineRegistryUtils::getParameterIndex( WorkflowDesignerPlugin::RUN_WORKFLOW );
if(taskOptionIdx != -1) {
processLoadSchemaTask( cmdLineRegistry->getParameterValue( WorkflowDesignerPlugin::RUN_WORKFLOW, taskOptionIdx ), taskOptionIdx );
}
if( loadTask == NULL ) {
setError( tr( "no task to run" ) );
return;
}
addSubTask( loadTask );
}
void DatasetsListWidget::sl_newDataset() {
GCOUNTER(cvar, tvar, "WD::Dataset::New Dataset");
QString error;
QString text = getTip();
do {
bool ok = false;
text = QInputDialog::getText(this,
tr("Enter Dataset Name"),
tr("New dataset name:"),
QLineEdit::Normal,
text, &ok);
if (!ok) {
return;
}
U2OpStatusImpl os;
ctrl->addDataset(text, os);
error = os.getError();
if (!error.isEmpty()) {
QMessageBox::critical(this, tr("Error"), error);
}
} while (!error.isEmpty());
// activate the tab after adding
tabs->setCurrentIndex(tabs->count() - 1);
}
void DatasetsListWidget::sl_renameDataset() {
GCOUNTER(cvar, tvar, "WD::Dataset::Rename Dataset");
QAction *a = dynamic_cast<QAction*>(sender());
CHECK(NULL != a, );
int idx = a->property("idx").toInt();
CHECK(idx < tabs->count(), );
bool error = false;
QString text = tabs->tabText(idx);
do {
bool ok = false;
text = QInputDialog::getText(this,
tr("Rename Dataset"),
tr("New dataset name:"),
QLineEdit::Normal,
text, &ok);
if (!ok) {
return;
}
U2OpStatusImpl os;
ctrl->renameDataset(idx, text, os);
if (os.hasError()) {
QMessageBox::critical(this, tr("Error"), os.getError());
}
error = os.hasError();
} while (error);
tabs->setTabText(idx, text);
}
void DatasetsListWidget::sl_deleteDataset(int idx) {
GCOUNTER(cvar, tvar, "WD::Dataset::Delete Dataset");
QWidget *w = tabs->widget(idx);
tabs->removeTab(idx);
ctrl->deleteDataset(idx);
delete w;
}
HMMCalibrateTask::HMMCalibrateTask(plan7_s* hmm, const UHMMCalibrateSettings& s)
: HMMCalibrateAbstractTask("", hmm, s)
{
GCOUNTER( cvar, tvar, "HMMCalibrateTask" );
setTaskName(tr("HMM calibrate '%1'").arg(hmm->name));
tpm = Task::Progress_Manual;
}
BlastDBCmdSupportTask::BlastDBCmdSupportTask(const BlastDBCmdSupportTaskSettings& _settings) :
Task("Run NCBI BlastDBCmd task", TaskFlags_NR_FOSCOE),settings(_settings)
{
GCOUNTER( cvar, tvar, "BlastDBCmdSupportTask" );
blastDBCmdTask=NULL;
toolName = ET_BLASTDBCMD;
}
ExportMSA2SequencesTask::ExportMSA2SequencesTask(const MultipleSequenceAlignment& _ma, const QString& _url, bool _trimAli, DocumentFormatId _format)
: DocumentProviderTask(tr("Export alignment to sequence: %1").arg(_url), TaskFlag_None),
ma(_ma->getCopy()), url(_url), trimAli(_trimAli), format(_format)
{
GCOUNTER( cvar, tvar, "ExportMSA2SequencesTask");
setVerboseLogMode(true);
}
ORFFindTask::ORFFindTask(const ORFAlgorithmSettings& s,const U2EntityRef& _entityRef)
: Task (tr("ORF find"), TaskFlag_None),config(s),entityRef(_entityRef)
{
GCOUNTER( cvar, tvar, "ORFFindTask" );
tpm = Progress_Manual;
assert(config.proteinTT && config.proteinTT->isThree2One());
}
PrimersDetailsDialog::PrimersDetailsDialog(QWidget *parent, const QString &details)
: QDialog(parent)
{
GCOUNTER(cvar, tvar, "PrimersDetailsDialog");
setupUi(this);
new HelpButton(this, buttonBox, "17469030");
textEdit->setText(details);
}
SaveMSA2SequencesTask::SaveMSA2SequencesTask(const MAlignment& _ma, const QString& _url, bool _trimAli, DocumentFormatId _format)
: Task(tr("Export alignment to sequence: %1").arg(_url), TaskFlag_None),
ma(_ma), url(_url), trimAli(_trimAli), format(_format)
{
GCOUNTER( cvar, tvar, "ExportMSA2SequencesTask" );
setVerboseLogMode(true);
stateInfo.setProgress(0);
}
FormatDBSupportTask::FormatDBSupportTask(const QString& name, const FormatDBSupportTaskSettings& _settings) :
Task(tr("Run NCBI FormatDB task"), TaskFlags_NR_FOSE_COSC | TaskFlag_ReportingIsSupported | TaskFlag_ReportingIsEnabled),
prepareTask(NULL),
formatDBTask(NULL),
toolName(name),
settings(_settings)
{
GCOUNTER(cvar, tvar, "FormatDBSupportTask");
}
//////////////////////////////////////////////////////////////////////////
// DNAExportAlignmentTask
ExportAlignmentTask::ExportAlignmentTask(const MultipleSequenceAlignment& _ma, const QString& _fileName, DocumentFormatId _f)
: DocumentProviderTask("", TaskFlag_None), ma(_ma->getCopy()), fileName(_fileName), format(_f)
{
GCOUNTER( cvar, tvar, "ExportAlignmentTask" );
setTaskName(tr("Export alignment to '%1'").arg(QFileInfo(fileName).fileName()));
setVerboseLogMode(true);
assert(!ma->isEmpty());
}
void EditPrimerDialog::init() {
GCOUNTER(cvar, tvar, "Add primer in library");
setupUi(this);
new HelpButton(this, buttonBox, "17467823");
primerEdit->setValidator(new PrimerValidator(this));
connect(primerEdit, SIGNAL(textEdited(const QString &)), SLOT(sl_onPrimerChanged(const QString &)));
connect(primerEdit, SIGNAL(textChanged(const QString &)), SLOT(sl_validate()));
connect(nameEdit, SIGNAL(textChanged(const QString &)), SLOT(sl_validate()));
sl_validate();
}
DNASequenceGeneratorTask::DNASequenceGeneratorTask(const DNASequenceGeneratorConfig& cfg)
: Task(tr("Generate sequence task"), TaskFlag_NoRun),
cfg(cfg),
loadRefTask(NULL),
evalTask(NULL),
generateTask(NULL),
saveTask(NULL) {
GCOUNTER( cvar, tvar, "DNASequenceGeneratorTask" );
if (cfg.useReference()) {
// do not load reference file if it is already in project and has loaded state
const QString& docUrl = cfg.getReferenceUrl();
Project* prj = AppContext::getProject();
if (prj) {
Document* doc = prj->findDocumentByURL(docUrl);
if (doc && doc->isLoaded()) {
QString err;
evalTask = createEvaluationTask(doc, err);
if (evalTask) {
addSubTask(evalTask);
} else {
stateInfo.setError(err);
}
return;
}
}
loadRefTask = LoadDocumentTask::getDefaultLoadDocTask(GUrl(docUrl));
if (loadRefTask) {
addSubTask(loadRefTask);
} else {
stateInfo.setError(tr("Incorrect reference file"));
return;
}
} else {
generateTask = new GenerateDNASequenceTask(cfg.getContent(), cfg.getLength(), cfg.window, cfg.getNumberOfSequences(), cfg.seed);
addSubTask(generateTask);
}
}
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")), );
}
WorkflowEditor::WorkflowEditor(WorkflowView *p)
: QWidget(p),
owner(p),
custom(NULL),
customWidget(NULL),
subject(NULL),
actor(NULL),
onFirstTableShow(true)
{
GCOUNTER( cvar, tvar, "WorkflowEditor" );
setupUi(this);
specialParameters = new SpecialParametersPanel(this);
tableSplitter->insertWidget(0, specialParameters);
specialParameters->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Maximum);
table->setSizePolicy(QSizePolicy::Preferred, QSizePolicy::Expanding);
specialParameters->hide();
#ifdef Q_OS_MAC
QString style("QGroupBox::title {margin-top: 1px; margin-left: 15px;}");
editorBox->setStyleSheet(style);
#endif
QVBoxLayout *inputScrollAreaContainerLayout = new QVBoxLayout();
inputScrollAreaContainerLayout->setContentsMargins(0, 0, 0, 0);
inputScrollAreaContainerLayout->setSpacing(0);
inputScrollAreaContainerLayout->setSizeConstraint(QLayout::SetMinAndMaxSize);
inputScrollAreaContainer->setLayout(inputScrollAreaContainerLayout);
inputPortBox->setEnabled(false);
inputPortBox->setVisible(true);
connect(inputPortBox, SIGNAL(toggled(bool)), SLOT(sl_changeVisibleInput(bool)));
QVBoxLayout *outputScrollAreaContainerLayout = new QVBoxLayout();
outputScrollAreaContainerLayout->setContentsMargins(0, 0, 0, 0);
outputScrollAreaContainerLayout->setSpacing(0);
outputScrollAreaContainerLayout->setSizeConstraint(QLayout::SetMinAndMaxSize);
outputScrollAreaContainer->setLayout(outputScrollAreaContainerLayout);
outputPortBox->setEnabled(false);
outputPortBox->setVisible(true);
connect(outputPortBox, SIGNAL(toggled(bool)), SLOT(sl_changeVisibleOutput(bool)));
caption->setMinimumHeight(nameEdit->sizeHint().height());
actorModel = new ActorCfgModel(this, owner);
proxyModel = new ActorCfgFilterProxyModel(this);
proxyModel->setSourceModel(actorModel);
table->setModel(proxyModel);
table->horizontalHeader()->setSectionsClickable(false);
table->horizontalHeader()->setSectionResizeMode(QHeaderView::Interactive);
table->verticalHeader()->hide();
table->verticalHeader()->setDefaultSectionSize(QFontMetrics(QFont()).height() + 6);
table->setItemDelegate(new SuperDelegate(this));
table->installEventFilter(this);
reset();
doc->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
propDoc->setSizePolicy(QSizePolicy::Expanding, QSizePolicy::Expanding);
doc->installEventFilter(this);
connect(nameEdit, SIGNAL(editingFinished()), SLOT(editingLabelFinished()));
connect(table->selectionModel(), SIGNAL(currentChanged(QModelIndex, QModelIndex)), SLOT(sl_showPropDoc()));
connect(table->model(), SIGNAL(dataChanged(QModelIndex, QModelIndex)), SLOT(handleDataChanged(QModelIndex, QModelIndex)));
// FIXME
//connect(doc, SIGNAL(customContextMenuRequested(const QPoint &)), SLOT(sl_contextMenuForDoc(const QPoint &)));
table->setTabKeyNavigation(true);
}
//////////////////////////////////////////////////////
//CASAVAFilterTask
CASAVAFilterTask::CASAVAFilterTask(const BaseNGSSetting &settings)
:BaseNGSTask(settings){
GCOUNTER(cvar, tvar, "NGS:CASAVAFilterTask");
}
//////////////////////////////////////////////////////
//QualityTrimTask
QualityTrimTask::QualityTrimTask(const BaseNGSSetting &settings)
:BaseNGSTask(settings){
GCOUNTER(cvar, tvar, "NGS:FASTQQualityTrimmerTask");
}
//////////////////////////////////////////////////////
//MergeFastqTask
MergeFastqTask::MergeFastqTask(const BaseNGSSetting &settings)
:BaseNGSTask(settings){
GCOUNTER(cvar, tvar, "NGS:FASTQMergeFastqmerTask");
}
void CreateAnnotationOptionsPanelWidget::countDescriptionUsage() const {
if (!leDescription->text().isEmpty()) {
GCOUNTER(cvar, tvar, "CreateAnnotationOptionsPanelWidget: description is used");
}
}
SolventAccessibleSurface::SolventAccessibleSurface()
{
GCOUNTER( cvar, tvar, "SolventAccessibleSurface" );
}