bool Version::IsInRange(const wstring& sAssemblyVersion, const wstring& sOldVersion)
{
wstring sHigh = sOldVersion;
Version assemblyVersion(sAssemblyVersion);
std::string::size_type pos = sHigh.find(L"-");
if (pos != std::wstring::npos) {
Version lowVersion(sHigh.substr(0, pos));
Version highVersion(sHigh.substr(pos + 1));
if (lowVersion <= assemblyVersion && assemblyVersion <= highVersion) {
return true;
}
}
else {
Version aHightVer(sHigh);
if (assemblyVersion == aHightVer) {
return true;
}
}
return false;
}
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());
}
