virtual void main()
{
//init
QString psname = getString("psname");
if (psname=="") psname = getInfile("in");
//load
VariantList variants;
variants.load(getInfile("in"));
//annotate
bool test = getFlag("test");
QString mode = getEnum("mode");
if(mode=="germline")
{
NGSD(test).annotate(variants, psname);
}
else if(mode=="somatic")
{
NGSD(test).annotateSomatic(variants, psname);
}
//store
variants.store(getOutfile("out"));
}
void RandomFire::load(const VariantMap& stream)
{
VariantList vl = stream.get( lc_population ).toList();
_d->minPopulation = vl.get( 0, 0 ).toInt();
_d->maxPopulation = vl.get( 1, 999999 ).toInt();
_d->strong = stream.get( lc_strong, 10 );
}
void MoveButtonState::OnPressToggle(bool bDown, boost::signal<void (VariantList*)> *pCustomSignal)
{
VariantList v;
if (bDown)
{
if (!m_bIsDown)
{
m_bIsDown = true;
v.Get(0).Set(uint32(m_keyType));
v.Get(1).Set(uint32(VIRTUAL_KEY_PRESS));
if (pCustomSignal)
{
(*pCustomSignal)(&v);
} else
{
GetBaseApp()->m_sig_arcade_input(&v);
}
}
m_releaseTimer = rt_max(GetTick(TIMER_SYSTEM), m_releaseTimer);
m_releaseTimer += 1000*60;
} else
{
ReleaseIfNeeded(pCustomSignal);
}
}
virtual void load(const VariantList& stream)
{
for (const auto& item : stream) {
VariantList vl = item.toList();
(*this)[ vl.get(0) ] = vl.get(1);
}
}
void Base::load(const VariantList& stream)
{
type = (Type)stream.get( ftype ).toInt();
date = stream.get( fdate ).toDateTime();
objectName = stream.get( fname ).toString();
message = stream.get( fmessage ).toString();
location = stream.get( flocation ).toPoint();
}
void load( const VariantList& stream )
{
for( unsigned int i=0; i < stream.size(); i+=2 )
{
Service::Type type = Service::Type( stream.get( i ).toInt() );
at( type )->set( stream.get( i+1 ).toFloat() ); //serviceValue
}
}
bool NGSD::removeColumnIfPresent(VariantList& variants, QString name, bool exact_name_match)
{
int index = variants.annotationIndexByName(name, exact_name_match, false);
if (index==-1) return false;
variants.removeAnnotation(index);
return true;
}
void Addressable::onDeserialize(VariantList& variants) {
if(variants.hasKey("class")) {
addClasses(variants.get("class").asStringList());
}
if(variants.hasKey("id")) {
setId(variants.get("id"));
}
}
void RandomDamage::load(const VariantMap& stream)
{
VariantList vl = stream.get( lc_population ).toList();
_d->minPopulation = vl.get( 0, 0 ).toInt();
_d->maxPopulation = vl.get( 1, 999999 ).toInt();
VARIANT_LOAD_ANY_D( _d, strong, stream );
VARIANT_LOAD_ANY_D( _d, priority, stream );
}
VariantList GoodStock::save() const
{
VariantList stream;
stream.push_back( (int)_type );
stream.push_back( _maxQty );
stream.push_back( _currentQty );
return stream;
}
virtual VariantList save() const
{
VariantList ret;
for (const auto& item : *this) {
ret.push_back(VariantList(item.first, item.second));
}
return ret;
}
void GoodStock::load( const VariantList& stream )
{
if( stream.size() < 3 )
return;
VariantList::const_iterator it=stream.begin();
_type = (Good::Type)(*it).toInt(); it++;
_maxQty = (*it).toInt(); it++;
_currentQty = math::clamp( (*it).toInt(), 0, _maxQty );
}
VariantList save() const
{
VariantList ret;
for( auto& mapItem : *this )
{
ret.push_back( Variant( (int)mapItem.first ) );
ret.push_back( Variant( mapItem.second->value() ) );
}
return ret;
}
int NGSD::addColumn(VariantList& variants, QString name, QString description)
{
variants.annotations().append(VariantAnnotationHeader(name));
for (int i=0; i<variants.count(); ++i)
{
variants[i].annotations().append("");
}
variants.annotationDescriptions().append(VariantAnnotationDescription(name, description));
return variants.annotations().count() - 1;
}
void ArcadeInputComponent::ActivateBinding(ArcadeKeyBind *pBind, bool bDown)
{
//special handling for directional keys, so they work in tandem with the trackball or whatever else also does directions
bool bWasDirectionalKey = true;
switch (pBind->m_outputkeycode)
{
case VIRTUAL_KEY_DIR_LEFT: m_buttons[MOVE_BUTTON_DIR_LEFT].OnPressToggle(bDown, m_customSignal); break;
case VIRTUAL_KEY_DIR_RIGHT: m_buttons[MOVE_BUTTON_DIR_RIGHT].OnPressToggle(bDown, m_customSignal); break;
case VIRTUAL_KEY_DIR_UP: m_buttons[MOVE_BUTTON_DIR_UP].OnPressToggle(bDown, m_customSignal); break;
case VIRTUAL_KEY_DIR_DOWN: m_buttons[MOVE_BUTTON_DIR_DOWN].OnPressToggle(bDown, m_customSignal); break;
default:
bWasDirectionalKey = false;
break;
}
if (bWasDirectionalKey)
{
//avoid sending it twice, we already would above
return;
}
//for other keys, just send it through the arcade signal:
VariantList v;
v.Get(0).Set(pBind->m_outputkeycode);
v.Get(1).Set(uint32(bDown));
if (m_customSignal)
{
(*m_customSignal)(&v);
} else
{
GetBaseApp()->m_sig_arcade_input(&v);
}
if (bDown)
{
//send as normal key, only on the keydown
VariantList v2;
v2.Get(0).Set((float)MESSAGE_TYPE_GUI_CHAR);
v2.Get(1).Set(0,0);
v2.Get(2).Set(uint32(pBind->m_outputkeycode));
GetBaseApp()->m_sig_input(&v2);
}
if (pBind->m_bOutputAsNormalKeyToo)
{
//also send as regular global key
GetBaseApp()->m_sig_raw_keyboard(&v);
}
}
void JSAPIImpl::FireJSEvent( const std::string& eventName, const VariantMap &members, const VariantList &arguments )
{
if (!m_valid) // When invalidated, do nothing more
return;
{
JSAPIImplPtr self(shared_from_this());
boost::recursive_mutex::scoped_lock _l(m_proxyMutex);
ProxyList::iterator proxyIt = m_proxies.begin();
while (proxyIt != m_proxies.end()) {
JSAPIImplPtr proxy(proxyIt->lock());
if (!proxy) {
// Since you can't use a shared_ptr in a destructor, there
// is no way for the proxy object to let us know when it goes
// away; thus when we find them, we remove them for efficiency
proxyIt = m_proxies.erase(proxyIt);
continue;
}
VariantList newArgs = proxyProcessList(arguments, self, proxy);
VariantMap newMap = proxyProcessMap(members, self, proxy);
proxy->FireJSEvent(eventName, newMap, newArgs);
proxyIt++;
}
}
VariantList args;
args.push_back(CreateEvent(shared_from_this(), eventName, members, arguments));
{
boost::recursive_mutex::scoped_lock _l(m_eventMutex);
EventContextMap::iterator it(m_eventMap.begin());
while (it != m_eventMap.end()) {
std::pair<EventMultiMap::iterator, EventMultiMap::iterator> range = it->second.equal_range(eventName);
for (EventMultiMap::const_iterator eventIt = range.first; eventIt != range.second; eventIt++) {
eventIt->second->InvokeAsync("", args);
}
++it;
}
}
// Some events are registered as a jsapi object with a method of the same name as the event
{
boost::recursive_mutex::scoped_lock _l(m_eventMutex);
EventIfaceContextMap::iterator it(m_evtIfaces.begin());
while (it != m_evtIfaces.end()) {
for (EventIFaceMap::const_iterator ifaceIt = it->second.begin(); ifaceIt != it->second.end(); ifaceIt++) {
ifaceIt->second->InvokeAsync(eventName, args);
}
}
}
}
void TileOverlay::save( VariantMap& stream ) const
{
VariantList config;
config.push_back( (int)_d->overlayType );
config.push_back( Variant( MetaDataHolder::instance().getData( _d->overlayType ).getName() ) );
config.push_back( getTile().getIJ() );
stream[ "config" ] = config;
stream[ "picture" ] = Variant( _d->picture.getName() );
stream[ "pictureOffset" ] = _d->picture.getOffset();
stream[ "size" ] = _d->size;
stream[ "isDeleted" ] = _d->isDeleted;
stream[ "name" ] = Variant( _d->name );
}
VariantMap Storage::save() const
{
VariantMap stream = good::Store::save();
stream[ "max" ] = _gsd->capacity;
VariantList stockSave;
for( auto& stockInfo : _gsd->stocks )
stockSave.push_back( stockInfo->save() );
stream[ "stock" ] = stockSave;
return stream;
}
void Stock::load( const VariantList& stream )
{
if( stream.empty())
return;
_type = stream.get( 0 ).toInt();
if( _type >= good::goodCount.toInt() )
{
Logger::warning( "GoodStock: wrong type of good %d", _type );
_type = good::none.toInt();
}
_capacity = (int)stream.get( 1 );
_qty = math::clamp( (int)stream.get( 2 ), 0, _capacity );
}
void SimpleGoodStore::load( const VariantMap& stream )
{
_goodStockList.clear();
GoodStore::load( stream );
_maxQty = (int)stream.get( "max" );
VariantList stockSave = stream.get( "stock" ).toList();
for( VariantList::iterator it=stockSave.begin(); it!=stockSave.end(); it++ )
{
GoodStock restored;
restored.load( (*it).toList() );
_goodStockList.push_back( restored );
}
}
const VariantList Database::getValueForItemNameAsVector( const std::string &item) const
{
VariantList list;
std::istringstream f( getValueForItemName( item )->getString() );
std::string s;
while (getline(f, s, ' '))
{
if ( !s.empty() )
list.push_back( s );
}
return list;
}
VariantMap SimpleGoodStore::save() const
{
VariantMap stream = GoodStore::save();
stream[ "max" ] = _maxQty;
VariantList stockSave;
for( std::vector<GoodStock>::const_iterator itStock = _goodStockList.begin(); itStock != _goodStockList.end(); itStock++)
{
stockSave.push_back( (*itStock).save() );
}
stream[ "stock" ] = stockSave;
return stream;
}
VariantList save()
{
VariantList ret;
ret.push_back( sellPrice );
ret.push_back( buyPrice );
ret.push_back( exportLimit );
ret.push_back( importLimit );
ret.push_back( soldGoods );
ret.push_back( bougthGoods );
ret.push_back( stacking );
ret.push_back( order );
ret.push_back( vendor );
return ret;
}
void MoveButtonState::ReleaseIfNeeded(boost::signal<void (VariantList*)> *pCustomSignal)
{
if (m_bIsDown)
{
m_bIsDown = false;
VariantList v;
v.Get(0).Set(uint32(m_keyType));
v.Get(1).Set(uint32(VIRTUAL_KEY_RELEASE));
if (pCustomSignal)
{
(*pCustomSignal)(&v);
} else
{
GetBaseApp()->m_sig_arcade_input(&v);
}
}
}
void load( const VariantList& stream )
{
if( stream.size() != 9 )
{
Logger::warning( "%s [%s %d]", "Incorrect argument number in ", __FILE__, __LINE__ );
return;
}
VariantList::const_iterator it=stream.begin();
sellPrice = it->toUInt(); ++it;
buyPrice = it->toUInt(); ++it;
exportLimit = it->toUInt(); ++it;
importLimit = it->toUInt(); ++it;
soldGoods = it->toUInt(); ++it;
bougthGoods = it->toUInt(); ++it;
stacking = it->toBool(); ++it;
order = (trade::Order)it->toInt(); ++it;
vendor = it->toBool();
}
void NGSD::setReportVariants(const QString& filename, const VariantList& variants, QSet<int> selected_indices)
{
QString ps_id = processedSampleId(filename);
//get variant ID
for(int i=0; i<variants.count(); ++i)
{
getQuery().exec("UPDATE detected_variant SET report=" + QString(selected_indices.contains(i) ? "1" : "0" ) + " WHERE processed_sample_id='" + ps_id + "' AND variant_id='" + variantId(variants[i]) + "'");
}
}
void load( const VariantList& stream )
{
if( stream.size() != 9 )
{
StringHelper::debug( 0xff, "%s [%s %d]", "Incorrect argument number in ", __FILE__, __LINE__ );
return;
}
VariantList::const_iterator it=stream.begin();
sellPrice = it->toUInt(); it++;
buyPrice = it->toUInt(); it++;
exportLimit = it->toUInt(); it++;
importLimit = it->toUInt(); it++;
soldGoods = it->toUInt(); it++;
bougthGoods = it->toUInt(); it++;
stacking = it->toBool(); it++;
order = (CityTradeOptions::Order)it->toInt(); it++;
vendor = it->toBool();
}
void PictureBank::Impl::loadAtlas(const vfs::Path& filePath)
{
if( !filePath.exist() )
{
Logger::warning( "PictureBank: cant find atlas " + filePath.toString() );
return;
}
VariantMap info = config::load( filePath );
vfs::Path texturePath = info.get( "texture" ).toString();
vfs::NFile file = vfs::NFile::open( texturePath );
Picture mainTexture;
if( file.isOpen() )
{
mainTexture = PictureLoader::instance().load( file );
}
else
{
Logger::warning( "PictureBank: load atlas failed for texture" + texturePath.toString() );
mainTexture = Picture::getInvalid();
}
//SizeF mainRectSize = mainTexture.size().toSizeF();
if( !info.empty() )
{
VariantMap items = info.get( framesSection ).toMap();
for( auto& i : items )
{
VariantList rInfo = i.second.toList();
Picture pic = mainTexture;
Point start( rInfo.get( 0 ).toInt(), rInfo.get( 1 ).toInt() );
Size size( rInfo.get( 2 ).toInt(), rInfo.get( 3 ).toInt() );
pic.setOriginRect( Rect( start, size ) );
setPicture( i.first, pic );
}
}
}
/**
* parseArray
*/
Variant Json::parseArray(const std::string &json, int &index, bool &success)
{
VariantList list;
Json::nextToken(json, index);
bool done = false;
while(!done)
{
int token = Json::lookAhead(json, index);
if(token == JsonTokenNone)
{
success = false;
return VariantList();
}
else if(token == JsonTokenComma)
{
Json::nextToken(json, index);
}
else if(token == JsonTokenSquaredClose)
{
Json::nextToken(json, index);
break;
}
else
{
Variant value = Json::parseValue(json, index, success);
if(!success)
{
return VariantList();
}
list.push_back(value);
}
}
return Variant(list);
}
void PictureInfoBank::initialize(vfs::Path filename)
{
Logger::warning( "PictureInfoBank: start load offsets from " + filename.toString() );
VariantMap m = config::load( filename );
foreach( it, m )
{
Variant v = it->second;
Logger::warning( "Set offset for " + it->first );
if( v.type() == Variant::Map )
{
VariantMap vm = v.toMap();
int startIndex = vm[ "start" ];
int stopIndex = vm[ "stop" ];
std::string rc = vm[ "rc" ].toString();
Point offset = vm[ "offset" ].toPoint();
_d->setRange( rc.empty() ? it->first : rc, startIndex, stopIndex, offset );
}
else if( v.type() == Variant::List )
{
VariantList vl = v.toList();
_d->setOne( it->first, vl.get( idxIndex ), vl.get( idxXOffset ), vl.get( idxYOffset ) );
}
}
