// static
bool ProfilesDialog::existingProfileDescription(const QString &desc)
{
QStringList profilesFilter;
profilesFilter << "*";
// List the Mlt profiles
QDir mltDir(KdenliveSettings::mltpath());
QStringList profilesFiles = mltDir.entryList(profilesFilter, QDir::Files);
for (int i = 0; i < profilesFiles.size(); ++i) {
KConfig confFile(mltDir.absoluteFilePath(profilesFiles.at(i)), KConfig::SimpleConfig);
if (desc == confFile.entryMap().value("description")) return true;
}
// List custom profiles
QStringList customProfiles = QStandardPaths::locateAll(QStandardPaths::DataLocation, "/profiles/", QStandardPaths::LocateDirectory);
for (int i = 0; i < customProfiles.size(); ++i) {
QDir customDir(customProfiles.at(i));
profilesFiles = customDir.entryList(profilesFilter, QDir::Files);
for (int j = 0; j < profilesFiles.size(); ++j) {
KConfig confFile(customDir.absoluteFilePath(profilesFiles.at(j)), KConfig::SimpleConfig);
if (desc == confFile.entryMap().value("description")) return true;
}
}
return false;
}
static QString remoteTmpDir()
{
QString customDir(qgetenv("KIO_JOBREMOTETEST_REMOTETMP"));
if (customDir.isEmpty()) {
return QFile::decodeName(qgetenv("KDEHOME")) + "/jobremotetest/";
} else {
return customDir;
}
}
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());
}
