Exemplo n.º 1
0
/*******************************************
* 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 );
}
Exemplo n.º 2
0
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);
}
Exemplo n.º 3
0
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);
}
Exemplo n.º 4
0
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;
}
Exemplo n.º 5
0
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;
}
Exemplo n.º 7
0
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);
}
Exemplo n.º 8
0
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());
}
Exemplo n.º 9
0
PrimersDetailsDialog::PrimersDetailsDialog(QWidget *parent, const QString &details)
: QDialog(parent)
{
    GCOUNTER(cvar, tvar, "PrimersDetailsDialog");
    setupUi(this);
    new HelpButton(this, buttonBox, "17469030");
    textEdit->setText(details);
}
Exemplo n.º 10
0
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);
}
Exemplo n.º 11
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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");
}
Exemplo n.º 12
0
//////////////////////////////////////////////////////////////////////////
// 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());
}
Exemplo n.º 13
0
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();
}
Exemplo n.º 14
0
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);
    }
}
Exemplo n.º 15
0
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")), );
    }
Exemplo n.º 16
0
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);
}
Exemplo n.º 17
0
//////////////////////////////////////////////////////
//CASAVAFilterTask
CASAVAFilterTask::CASAVAFilterTask(const BaseNGSSetting &settings)
    :BaseNGSTask(settings){
    GCOUNTER(cvar, tvar, "NGS:CASAVAFilterTask");
}
Exemplo n.º 18
0
//////////////////////////////////////////////////////
//QualityTrimTask
QualityTrimTask::QualityTrimTask(const BaseNGSSetting &settings)
    :BaseNGSTask(settings){

    GCOUNTER(cvar, tvar, "NGS:FASTQQualityTrimmerTask");
}
Exemplo n.º 19
0
//////////////////////////////////////////////////////
//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");
    }
}
Exemplo n.º 21
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SolventAccessibleSurface::SolventAccessibleSurface()
{
    GCOUNTER( cvar, tvar, "SolventAccessibleSurface" );
}