C++ (Cpp) setVerboseLogMode Examples

Example #1

File: ExportTasks.cpp Project: ggrekhov/ugene

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);
}

Example #2

File: ExportTasks.cpp Project: ugeneunipro/ugene-old

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);
}

Example #3

File: ExportTasks.cpp Project: ggrekhov/ugene

//////////////////////////////////////////////////////////////////////////
// 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());
}

Example #4

File: HMMCalibrateTask.cpp Project: ugeneunipro/ugene-old

//////////////////////////////////////////////////////////////////////////
// task to save calibration results to file
HMMCalibrateToFileTask::HMMCalibrateToFileTask(const QString& _inFile, const QString& _outFile, const UHMMCalibrateSettings& s)
: Task("", TaskFlags_NR_FOSCOE|TaskFlag_ReportingIsSupported), hmm(NULL), inFile(_inFile), outFile(_outFile), settings(s) 
{
    setVerboseLogMode(true);
    QString tn = tr("HMM calibrate '%1'").arg(QFileInfo(inFile).fileName());
    setTaskName(tn);
    readTask = NULL;
    calibrateTask = NULL;
}

Example #5

File: PairwiseAlignmentHirschbergTask.cpp Project: ugeneunipro/ugene-old

PairwiseAlignmentHirschbergTask::PairwiseAlignmentHirschbergTask(PairwiseAlignmentHirschbergTaskSettings* _settings) :
    PairwiseAlignmentTask(TaskFlag_NoRun), settings(_settings), kalignSubTask(NULL), workflowKalignSubTask(NULL), ma(NULL) {

    SAFE_POINT(settings != NULL, "Task settings are not defined.", );
    SAFE_POINT(settings->convertCustomSettings() && settings->isValid(), "Invalide task settings.", );

    U2OpStatus2Log os;
    DbiConnection con(settings->msaRef.dbiRef, os);
    CHECK_OP(os, );
    U2Sequence sequence = con.dbi->getSequenceDbi()->getSequenceObject(settings->firstSequenceRef.entityId, os);
    CHECK_OP(os, );
    first = con.dbi->getSequenceDbi()->getSequenceData(sequence.id, U2Region(0, sequence.length), os);
    CHECK_OP(os, );
    QString firstName = sequence.visualName;

    sequence = con.dbi->getSequenceDbi()->getSequenceObject(settings->secondSequenceRef.entityId, os);
    CHECK_OP(os, );
    second = con.dbi->getSequenceDbi()->getSequenceData(sequence.id, U2Region(0, sequence.length), os);
    CHECK_OP(os, );
    QString secondName = sequence.visualName;
    con.close(os);

    alphabet = U2AlphabetUtils::getById(settings->alphabet);
    SAFE_POINT(alphabet != NULL, "Albhabet is invalid.", );

    ma = new MAlignment(firstName + " vs. " + secondName, alphabet);
    ma->addRow(firstName, first, os);
    CHECK_OP(os, );
    ma->addRow(secondName, second, os);
    CHECK_OP(os, );

    KalignTaskSettings kalignSettings;
    kalignSettings.gapOpenPenalty = settings->gapOpen;
    kalignSettings.gapExtenstionPenalty = settings->gapExtd;
    kalignSettings.termGapPenalty = settings->gapTerm;
    kalignSettings.secret = settings->bonusScore;

    kalignSubTask = new KalignTask(*ma, kalignSettings);
    setUseDescriptionFromSubtask(true);
    setVerboseLogMode(true);
    addSubTask(kalignSubTask);
}