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;
}
IMPLEMENT_TEST(MsaImporterExporterUnitTests, importExportAlignment) {
const U2DbiRef& dbiRef = MsaImporterExporterTestData::getDbiRef();
U2OpStatusImpl os;
// Init an alignment
QString alignmentName = "Test alignment";
DNAAlphabetRegistry* alphabetRegistry = AppContext::getDNAAlphabetRegistry();
const DNAAlphabet* alphabet = alphabetRegistry->findById(BaseDNAAlphabetIds::NUCL_DNA_DEFAULT());
QByteArray firstSequence("---AG-T");
QByteArray secondSequence("AG-CT-TAA");
MultipleSequenceAlignment al(alignmentName, alphabet);
al->addRow("First row", firstSequence);
al->addRow("Second row", secondSequence);
// Import the alignment
QScopedPointer<MultipleSequenceAlignmentObject> msaObj(MultipleSequenceAlignmentImporter::createAlignment(dbiRef, al, os));
CHECK_NO_ERROR(os);
// Export the alignment
MultipleSequenceAlignmentExporter alExporter;
MultipleSequenceAlignment alActual = alExporter.getAlignment(dbiRef, msaObj->getEntityRef().entityId, os);
CHECK_NO_ERROR(os);
bool alsEqual = (*al == *alActual);
CHECK_TRUE(alsEqual, "Actual alignment doesn't equal to the original!");
CHECK_EQUAL(alignmentName, alActual->getName(), "alignment name");
}
Task* ClustalOWorker::tick() {
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
if (inputMessage.isEmpty()) {
output->transit();
return NULL;
}
cfg.numIterations=actor->getParameter(NUM_ITERATIONS)->getAttributeValue<int>(context);
cfg.maxGuidetreeIterations=actor->getParameter(MAX_GT_ITERATIONS)->getAttributeValue<int>(context);
cfg.maxHMMIterations=actor->getParameter(MAX_HMM_ITERATIONS)->getAttributeValue<int>(context);
cfg.setAutoOptions=actor->getParameter(SET_AUTO)->getAttributeValue<bool>(context);
cfg.numberOfProcessors=AppContext::getAppSettings()->getAppResourcePool()->getIdealThreadCount();
QString path=actor->getParameter(EXT_TOOL_PATH)->getAttributeValue<QString>(context);
if(QString::compare(path, "default", Qt::CaseInsensitive) != 0){
AppContext::getExternalToolRegistry()->getByName(ET_CLUSTALO)->setPath(path);
}
path=actor->getParameter(TMP_DIR_PATH)->getAttributeValue<QString>(context);
if(QString::compare(path, "default", Qt::CaseInsensitive) != 0){
AppContext::getAppSettings()->getUserAppsSettings()->setUserTemporaryDirPath(path);
}
QVariantMap qm = inputMessage.getData().toMap();
SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<MultipleSequenceAlignmentObject> msaObj(StorageUtils::getMsaObject(context->getDataStorage(), msaId));
SAFE_POINT(!msaObj.isNull(), "NULL MSA Object!", NULL);
const MultipleSequenceAlignment msa = msaObj->getMultipleAlignment();
if (msa->isEmpty()) {
algoLog.error(tr("An empty MSA '%1' has been supplied to ClustalO.").arg(msa->getName()));
return NULL;
}
ClustalOSupportTask* supportTask = new ClustalOSupportTask(msa, GObjectReference(), cfg);
supportTask->addListeners(createLogListeners());
Task *t = new NoFailTaskWrapper(supportTask);
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
return t;
} else if (input->isEnded()) {
setDone();
output->setEnded();
}
return NULL;
}
Task* ClustalWWorker::tick() {
if (input->hasMessage()) {
Message inputMessage = getMessageAndSetupScriptValues(input);
if (inputMessage.isEmpty()) {
output->transit();
return NULL;
}
cfg.gapOpenPenalty=actor->getParameter(GAP_OPEN_PENALTY)->getAttributeValue<float>(context);
cfg.gapExtenstionPenalty=actor->getParameter(GAP_EXT_PENALTY)->getAttributeValue<float>(context);
cfg.gapDist=actor->getParameter(GAP_DIST)->getAttributeValue<float>(context);
cfg.endGaps=actor->getParameter(END_GAPS)->getAttributeValue<bool>(context);
cfg.noHGaps=actor->getParameter(NO_HGAPS)->getAttributeValue<bool>(context);
cfg.noPGaps=actor->getParameter(NO_PGAPS)->getAttributeValue<bool>(context);
if(actor->getParameter(ITERATION)->getAttributeValue<int>(context) != 0){
if(actor->getParameter(ITERATION)->getAttributeValue<int>(context) == 1){
cfg.iterationType="TREE";
}else if(actor->getParameter(ITERATION)->getAttributeValue<int>(context) == 2){
cfg.iterationType="ALIGNMENT";
}
if(actor->getParameter(NUM_ITERATIONS)->getAttributeValue<int>(context) != 3){
cfg.numIterations=actor->getParameter(NUM_ITERATIONS)->getAttributeValue<int>(context);
}
}
if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == -1){
if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 0){
cfg.matrix="IUB";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 1){
cfg.matrix="CLUSTALW";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 2){
cfg.matrix="BLOSUM";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 3){
cfg.matrix="PAM";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 4){
cfg.matrix="GONNET";
}else if(actor->getParameter(MATRIX)->getAttributeValue<int>(context) == 5){
cfg.matrix="ID";
}
}
QString path=actor->getParameter(EXT_TOOL_PATH)->getAttributeValue<QString>(context);
if(QString::compare(path, "default", Qt::CaseInsensitive) != 0){
AppContext::getExternalToolRegistry()->getByName(ET_CLUSTAL)->setPath(path);
}
path=actor->getParameter(TMP_DIR_PATH)->getAttributeValue<QString>(context);
if(QString::compare(path, "default", Qt::CaseInsensitive) != 0){
AppContext::getAppSettings()->getUserAppsSettings()->setUserTemporaryDirPath(path);
}
QVariantMap qm = inputMessage.getData().toMap();
SharedDbiDataHandler msaId = qm.value(BaseSlots::MULTIPLE_ALIGNMENT_SLOT().getId()).value<SharedDbiDataHandler>();
QScopedPointer<MultipleSequenceAlignmentObject> msaObj(StorageUtils::getMsaObject(context->getDataStorage(), msaId));
SAFE_POINT(!msaObj.isNull(), "NULL MSA Object!", NULL);
const MultipleSequenceAlignment msa = msaObj->getMultipleAlignment();
if (msa->isEmpty()) {
algoLog.error(tr("An empty MSA '%1' has been supplied to ClustalW.").arg(msa->getName()));
return NULL;
}
ClustalWSupportTask* supportTask = new ClustalWSupportTask(msa, GObjectReference(), cfg);
supportTask->addListeners(createLogListeners());
Task *t = new NoFailTaskWrapper(supportTask);
connect(t, SIGNAL(si_stateChanged()), SLOT(sl_taskFinished()));
return t;
} else if (input->isEnded()) {
setDone();
output->setEnded();
}
return NULL;
}
