void Server::slotSendMsg(qintptr sockd, char *outbuf, uint outlen, quint16 shPdu)
{
QByteArray outBa;
QDataStream outD(&outBa, QIODevice::ReadWrite);
outD << shPdu;
outD.writeRawData(outbuf, outlen);
outlen = outBa.length();
QDataStream chkD(&outBa, QIODevice::ReadOnly);
qint16 shRet;
chkD >> shPdu;
chkD >> shRet;
QMap<qintptr, TcpClientSocket*>::iterator clientIt;
clientIt = clientList.find(sockd);
if (clientIt != clientList.end())
{
(clientIt.value())->write(outBa.data(), (qint64)outlen);
qDebug() << "void Server::slotSendMsg() - outlen=[" << outlen << "], sockd=" << sockd << " ,shPdu=" << shPdu << " ,shRet" << shRet;
}
}
void Server::slotSendMsg(QString szClientName, char *outbuf, uint outlen, quint16 shPdu)
{
QByteArray outBa;
QDataStream outD(&outBa, QIODevice::ReadWrite);
outD << shPdu;
outD.writeRawData(outbuf, outlen);
outlen = outBa.length();
QDataStream chkD(&outBa, QIODevice::ReadOnly);
chkD >> shPdu;
QMap<qintptr, TcpClientSocket*>::iterator clientIt = clientList.begin();
for (; clientIt!=clientList.end(); clientIt++)
{
if ((clientIt.value())->getClientName() == szClientName)
{
(clientIt.value())->write(outBa.data(), (qint64)outlen);
qDebug() << "void Server::slotSendMsg(username) - outlen=[" << outlen << "] ,shPdu=" << shPdu;
break;
}
}
}
void MergeFastqWorkerFactory::init() {
Descriptor desc( ACTOR_ID, MergeFastqWorker::tr("FASTQ Merger"),
MergeFastqWorker::tr("Merges input sequences to one output file") );
QList<PortDescriptor*> p;
{
Descriptor inD(BaseNGSWorker::INPUT_PORT, MergeFastqWorker::tr("Input File"),
MergeFastqWorker::tr("Set of FASTQ reads files"));
Descriptor outD(BaseNGSWorker::OUTPUT_PORT, MergeFastqWorker::tr("Output File"),
MergeFastqWorker::tr("Output FASTQ file"));
QMap<Descriptor, DataTypePtr> inM;
inM[BaseSlots::URL_SLOT()] = BaseTypes::STRING_TYPE();
p << new PortDescriptor(inD, DataTypePtr(new MapDataType("cf.input-url", inM)), true);
QMap<Descriptor, DataTypePtr> outM;
outM[BaseSlots::URL_SLOT()] = BaseTypes::STRING_TYPE();
p << new PortDescriptor(outD, DataTypePtr(new MapDataType("cf.output-url", outM)), false, true);
}
QList<Attribute*> a;
{
Descriptor outDir(BaseNGSWorker::OUT_MODE_ID, MergeFastqWorker::tr("Output directory"),
MergeFastqWorker::tr("Select an output directory. <b>Custom</b> - specify the output directory in the 'Custom directory' parameter. "
"<b>Workflow</b> - internal workflow directory. "
"<b>Input file</b> - the directory of the input file."));
Descriptor customDir(BaseNGSWorker::CUSTOM_DIR_ID, MergeFastqWorker::tr("Custom directory"),
MergeFastqWorker::tr("Select the custom output directory."));
Descriptor outName(BaseNGSWorker::OUT_NAME_ID, MergeFastqWorker::tr("Output file name"),
MergeFastqWorker::tr("A name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention."));
a << new Attribute(outDir, BaseTypes::NUM_TYPE(), false, QVariant(FileAndDirectoryUtils::WORKFLOW_INTERNAL));
Attribute* customDirAttr = new Attribute(customDir, BaseTypes::STRING_TYPE(), false, QVariant(""));
customDirAttr->addRelation(new VisibilityRelation(BaseNGSWorker::OUT_MODE_ID, FileAndDirectoryUtils::CUSTOM));
a << customDirAttr;
a << new Attribute( outName, BaseTypes::STRING_TYPE(), false, QVariant(BaseNGSWorker::DEFAULT_NAME));
}
QMap<QString, PropertyDelegate*> delegates;
{
QVariantMap directoryMap;
QString fileDir = MergeFastqWorker::tr("Input file");
QString workflowDir = MergeFastqWorker::tr("Workflow");
QString customD = MergeFastqWorker::tr("Custom");
directoryMap[fileDir] = FileAndDirectoryUtils::FILE_DIRECTORY;
directoryMap[workflowDir] = FileAndDirectoryUtils::WORKFLOW_INTERNAL;
directoryMap[customD] = FileAndDirectoryUtils::CUSTOM;
delegates[BaseNGSWorker::OUT_MODE_ID] = new ComboBoxDelegate(directoryMap);
delegates[BaseNGSWorker::CUSTOM_DIR_ID] = new URLDelegate("", "", false, true);
}
ActorPrototype* proto = new IntegralBusActorPrototype(desc, p, a);
proto->setEditor(new DelegateEditor(delegates));
proto->setPrompter(new MergeFastqPrompter());
WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_NGS_BASIC(), proto);
DomainFactory *localDomain = WorkflowEnv::getDomainRegistry()->getById(LocalDomainFactory::ID);
localDomain->registerEntry(new MergeFastqWorkerFactory());
}
void QualityTrimWorkerFactory::init() {
Descriptor desc( ACTOR_ID, QualityTrimWorker::tr("FASTQ Quality Trimmer"),
QualityTrimWorker::tr("The workflow scans each input sequence from the end to find the first position where the quality is greater or equal to the minimum quality threshold. "
"Then it trims the sequence to that position. If a the whole sequence has quality less than the threshold or the length of the output sequence less than "
"the minimum length threshold then the sequence is skipped.") );
QList<PortDescriptor*> p;
{
Descriptor inD(BaseNGSWorker::INPUT_PORT, QualityTrimWorker::tr("Input File"),
QualityTrimWorker::tr("Set of FASTQ reads files"));
Descriptor outD(BaseNGSWorker::OUTPUT_PORT, QualityTrimWorker::tr("Output File"),
QualityTrimWorker::tr("Output FASTQ files"));
QMap<Descriptor, DataTypePtr> inM;
inM[BaseSlots::URL_SLOT()] = BaseTypes::STRING_TYPE();
p << new PortDescriptor(inD, DataTypePtr(new MapDataType("cf.input-url", inM)), true);
QMap<Descriptor, DataTypePtr> outM;
outM[BaseSlots::URL_SLOT()] = BaseTypes::STRING_TYPE();
p << new PortDescriptor(outD, DataTypePtr(new MapDataType("cf.output-url", outM)), false, true);
}
QList<Attribute*> a;
{
Descriptor outDir(BaseNGSWorker::OUT_MODE_ID, QualityTrimWorker::tr("Output directory"),
QualityTrimWorker::tr("Select an output directory. <b>Custom</b> - specify the output directory in the 'Custom directory' parameter. "
"<b>Workflow</b> - internal workflow directory. "
"<b>Input file</b> - the directory of the input file."));
Descriptor customDir(BaseNGSWorker::CUSTOM_DIR_ID, QualityTrimWorker::tr("Custom directory"),
QualityTrimWorker::tr("Select the custom output directory."));
Descriptor outName(BaseNGSWorker::OUT_NAME_ID, QualityTrimWorker::tr("Output file name"),
QualityTrimWorker::tr("A name of an output file. If default of empty value is provided the output name is the name of the first file with additional extention."));
Descriptor qualT(QUALITY_ID, QualityTrimWorker::tr("Quality threshold"),
QualityTrimWorker::tr("Quality threshold for trimming."));
Descriptor lenT(LEN_ID, QualityTrimWorker::tr("Min Length"),
QualityTrimWorker::tr("Too short reads are discarded by the filter."));
Descriptor bothD(BOTH_ID, QualityTrimWorker::tr("Trim both ends"),
QualityTrimWorker::tr("Trim the both ends of a read or not. Usually, you need to set <b>True</b> for <b>Sanger</b> sequencing and <b>False</b> for <b>NGS</b>"));
a << new Attribute(outDir, BaseTypes::NUM_TYPE(), false, QVariant(FileAndDirectoryUtils::WORKFLOW_INTERNAL));
Attribute* customDirAttr = new Attribute(customDir, BaseTypes::STRING_TYPE(), false, QVariant(""));
customDirAttr->addRelation(new VisibilityRelation(BaseNGSWorker::OUT_MODE_ID, FileAndDirectoryUtils::CUSTOM));
a << customDirAttr;
a << new Attribute( outName, BaseTypes::STRING_TYPE(), false, QVariant(BaseNGSWorker::DEFAULT_NAME));
a << new Attribute( qualT, BaseTypes:: NUM_TYPE(), false, QVariant(30));
a << new Attribute( lenT, BaseTypes::NUM_TYPE(), false, QVariant(0));
a << new Attribute( bothD, BaseTypes::BOOL_TYPE(), false, true);
}
QMap<QString, PropertyDelegate*> delegates;
{
QVariantMap directoryMap;
QString fileDir = QualityTrimWorker::tr("Input file");
QString workflowDir = QualityTrimWorker::tr("Workflow");
QString customD = QualityTrimWorker::tr("Custom");
directoryMap[fileDir] = FileAndDirectoryUtils::FILE_DIRECTORY;
directoryMap[workflowDir] = FileAndDirectoryUtils::WORKFLOW_INTERNAL;
directoryMap[customD] = FileAndDirectoryUtils::CUSTOM;
delegates[BaseNGSWorker::OUT_MODE_ID] = new ComboBoxDelegate(directoryMap);
delegates[BaseNGSWorker::CUSTOM_DIR_ID] = new URLDelegate("", "", false, true);
QVariantMap len; len["minimum"] = 0; len["maximum"] = INT_MAX;
delegates[QUALITY_ID] = new SpinBoxDelegate(len);
delegates[LEN_ID] = new SpinBoxDelegate(len);
}
ActorPrototype* proto = new IntegralBusActorPrototype(desc, p, a);
proto->setEditor(new DelegateEditor(delegates));
proto->setPrompter(new QualityTrimPrompter());
WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_NGS_BASIC(), proto);
DomainFactory *localDomain = WorkflowEnv::getDomainRegistry()->getById(LocalDomainFactory::ID);
localDomain->registerEntry(new QualityTrimWorkerFactory());
}
