TrajectoryFrame
TrajectoryFrameReader::frame()
{
TrajectoryFrame frame;
if (!haveProbedForNextFrame_)
{
readNextFrame();
}
if (!nextFrameExists_)
{
GMX_THROW(APIError("There is no next frame, so there should have been no attempt to use the data, e.g. by reacting to a call to readNextFrame()."));
}
// Prepare for reading future frames
haveProbedForNextFrame_ = false;
nextFrameExists_ = false;
// The probe filled trxframeGuard_ with new data, so return it
frame.frame_ = trxframeGuard_.get();
if (!frame.frame_->bStep)
{
GMX_THROW(APIError("Cannot handle trajectory frame that lacks a step number"));
}
if (!frame.frame_->bTime)
{
GMX_THROW(APIError("Cannot handle trajectory frame that lacks a time"));
}
return frame;
}
void SearchController::resultsAction()
{
checkParams({"id"});
const int id = params()["id"].toInt();
int limit = params()["limit"].toInt();
int offset = params()["offset"].toInt();
const auto searchHandlers = sessionManager()->session()->getData<SearchHandlerDict>(SEARCH_HANDLERS);
if (!searchHandlers.contains(id))
throw APIError(APIErrorType::NotFound);
const SearchHandlerPtr searchHandler = searchHandlers[id];
const QList<SearchResult> searchResults = searchHandler->results();
const int size = searchResults.size();
if (offset > size)
throw APIError(APIErrorType::Conflict, tr("Offset is out of range"));
// normalize values
if (offset < 0)
offset = size + offset;
if (offset < 0) // check again
throw APIError(APIErrorType::Conflict, tr("Offset is out of range"));
if (limit <= 0)
limit = -1;
if ((limit > 0) || (offset > 0))
setResult(getResults(searchResults.mid(offset, limit), searchHandler->isActive(), size));
else
setResult(getResults(searchResults, searchHandler->isActive(), size));
}
void
AnalysisDataDisplacementModule::frameStarted(const AnalysisDataFrameHeader &header)
{
// Initialize times.
if (_impl->bFirst)
{
_impl->t0 = header.x();
}
else if (_impl->dt <= 0)
{
_impl->dt = header.x() - _impl->t0;
if (_impl->dt < 0 || gmx_within_tol(_impl->dt, 0.0, GMX_REAL_EPS))
{
GMX_THROW(APIError("Identical or decreasing frame times"));
}
}
else
{
if (!gmx_within_tol(header.x() - _impl->t, _impl->dt, GMX_REAL_EPS))
{
GMX_THROW(APIError("Frames not evenly spaced"));
}
}
_impl->t = header.x();
// Allocate memory for all the positions once it is possible.
if (_impl->max_store == -1 && !_impl->bFirst)
{
_impl->max_store = _impl->nmax * (int)(_impl->tmax/_impl->dt + 1);
srenew(_impl->oldval, _impl->max_store);
}
// Increment the index where current positions are stored.
_impl->ci += _impl->nmax;
if (_impl->ci >= _impl->max_store)
{
_impl->ci = 0;
}
/*
for (int i = 0; i < _impl->nmax; ++i)
{
_impl->p[_impl->ci + i].bPres = false;
}
*/
_impl->nstored++;
_impl->bFirst = false;
}
EnergyFrame
EnergyFrameReader::frame()
{
EnergyFrame energyFrame;
if (!haveProbedForNextFrame_)
{
readNextFrame();
}
if (!nextFrameExists_)
{
GMX_THROW(APIError("There is no next frame, so there should have been no attempt to use the data, e.g. by reacting to a call to readNextFrame()."));
}
// The probe filled enxframe_ with new data, so now we use that data to fill energyFrame
t_enxframe *enxframe = enxframeGuard_.get();
energyFrame.time_ = enxframe->t;
energyFrame.step_ = enxframe->step;
for (auto &index : indicesOfEnergyFields_)
{
if (index.second >= enxframe->nre)
{
GMX_THROW(InternalError(formatString("Index %d for energy %s not present in energy frame with %d energies",
index.second, index.first.c_str(), enxframe->nre)));
}
energyFrame.values_[index.first] = enxframe->ener[index.second].e;
}
// Prepare for reading future frames
haveProbedForNextFrame_ = false;
nextFrameExists_ = false;
return energyFrame;
}
void
AnalysisDataModuleManager::notifyPointsAdd(const AnalysisDataPointSetRef &points) const
{
GMX_ASSERT(impl_->state_ == Impl::eInFrame, "notifyFrameStart() not called");
// TODO: Add checks for column spans (requires passing the information
// about the column counts from somewhere).
//GMX_ASSERT(points.lastColumn() < columnCount(points.dataSetIndex()),
// "Invalid columns");
GMX_ASSERT(points.frameIndex() == impl_->currIndex_,
"Points do not correspond to current frame");
if (impl_->bSerialModules_)
{
if (!impl_->bAllowMissing_ && !points.allPresent())
{
GMX_THROW(APIError("Missing data not supported by a module"));
}
Impl::ModuleList::const_iterator i;
for (i = impl_->modules_.begin(); i != impl_->modules_.end(); ++i)
{
if (!i->bParallel)
{
i->module->pointsAdded(points);
}
}
}
}
void
AbstractAnalysisData::Impl::presentData(AbstractAnalysisData *data,
AnalysisDataModuleInterface *module)
{
module->dataStarted(data);
bool bCheckMissing = bAllowMissing_
&& !(module->flags() & AnalysisDataModuleInterface::efAllowMissing);
for (int i = 0; i < data->frameCount(); ++i)
{
AnalysisDataFrameRef frame = data->getDataFrame(i);
GMX_RELEASE_ASSERT(frame.isValid(), "Invalid data frame returned");
// TODO: Check all frames before doing anything for slightly better
// exception behavior.
if (bCheckMissing && !frame.allPresent())
{
GMX_THROW(APIError("Missing data not supported by a module"));
}
module->frameStarted(frame.header());
module->pointsAdded(frame.points());
module->frameFinished(frame.header());
}
if (!bInData_)
{
module->dataFinished();
}
}
void
AnalysisDataModuleManager::notifyParallelPointsAdd(
const AnalysisDataPointSetRef &points) const
{
// TODO: Add checks for column spans (requires passing the information
// about the column counts from somewhere).
//GMX_ASSERT(points.lastColumn() < columnCount(points.dataSetIndex()),
// "Invalid columns");
if (impl_->bParallelModules_)
{
if (!impl_->bAllowMissing_ && !points.allPresent())
{
GMX_THROW(APIError("Missing data not supported by a module"));
}
Impl::ModuleList::const_iterator i;
for (i = impl_->modules_.begin(); i != impl_->modules_.end(); ++i)
{
if (i->bParallel)
{
i->module->pointsAdded(points);
}
}
}
}
void Application::createDisplay(uint width, uint height,
uint redBits, uint greenBits, uint blueBits,
uint alphaBits, uint depthBits, uint stencilBits,
DisplayMode mode, const std::string &title)
{
GLboolean status;
status = glfwOpenWindow(width, height, redBits, greenBits, blueBits,
alphaBits, depthBits, stencilBits,
mode == DISP_FULLSCREEN ? GLFW_FULLSCREEN : GLFW_WINDOW);
if(status == GL_FALSE)
{
throw APIError("Failed to create display.");
}
// fetch window size (fixes X11 fullscreen bug)
glfwGetWindowSize(reinterpret_cast<int*>(&displayWidth_),
reinterpret_cast<int*>(&displayHeight_));
glfwSetWindowTitle(title.c_str()); // title is set separately
initOpenGL();
setOrthoView();
// register the callbacks (after a window is open)
glfwSetKeyCallback(Application::keyCallback);
//glfwSetCharCallback(Application::charCallback);
glfwSetMouseButtonCallback(Application::mouseButtonCallback);
glfwSetMousePosCallback(Application::mouseMoveCallback);
glfwSetMouseWheelCallback(Application::mouseWheelCallback);
quit_ = false;
}
void
AnalysisDataModuleManager::Impl::presentData(AbstractAnalysisData *data,
AnalysisDataModuleInterface *module)
{
if (state_ == eNotStarted)
{
return;
}
GMX_RELEASE_ASSERT(state_ != eInFrame,
"Cannot apply a modules in mid-frame");
module->dataStarted(data);
const bool bCheckMissing = bAllowMissing_
&& !(module->flags() & AnalysisDataModuleInterface::efAllowMissing);
for (int i = 0; i < data->frameCount(); ++i)
{
AnalysisDataFrameRef frame = data->getDataFrame(i);
GMX_RELEASE_ASSERT(frame.isValid(), "Invalid data frame returned");
// TODO: Check all frames before doing anything for slightly better
// exception behavior.
if (bCheckMissing && !frame.allPresent())
{
GMX_THROW(APIError("Missing data not supported by a module"));
}
module->frameStarted(frame.header());
for (int j = 0; j < frame.pointSetCount(); ++j)
{
module->pointsAdded(frame.pointSet(j));
}
module->frameFinished(frame.header());
}
if (state_ == eFinished)
{
module->dataFinished();
}
}
void
AnalysisDataVectorPlotModule::pointsAdded(const AnalysisDataPointSetRef &points)
{
if (points.firstColumn() % DIM != 0 || points.columnCount() % DIM != 0)
{
GMX_THROW(APIError("Partial data points"));
}
if (!isFileOpen())
{
return;
}
for (int i = 0; i < points.columnCount(); i += 3)
{
for (int d = 0; d < DIM; ++d)
{
if (bWrite_[i])
{
writeValue(points.values()[i + d]);
}
}
if (bWrite_[DIM])
{
const rvec y = { points.y(i), points.y(i + 1), points.y(i + 2) };
AnalysisDataValue value(norm(y));
writeValue(value);
}
}
}
void
AbstractAnalysisData::notifyPointsAdd(int firstcol, int n,
const real *y, const real *dy,
const bool *present) const
{
GMX_ASSERT(_impl->_bInData, "notifyDataStart() not called");
GMX_ASSERT(_impl->_bInFrame, "notifyFrameStart() not called");
GMX_ASSERT(firstcol >= 0 && n > 0 && firstcol + n <= _ncol, "Invalid column");
if (present && !_impl->_bAllowMissing)
{
for (int i = 0; i < n; ++i)
{
if (!present[i])
{
GMX_THROW(APIError("Missing data not supported by a module"));
}
}
}
Impl::ModuleList::const_iterator i;
for (i = _impl->_modules.begin(); i != _impl->_modules.end(); ++i)
{
(*i)->pointsAdded(_impl->_currx, _impl->_currdx, firstcol, n,
y, dy, present);
}
}
EnergyFrameReaderPtr
openEnergyFileToReadFields(const std::string &filename,
const std::vector<std::string> &namesOfRequiredEnergyFields)
{
ener_file_ptr energyFile(open_enx(filename.c_str(), "r"));
if (!energyFile)
{
GMX_THROW(FileIOError("Could not open energy file " + filename + " for reading"));
}
/* Read in the names of energy fields used in this file. The
* resulting data structure would leak if an exception was thrown,
* so transfer the contents that we actually need to a map we can
* keep.
*
* TODO Technically, the insertions into the map could throw
* std::bad_alloc and we could leak memory allocated by
* do_enxnms(), but there's nothing we can do about this right
* now. */
std::map<std::string, int> indicesOfEnergyFields;
{
int numEnergyTerms;
gmx_enxnm_t *energyNames = nullptr;
do_enxnms(energyFile.get(), &numEnergyTerms, &energyNames);
for (int i = 0; i != numEnergyTerms; ++i)
{
const char *name = energyNames[i].name;
auto requiredEnergy = std::find_if(std::begin(namesOfRequiredEnergyFields),
std::end(namesOfRequiredEnergyFields),
[name](const std::string &n){
return 0 == n.compare(name);
});
if (requiredEnergy != namesOfRequiredEnergyFields.end())
{
indicesOfEnergyFields[name] = i;
}
}
// Clean up old data structures
free_enxnms(numEnergyTerms, energyNames);
}
// Throw if we failed to find the fields we need
if (indicesOfEnergyFields.size() != namesOfRequiredEnergyFields.size())
{
std::string requiredEnergiesNotFound = "Did not find the following required energies in mdrun output:\n";
for (auto &name : namesOfRequiredEnergyFields)
{
auto possibleIndex = indicesOfEnergyFields.find(name);
if (possibleIndex == indicesOfEnergyFields.end())
{
requiredEnergiesNotFound += name + "\n";
}
}
GMX_THROW(APIError(requiredEnergiesNotFound));
}
return EnergyFrameReaderPtr(new EnergyFrameReader(indicesOfEnergyFields, energyFile.release()));
}
void SearchController::startAction()
{
checkParams({"pattern", "category", "plugins"});
if (!Utils::ForeignApps::pythonInfo().isValid())
throw APIError(APIErrorType::Conflict, "Python must be installed to use the Search Engine.");
const QString pattern = params()["pattern"].trimmed();
const QString category = params()["category"].trimmed();
const QStringList plugins = params()["plugins"].split('|');
QStringList pluginsToUse;
if (plugins.size() == 1) {
const QString pluginsLower = plugins[0].toLower();
if (pluginsLower == "all")
pluginsToUse = SearchPluginManager::instance()->allPlugins();
else if ((pluginsLower == "enabled") || (pluginsLower == "multi"))
pluginsToUse = SearchPluginManager::instance()->enabledPlugins();
else
pluginsToUse << plugins;
}
else {
pluginsToUse << plugins;
}
ISession *const session = sessionManager()->session();
auto activeSearches = session->getData<QSet<int>>(ACTIVE_SEARCHES);
if (activeSearches.size() >= MAX_CONCURRENT_SEARCHES)
throw APIError(APIErrorType::Conflict, QString("Unable to create more than %1 concurrent searches.").arg(MAX_CONCURRENT_SEARCHES));
const auto id = generateSearchId();
const SearchHandlerPtr searchHandler {SearchPluginManager::instance()->startSearch(pattern, category, pluginsToUse)};
QObject::connect(searchHandler.data(), &SearchHandler::searchFinished, this, [session, id, this]() { searchFinished(session, id); });
QObject::connect(searchHandler.data(), &SearchHandler::searchFailed, this, [session, id, this]() { searchFailed(session, id); });
auto searchHandlers = session->getData<SearchHandlerDict>(SEARCH_HANDLERS);
searchHandlers.insert(id, searchHandler);
session->setData(SEARCH_HANDLERS, QVariant::fromValue(searchHandlers));
activeSearches.insert(id);
session->setData(ACTIVE_SEARCHES, QVariant::fromValue(activeSearches));
const QJsonObject result = {{"id", id}};
setResult(result);
}
AbstractAnalysisData &TrajectoryAnalysisModule::datasetFromName(const char *name) const
{
Impl::DatasetContainer::const_iterator item = impl_->datasets_.find(name);
if (item == impl_->datasets_.end())
{
GMX_THROW(APIError("Unknown data set name"));
}
return *item->second;
}
bool
EnergyFrameReader::readNextFrame()
{
if (haveProbedForNextFrame_)
{
if (nextFrameExists_)
{
GMX_THROW(APIError("This frame has already been probed for, it should be used before probing again."));
}
else
{
GMX_THROW(APIError("This frame has already been probed for, it doesn't exist, so there should not be subsequent attempts to probe for it."));
}
}
haveProbedForNextFrame_ = true;
// If there's a next frame, read it into enxframe_, and report the result.
return nextFrameExists_ = do_enx(energyFileGuard_.get(), enxframeGuard_.get());
}
const real &EnergyFrame::at(const std::string &name) const
{
auto valueIterator = values_.find(name);
if (valueIterator == values_.end())
{
GMX_THROW(APIError("Cannot get energy value " + name + " unless previously registered when constructing EnergyFrameReader"));
}
return valueIterator->second;
}
AnalysisDataFrameRef
AbstractAnalysisData::getDataFrame(int index) const
{
AnalysisDataFrameRef frame = tryGetDataFrame(index);
if (!frame.isValid())
{
GMX_THROW(APIError("Invalid frame accessed"));
}
return frame;
}
OptionInfo *Options::addOption(const AbstractOption &settings)
{
AbstractOptionStoragePointer option(settings.createStorage());
if (impl_->findOption(option->name().c_str()) != NULL)
{
GMX_THROW(APIError("Duplicate option: " + option->name()));
}
impl_->options_.push_back(move(option));
return &impl_->options_.back()->optionInfo();
}
util::VersionInfo Application::initGLFW()
{
int maj,min,patch;
if(glfwInit() == GL_FALSE)
{
throw APIError("Initialization of GLFW failed!");
}
glfwGetVersion(&maj,&min,&patch);
return util::VersionInfo(maj,min,patch);
}
// GET param:
// - hash (string): torrent hash
// - rid (int): last response id
void SyncController::torrentPeersAction()
{
auto lastResponse = sessionManager()->session()->getData(QLatin1String("syncTorrentPeersLastResponse")).toMap();
auto lastAcceptedResponse = sessionManager()->session()->getData(QLatin1String("syncTorrentPeersLastAcceptedResponse")).toMap();
const QString hash {params()["hash"]};
BitTorrent::TorrentHandle *const torrent = BitTorrent::Session::instance()->findTorrent(hash);
if (!torrent)
throw APIError(APIErrorType::NotFound);
QVariantMap data;
QVariantHash peers;
const QList<BitTorrent::PeerInfo> peersList = torrent->peers();
#ifndef DISABLE_COUNTRIES_RESOLUTION
bool resolvePeerCountries = Preferences::instance()->resolvePeerCountries();
#else
bool resolvePeerCountries = false;
#endif
data[KEY_SYNC_TORRENT_PEERS_SHOW_FLAGS] = resolvePeerCountries;
for (const BitTorrent::PeerInfo &pi : peersList) {
if (pi.address().ip.isNull()) continue;
QVariantMap peer;
#ifndef DISABLE_COUNTRIES_RESOLUTION
if (resolvePeerCountries) {
peer[KEY_PEER_COUNTRY_CODE] = pi.country().toLower();
peer[KEY_PEER_COUNTRY] = Net::GeoIPManager::CountryName(pi.country());
}
#endif
peer[KEY_PEER_IP] = pi.address().ip.toString();
peer[KEY_PEER_PORT] = pi.address().port;
peer[KEY_PEER_CLIENT] = pi.client();
peer[KEY_PEER_PROGRESS] = pi.progress();
peer[KEY_PEER_DOWN_SPEED] = pi.payloadDownSpeed();
peer[KEY_PEER_UP_SPEED] = pi.payloadUpSpeed();
peer[KEY_PEER_TOT_DOWN] = pi.totalDownload();
peer[KEY_PEER_TOT_UP] = pi.totalUpload();
peer[KEY_PEER_CONNECTION_TYPE] = pi.connectionType();
peer[KEY_PEER_FLAGS] = pi.flags();
peer[KEY_PEER_FLAGS_DESCRIPTION] = pi.flagsDescription();
peer[KEY_PEER_RELEVANCE] = pi.relevance();
peer[KEY_PEER_FILES] = torrent->info().filesForPiece(pi.downloadingPieceIndex()).join(QLatin1String("\n"));
peers[pi.address().ip.toString() + ':' + QString::number(pi.address().port)] = peer;
}
data["peers"] = peers;
const int acceptedResponseId {params()["rid"].toInt()};
setResult(QJsonObject::fromVariantMap(generateSyncData(acceptedResponseId, data, lastAcceptedResponse, lastResponse)));
sessionManager()->session()->setData(QLatin1String("syncTorrentPeersLastResponse"), lastResponse);
sessionManager()->session()->setData(QLatin1String("syncTorrentPeersLastAcceptedResponse"), lastAcceptedResponse);
}
static Any
get_clipboard_data(DisplayObj d, Name type)
{ HGLOBAL mem;
HENHMETAFILE hmf;
Any rval = FAIL;
OpenClipboard(CLIPBOARDWIN);
if ( type != NAME_winMetafile && (mem = GetClipboardData(CF_UNICODETEXT)) )
{ wchar_t *data = GlobalLock(mem);
wchar_t *copy, *q;
q = copy = pceMalloc((wcslen(data)+1)*sizeof(wchar_t));
for(; *data; data++)
{ if ( *data == '\r' && data[1] == '\n' )
{ data++;
*q++ = '\n';
} else
*q++ = *data;
}
*q = EOS;
rval = WCToString(copy, q-copy);
pceFree(copy);
GlobalUnlock(mem);
} else if ( type != NAME_winMetafile && (mem = GetClipboardData(CF_TEXT)) )
{ char far *data = GlobalLock(mem);
char *copy, *q;
q = copy = pceMalloc(strlen(data));
for(; *data; data++)
{ if ( *data == '\r' && data[1] == '\n' )
{ data++;
*q++ = '\n';
} else
*q++ = *data;
}
*q = EOS;
rval = CtoString(copy);
pceFree(copy);
GlobalUnlock(mem);
} else if ( type != NAME_text && (hmf = GetClipboardData(CF_ENHMETAFILE)) )
{ HENHMETAFILE copy = CopyEnhMetaFile(hmf, NULL);
if ( !copy )
{ errorPce(d, NAME_winMetafile, CtoName("CopyEnhMetaFile"), APIError());
fail;
}
rval = CtoWinMetafile(copy);
DeleteEnhMetaFile(hmf);
}
CloseClipboard();
return rval;
}
//==============================================================================
// main - this is the main module for our application. It handle the
// initialization of the window, going into a message loop for
// dispatching messages and terminates the window upon successful exit
// from the message loop
//==============================================================================
void cdecl main( void ) {
// initialize the main instance of our application
if (Main::Initialize()==FALSE)
APIError((HWND)NULL,(HWND)NULL);
{
AppWindow MainWnd; // initialize our application window
Main::FramehWnd = MainWnd.GetFrameHandle();
Main::MessageLoop(); // call our message handler for our app
}
Main::Terminate(); // terminate the application
}
AbstractAnalysisData &TrajectoryAnalysisModule::datasetFromIndex(int index) const
{
if (index < 0 || index >= datasetCount())
{
GMX_THROW(APIError("Out of range data set index"));
}
Impl::DatasetContainer::const_iterator item
= impl_->datasets_.find(impl_->datasetNames_[index]);
GMX_RELEASE_ASSERT(item != impl_->datasets_.end(),
"Inconsistent data set names");
return *item->second;
}
bool
TrajectoryFrameReader::readNextFrame()
{
if (haveProbedForNextFrame_)
{
if (nextFrameExists_)
{
GMX_THROW(APIError("This frame has already been probed for, it should be used before probing again."));
}
else
{
GMX_THROW(APIError("This frame has already been probed for, it doesn't exist, so there should not be subsequent attempts to probe for it."));
}
}
haveProbedForNextFrame_ = true;
// If there's a next frame, read it into trxframe_, and report the result.
if (!haveReadFirstFrame_)
{
t_trxstatus *trajectoryFile;
int flags = TRX_READ_X | TRX_READ_V | TRX_READ_F;
nextFrameExists_ = read_first_frame(oenvGuard_.get(),
&trajectoryFile,
filename_.c_str(),
trxframeGuard_.get(),
flags);
if (!trajectoryFile)
{
GMX_THROW(FileIOError("Could not open trajectory file " + filename_ + " for reading"));
}
trajectoryFileGuard_.reset(trajectoryFile);
haveReadFirstFrame_ = true;
}
else
{
nextFrameExists_ = read_next_frame(oenvGuard_.get(),
trajectoryFileGuard_.get(),
trxframeGuard_.get());
}
return nextFrameExists_;
}
void
AnalysisDataDisplacementModule::pointsAdded(const AnalysisDataPointSetRef &points)
{
if (points.firstColumn() % _impl->ndim != 0
|| points.columnCount() % _impl->ndim != 0)
{
GMX_THROW(APIError("Partial data points"));
}
for (int i = 0; i < points.columnCount(); ++i)
{
_impl->oldval[_impl->ci + points.firstColumn() + i] = points.y(i);
}
}
void
AnalysisDataDisplacementModule::pointsAdded(real x, real dx, int firstcol, int n,
const real *y, const real *dy,
const bool *present)
{
if (firstcol % _impl->ndim != 0 || n % _impl->ndim != 0)
{
GMX_THROW(APIError("Partial data points"));
}
for (int i = firstcol; i < firstcol + n; ++i)
{
_impl->oldval[_impl->ci + i] = y[i];
}
}
void
AbstractAnalysisData::applyModule(AnalysisDataModuleInterface *module)
{
if ((columnCount() > 1 && !(module->flags() & AnalysisDataModuleInterface::efAllowMulticolumn))
|| (isMultipoint() && !(module->flags() & AnalysisDataModuleInterface::efAllowMultipoint))
|| (!isMultipoint() && (module->flags() & AnalysisDataModuleInterface::efOnlyMultipoint)))
{
GMX_THROW(APIError("Data module not compatible with data object properties"));
}
GMX_RELEASE_ASSERT(_impl->_bDataStart && !_impl->_bInData,
"Data module can only be applied to ready data");
_impl->presentData(this, module);
}
void
AbstractAnalysisData::Impl::presentData(AbstractAnalysisData *data,
AnalysisDataModuleInterface *module)
{
module->dataStarted(data);
bool bCheckMissing = _bAllowMissing
&& !(module->flags() & AnalysisDataModuleInterface::efAllowMissing);
int ncol = data->columnCount();
for (int i = 0; i < data->frameCount(); ++i)
{
real x, dx;
const real *y, *dy;
const bool *present;
if (!data->getDataWErr(i, &x, &dx, &y, &dy, &present))
{
GMX_THROW(APIError("Data not available when module added"));
}
if (bCheckMissing && present)
{
for (int j = 0; j < ncol; ++j)
{
if (!present[j])
{
GMX_THROW(APIError("Missing data not supported by a module"));
}
}
}
module->frameStarted(x, dx);
module->pointsAdded(x, dx, 0, ncol, y, dy, present);
module->frameFinished();
}
if (!_bInData)
{
module->dataFinished();
}
}
void
AnalysisDataDisplacementModule::dataStarted(AbstractAnalysisData *data)
{
if (data->columnCount() % _impl->ndim != 0)
{
GMX_THROW(APIError("Data has incorrect number of columns"));
}
_impl->nmax = data->columnCount();
snew(_impl->oldval, _impl->nmax);
_impl->ci = -_impl->nmax;
int ncol = _impl->nmax / _impl->ndim + 1;
_impl->currValues_.reserve(ncol);
setColumnCount(ncol);
}
void
TopologyInformation::getTopologyConf(rvec **x, matrix box) const
{
if (box)
{
copy_mat(const_cast<rvec *>(boxtop_), box);
}
if (x)
{
if (!xtop_)
{
*x = NULL;
GMX_THROW(APIError("Topology coordinates requested without setting efUseTopX"));
}
*x = xtop_;
}
}
