void GetFileListWorkerFactory::init() {
QList<PortDescriptor*> portDescs;
{
QMap<Descriptor, DataTypePtr> outTypeMap;
outTypeMap[BaseSlots::URL_SLOT()] = BaseTypes::STRING_TYPE();
outTypeMap[BaseSlots::DATASET_SLOT()] = BaseTypes::STRING_TYPE();
DataTypePtr outTypeSet(new MapDataType(BasePorts::OUT_TEXT_PORT_ID(), outTypeMap));
portDescs << new PortDescriptor(Descriptor(OUT_PORT_ID, GetFileListWorker::tr("Output URL"), GetFileListWorker::tr("Paths read by the element.")), outTypeSet, false, true);
}
QList<Attribute*> attrs;
{
Descriptor inUrl(URL_ATTR,
GetFileListWorker::tr("Input URL"),
GetFileListWorker::tr("Input URL"));
attrs << new URLAttribute(BaseAttributes::URL_IN_ATTRIBUTE(), BaseTypes::URL_DATASETS_TYPE(), true);
}
Descriptor protoDesc(GetFileListWorkerFactory::ACTOR_ID,
GetFileListWorker::tr("File List"),
GetFileListWorker::tr("Produces URL(s) to files from specified folders."));
ActorPrototype *proto = new IntegralBusActorPrototype(protoDesc, portDescs, attrs);
proto->setEditor(new DelegateEditor(QMap<QString, PropertyDelegate*>()));
proto->setPrompter(new GetFileListPrompter());
proto->setValidator(new DatasetValidator());
if(AppContext::isGUIMode()) {
proto->setIcon( GUIUtils::createRoundIcon(QColor(85,85,255), 22));
}
WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_DATASRC(), proto);
WorkflowEnv::getDomainRegistry()->getById(LocalDomainFactory::ID)->registerEntry(new GetFileListWorkerFactory());
}
/*******************************
* Alignment2SequenceWorkerFactory
*******************************/
void Alignment2SequenceWorkerFactory::init() {
// ports description
QList<PortDescriptor*> portDescs;
{
QMap<Descriptor, DataTypePtr> inM;
inM[BaseSlots::MULTIPLE_ALIGNMENT_SLOT()] = BaseTypes::MULTIPLE_ALIGNMENT_TYPE();
DataTypePtr inSet(new MapDataType(ALN_2_SEQUENCE_IN_TYPE_ID, inM));
Descriptor inPortDesc(BasePorts::IN_MSA_PORT_ID(), Alignment2SequenceWorker::tr("Input alignment"),
Alignment2SequenceWorker::tr("A alignment which will be split into sequences"));
portDescs << new PortDescriptor(inPortDesc, inSet, true);
QMap<Descriptor, DataTypePtr> outM;
outM[BaseSlots::DNA_SEQUENCE_SLOT()] = BaseTypes::DNA_SEQUENCE_TYPE();
DataTypePtr outSet(new MapDataType(ALN_2_SEQUENCE_OUT_TYPE_ID, outM));
Descriptor outPortDesc(BasePorts::OUT_SEQ_PORT_ID(), Alignment2SequenceWorker::tr("Output sequences"),
Alignment2SequenceWorker::tr("Converted sequences"));
portDescs << new PortDescriptor(outPortDesc, outSet, false);
}
QList<Attribute*> attrs;
Descriptor protoDesc(Alignment2SequenceWorkerFactory::ACTOR_ID,
Alignment2SequenceWorker::tr("Split Alignment into Sequences"),
Alignment2SequenceWorker::tr("Splits input alignment into sequences"));
ActorPrototype * proto = new IntegralBusActorPrototype(protoDesc, portDescs, attrs);
proto->setPrompter(new Alignment2SequencePrompter());
WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_ALIGNMENT(), proto);
WorkflowEnv::getDomainRegistry()->getById( LocalDomainFactory::ID )->registerEntry( new Alignment2SequenceWorkerFactory() );
}
void ConservationPlotWorkerFactory::init() {
//init data path
U2DataPath* dataPath = NULL;
U2DataPathRegistry* dpr = AppContext::getDataPathRegistry();
if (dpr){
U2DataPath* dp = dpr->getDataPathByName(CONSERVATION_DATA_NAME);
if (dp && dp->isValid()){
dataPath = dp;
}
}
QList<PortDescriptor*> portDescs;
//in port
QMap<Descriptor, DataTypePtr> inTypeMap;
Descriptor treatDesc(ANNOT_SLOT_ID,
ConservationPlotWorker::tr("Input regions"),
ConservationPlotWorker::tr("Regions (centered at peak summits for better performance)."));
inTypeMap[treatDesc] = BaseTypes::ANNOTATION_TABLE_LIST_TYPE();
Descriptor inPortDesc(IN_PORT_DESCR,
ConservationPlotWorker::tr("conservation_plot data"),
ConservationPlotWorker::tr("Regions to plot the PhastCons scores profiles."));
DataTypePtr inTypeSet(new MapDataType(IN_TYPE_ID, inTypeMap));
portDescs << new PortDescriptor(inPortDesc, inTypeSet, true);
QList<Attribute*> attrs;
{
Descriptor outFile(OUTPUT_FILE,
ConservationPlotWorker::tr("Output file"),
ConservationPlotWorker::tr("File to store phastcons results (BMP)."));
Descriptor titleDescr(TITLE,
ConservationPlotWorker::tr("Title"),
ConservationPlotWorker::tr("Title of the figure (--title)."));
Descriptor labelDescr(LABEL,
ConservationPlotWorker::tr("Label"),
ConservationPlotWorker::tr("Label of data in the figure (--bed-label)."));
Descriptor assemblyVersion(ASSEMBLY_VER,
ConservationPlotWorker::tr("Assembly version"),
ConservationPlotWorker::tr("The directory to store phastcons scores (--phasdb)."));
Descriptor windowSizeDescr(WINDOW_S,
ConservationPlotWorker::tr("Window width"),
ConservationPlotWorker::tr("Window width centered at middle of regions (-w)."));
Descriptor heightDescr(HEIGHT,
ConservationPlotWorker::tr("Height"),
ConservationPlotWorker::tr("Height of plot (--height)."));
Descriptor widthDescr(WIDTH,
ConservationPlotWorker::tr("Width"),
ConservationPlotWorker::tr("Width of plot (--width)."));
attrs << new Attribute(outFile, BaseTypes::STRING_TYPE(), true, QVariant(""));
attrs << new Attribute(titleDescr, BaseTypes::STRING_TYPE(), true, QVariant("Average Phastcons around the Center of Sites"));
attrs << new Attribute(labelDescr, BaseTypes::STRING_TYPE(), true, QVariant("Conservation_at_peak_summits"));
Attribute* assemblyVerAttr = NULL;
if (dataPath){
const QList<QString>& dataNames = dataPath->getDataNames();
if (!dataNames.isEmpty()){
assemblyVerAttr = new Attribute(assemblyVersion, BaseTypes::STRING_TYPE(), true, dataPath->getPathByName(dataNames.first()));
}else{
assemblyVerAttr = new Attribute(assemblyVersion, BaseTypes::STRING_TYPE(), true);
}
}else{
assemblyVerAttr = new Attribute(assemblyVersion, BaseTypes::STRING_TYPE(), true);
}
attrs << assemblyVerAttr;
attrs << new Attribute(windowSizeDescr, BaseTypes::NUM_TYPE(), false, QVariant(1000));
attrs << new Attribute(heightDescr, BaseTypes::NUM_TYPE(), false, QVariant(1000));
attrs << new Attribute(widthDescr, BaseTypes::NUM_TYPE(), false, QVariant(1000));
}
QMap<QString, PropertyDelegate*> delegates;
{
delegates[OUTPUT_FILE] = new URLDelegate(DialogUtils::prepareFileFilter(ConservationPlotWorker::tr("Conservation plot file"), QStringList("bmp"), true), "", false, false);
{
QVariantMap vm;
vm["minimum"] = QVariant(0);
vm["maximum"] = INT_MAX;
vm["singleStep"] = QVariant(1000);
delegates[WINDOW_S] = new SpinBoxDelegate(vm);
delegates[HEIGHT] = new SpinBoxDelegate(vm);
delegates[WIDTH] = new SpinBoxDelegate(vm);
}
{
QVariantMap vm;
if (dataPath){
vm = dataPath->getDataItemsVariantMap();
}
delegates[ASSEMBLY_VER] = new ConservationPlotComboBoxWithUrlsDelegate(vm, true);
}
}
Descriptor protoDesc(ConservationPlotWorkerFactory::ACTOR_ID,
ConservationPlotWorker::tr("Build Conservation Plot"),
ConservationPlotWorker::tr("Plots the PhastCons scores profiles."));
ActorPrototype *proto = new IntegralBusActorPrototype(protoDesc, portDescs, attrs);
proto->setPrompter(new ConservationPlotPrompter());
proto->setEditor(new DelegateEditor(delegates));
proto->addExternalTool(ET_CONSERVATION_PLOT);
WorkflowEnv::getProtoRegistry()->registerProto(BaseActorCategories::CATEGORY_CHIP_SEQ(), proto);
WorkflowEnv::getDomainRegistry()->getById(LocalDomainFactory::ID)->registerEntry(new ConservationPlotWorkerFactory());
}
