EntityLoader::EntityLoader():
mLoaders()
{
registerLoader(new MeshComponentLoader());
registerLoader(new ParticleComponentLoader());
registerLoader(new PhysicsComponentLoader());
}
void CrosswordLoadSupportLocator::registerFormats()
{
// Load and save XWC files (v1.0.1)
registerLoader(new CrosswordFormat(XWC101), new XWCLoader());
registerSaver(new CrosswordFormat(XWC101), new XWCSaver());
// Load and save XWC3D files (v1.0.0)
registerLoader(new CrosswordFormat(XWC3D100), new XWC3DLoader());
registerSaver(new CrosswordFormat(XWC3D100), new XWC3DSaver());
// Across Lite Text support
//registerLoader(new CrosswordFormat(ACROSSLITETEXT), new AcrossLiteTextLoader());
// registerSaver(new CrosswordFormat(ACROSSLITETEXT), new AcrossLiteTextSaver());
// TODO More file support
}
bool ResCache::init() {
bool retValue = true;
for( ResourceFiles::iterator fileItr = m_files.begin(); fileItr != m_files.end(); ++fileItr ) {
if( !(*fileItr)->VOpen() ) {
GEN_FATAL("unable to load filename: " + (*fileItr)->VGetResourceFileName());
retValue = false;
}
}
if( retValue )
registerLoader(std::shared_ptr<IResourceLoader>(new DefaultResourceLoader()));
return retValue;
}//ResCache::init
void ResourceManager::setupResourceLoaders(Class* klass)
{
for( size_t i = 0; i < klass->childs.size(); i++ )
{
Class* child = klass->childs[i];
if( !child->childs.empty() )
setupResourceLoaders(child);
if( ClassIsAbstract(child ) ) continue;
auto loader = (ResourceLoader*) ClassCreateInstance(
child, GetResourcesAllocator());
registerLoader( loader );
}
}
int main(int argc, char ** argv)
{
lua_State * L = luaL_newstate();
if (!readTOC(L, argv[0]))
{
if (argc < 2)
{
// display usage message and exit
printf("This copy of enceladus has no embedded lua program to run\n");
printf("Please embed one: enceladus main.lua lib.lua ...\n");
return 1;
}
// parse command line and embed lua code, then exit
parse_args(&argc, &argv);
char * outname = embed(L, argc, argv);
if (outname)
{
printf("Embed successful. Output file: %s\n", outname);
} else {
fprintf(stderr, "Embed failed. Aborting.\n");
}
return 0;
}
// TOC read successful - we have an embedded lua program to run
// initialize standard libraries
luaL_openlibs(L);
// load any statically linked libraries
enceladus_init_static_libs(L);
// grab the entry point
// the name is on top of the stack and the table of packed files right
// below, thanks to readTOC
lua_gettable(L, -2); // toc{} main()
if (lua_type(L, -1) != LUA_TFUNCTION)
{
fprintf(stderr, "Error loading entry point: %s\n", lua_tostring(L, -1));
return 1;
}
// install our custom loader for the embedded libraries
lua_insert(L, -2);
if (!registerLoader(L))
{
fprintf(stderr, "Error registering custom loader: %s\n", lua_tostring(L, -1));
return 1;
}
// marshal arguments into lua
lua_newtable(L); // toc{} main() arg{}
for (int i = 0; i < argc; ++i)
{
lua_pushstring(L, argv[i]); // toc{} main() arg{} argv[i]
lua_rawseti(L, -2, i); // toc{} main() arg{}
}
lua_setglobal(L, "arg"); // toc{} main()
for (int i = 1; i < argc; ++i)
{
lua_pushstring(L, argv[i]); // toc{} main() argv[i]...
}
// call
lua_getglobal(L, "debug"); // ... debug
lua_getfield(L, -1, "traceback"); // ... debug debug.traceback
lua_insert(L, 1); // debug.traceback ... debug
lua_pop(L, 1); // debug.traceback ...
if (lua_pcall(L, argc-1, 0, 1) != 0)
{
// error handling
fprintf(stderr, "error: %s\n", lua_tostring(L, -1));
return 1;
}
return 0;
}
namespace Ms2Preproc {
class TopXInYRegionsAlgorithm : public libpipe::rtc::Algorithm
{
public:
static libpipe::rtc::Algorithm* create()
{
return new TopXInYRegionsAlgorithm;
}
virtual ~TopXInYRegionsAlgorithm()
{
}
void update(libpipe::Request& req)
{
boost::shared_ptr<libpipe::rtc::SharedData<mgf::MgfFile> > mgfInputFile =
boost::dynamic_pointer_cast<
libpipe::rtc::SharedData<mgf::MgfFile> >(
this->getPort("MGFInputFile"));
boost::shared_ptr<libpipe::rtc::SharedData<mgf::MgfFile> > mgfParsedFile =
boost::dynamic_pointer_cast<
libpipe::rtc::SharedData<mgf::MgfFile> >(
this->getPort("MGFParsedFile"));
LIBPIPE_PIPELINE_TRACE(req, "Starting TopXInYRegions");
mgfInputFile->shared_lock();
mgfParsedFile->lock();
// copy the file so that input is not changed.
mgfParsedFile->set(new mgf::MgfFile(*mgfInputFile->get()));
mgfInputFile->unlock();
// Top X in Y regions
for (mgf::MgfFile::iterator i = mgfParsedFile->get()->begin();
i != mgfParsedFile->get()->end(); ++i) {
// get a temporary object and make sure it is big enough
mgf::MgfSpectrum m;
m.resize(2 * i->size());
// get the top X in Y regions, including duplicated from overlaps
mgf::MgfSpectrum::iterator sEnd = run(i->begin(), i->end(),
m.begin(), LessThanMass(), LessThanAbundance());
// make sure we have enough space in the original object
i->resize(std::distance(m.begin(), sEnd));
// unique copy expectes a sorted range
std::sort(m.begin(), sEnd, LessThanMass());
// copy all unique peaks back into the original MgfSpectrum
mgf::MgfSpectrum::iterator iEnd = std::unique_copy(m.begin(),
sEnd, i->begin());
// crop to fit
i->resize(std::distance(i->begin(), iEnd));
}
mgfParsedFile->unlock();
LIBPIPE_PIPELINE_TRACE(req, "TopXInYRegions is finished");
}
protected:
private:
TopXInYRegionsAlgorithm() :
libpipe::rtc::Algorithm()
{
ports_["MGFInputFile"] = boost::make_shared<
libpipe::rtc::SharedData<mgf::MgfFile> >();
ports_["MGFParsedFile"] = boost::make_shared<
libpipe::rtc::SharedData<mgf::MgfFile> >(new mgf::MgfFile);
}
template<class In, class Out, class MassComp, class AbundanceComp>
Out run(In begin, In end, Out out, MassComp massComp,
AbundanceComp abundanceComp)
{
// sort a copy
std::vector<typename In::value_type> v(begin, end);
std::sort(v.begin(), v.end(), massComp);
// split the m/z domain in y_ equisized regions
double maxMz = (v.end() - 1)->first;
double minMz = (v.begin())->first;
double increment = (maxMz - minMz)
/ static_cast<double>(parameters_.get<unsigned int>(
"nregions"));
if (increment > 2.5) {
for (unsigned int k = 0;
k < parameters_.get<unsigned int>("nregions"); ++k) {
// iterate over all regions and apply TopX
double regionBegin = minMz + k * increment - 2.5;
regionBegin = regionBegin > minMz ? regionBegin : minMz;
double regionEnd = minMz + (k + 1) * increment + 2.5;
In regionBeginIt = std::lower_bound(v.begin(), v.end(),
regionBegin, massComp);
In regionEndIt = std::upper_bound(v.begin(), v.end(),
regionEnd, massComp);
// run TopX on region
Out nout = runTopX(regionBeginIt, regionEndIt, out,
abundanceComp);
out = nout;
}
} else {
Out nout = runTopX(v.begin(), v.end(), out, abundanceComp);
out = nout;
}
return out;
}
template<class In, class Out, class Comp>
Out runTopX(In begin, In end, Out out, Comp comp)
{
typename In::difference_type size = std::distance(begin, end);
unsigned int x = parameters_.get<unsigned int>("top");
// FIXME: Make the static_cast in the next step safe.
if (static_cast<unsigned int>(size) > x) {
// sort a copy
std::vector<typename In::value_type> v(begin, end);
std::sort(v.begin(), v.end(), comp);
std::copy(v.rbegin(), v.rbegin() + x, out);
std::advance(out, x);
} else {
// accept all peaks
std::copy(begin, end, out);
std::advance(out, size);
}
return out;
}
static const bool registerLoader()
{
std::string ids = "TopXInYRegionsAlgorithm";
return libpipe::rtc::AlgorithmFactory::instance().registerType(ids,
TopXInYRegionsAlgorithm::create);
}
/// true is class is registered in Algorithm Factory
static const bool registered_;
};
const bool TopXInYRegionsAlgorithm::registered_ = registerLoader();
}
