bool DynamicObjectImp::setAttributeByPath(QStringList pathComponents, DataVariant& value, bool swap)
{
if (!value.isValid())
{
return false;
}
QString finalName = pathComponents.back();
pathComponents.pop_back();
string loopType = "DynamicObject";
DynamicObject* pLoopObj = dynamic_cast<DynamicObject*>(this);
DynamicObject* pCurObj = pLoopObj;
for (QStringList::const_iterator iter = pathComponents.begin();
iter != pathComponents.end(); ++iter)
{
if (pLoopObj == NULL || loopType != "DynamicObject")
{
return false;
}
pCurObj = pLoopObj;
DataVariant& attrValue = pCurObj->getAttribute(iter->toStdString());
loopType = attrValue.getTypeName();
pLoopObj = attrValue.getPointerToValue<DynamicObject>();
if ((pLoopObj != NULL) && (loopType != "DynamicObject"))
{
return false;
}
if (pLoopObj == NULL)
{
FactoryResource<DynamicObject> pNewObj;
if (pCurObj != NULL)
{
pCurObj->setAttribute(iter->toStdString(), *pNewObj.get());
DataVariant& currentValue = pCurObj->getAttribute(iter->toStdString());
loopType = currentValue.getTypeName();
pLoopObj = currentValue.getPointerToValue<DynamicObject>();
}
}
}
if (pLoopObj == NULL || loopType != "DynamicObject")
{
return false;
}
pCurObj = pLoopObj;
DynamicObjectImp* const pCurObjImp = dynamic_cast<DynamicObjectImp*>(pCurObj);
VERIFY(pCurObjImp != NULL);
return pCurObjImp->setAttribute(finalName.toStdString(), value, swap);
}
void JointMotorI::getAllMotorState(MotorStateMap &mstateMap, const Ice::Current&)
{
for (QStringList::const_iterator name = jointIDs.constBegin() ; name != jointIDs.constEnd() ; ++name)
{
InnerModelNode *node = innerModel->getNode(*name);
if (dynamic_cast<InnerModelJoint*>(node) != NULL)
{
states[name->toStdString()].pos = dynamic_cast<InnerModelJoint*>(node)->getAngle();
}
else if (dynamic_cast<InnerModelPrismaticJoint*>(node) != NULL)
{
states[name->toStdString()].pos = dynamic_cast<InnerModelPrismaticJoint*>(node)->getPosition();
}
}
mstateMap = states;
}
const DataVariant& DynamicObjectImp::getAttributeByPath(QStringList pathComponents) const
{
static DataVariant sEmptyVariant;
QString finalName = pathComponents.back();
pathComponents.pop_back();
string loopType = "DynamicObject";
const DynamicObject* pCurrentObj = dynamic_cast<const DynamicObject*>(this);
for (QStringList::const_iterator iter = pathComponents.begin();
iter != pathComponents.end(); ++iter)
{
if ( (pCurrentObj == NULL) || loopType != "DynamicObject")
{
sEmptyVariant = DataVariant();
return sEmptyVariant;
}
const DataVariant& attrValue = pCurrentObj->getAttribute(iter->toStdString());
loopType = attrValue.getTypeName();
pCurrentObj = attrValue.getPointerToValue<DynamicObject>();
}
if (pCurrentObj == NULL)
{
sEmptyVariant = DataVariant();
return sEmptyVariant;
}
return pCurrentObj->getAttribute(finalName.toStdString());
}
bool SQLiteDatabaseConnection::createTables()
{
bool retVal = true;
//Liste von auszuführenden Statements erstellen
QStringList statements;
statements << "PRAGMA page_size = 4096;";
statements << "PRAGMA max_page_count = 2147483646;";
statements << "PRAGMA cache_size=50000;";
statements << "PRAGMA synchronous=OFF;";
statements << "PRAGMA journal_mode=MEMORY;";
statements << "PRAGMA temp_store = MEMORY;";
statements << "CREATE TABLE IF NOT EXISTS EDGES(ID INTEGER PRIMARY KEY, STARTNODE INTEGER NOT NULL, ENDNODE INTEGER NOT NULL, PROPERTIES INTEGER NOT NULL);";
statements << "CREATE TABLE IF NOT EXISTS NODES(ID INTEGER PRIMARY KEY, LAT, LON, BUCKETID);";
//TODO: Müssen noch Indicies erstellt werden? Laut Doku sollte es so schon schnell sein.
statements << "CREATE TABLE EDGES_STREETNAME(ID INTEGER PRIMARY KEY, STREETNAME VARCHAR);";
//Alle Statements der Liste ausführen in einer Transaktion
//retVal = this->beginTransaction();
QStringList::const_iterator it;
for (it = statements.constBegin(); it != statements.constEnd(); it++)
{
retVal &= execCreateTableStatement(it->toStdString());
}
//retVal &= this->endTransaction();
return retVal;
}
std::vector<std::string> const MergeGeometriesDialog::getSelectedGeometries() const
{
std::vector<std::string> indexList;
QStringList const& list (_selGeo->stringList());
for (QStringList::const_iterator it = list.begin(); it != list.end(); ++it)
indexList.push_back(it->toStdString());
return indexList;
}
StringList StringListUtils::fromQStringList(const QStringList& rhs)
{
StringList sl;
sl.reserve(rhs.size());
for (QStringList::const_iterator it = rhs.begin(); it != rhs.end(); ++it)
{
sl.push_back(it->toStdString());
}
return sl;
}
void DelaylineDetector::loadSettings(CASSSettings &s)
{
s.beginGroup(QString::fromStdString(_name));
DelaylineType delaylinetype
(static_cast<DelaylineType>(s.value("DelaylineType",Hex).toInt()));
s.beginGroup("MCP");
_mcp.loadSettings(s);
s.endGroup();
switch (delaylinetype)
{
case Hex:
s.beginGroup("ULayer");
_anodelayers['U'].loadSettings(s);
s.endGroup();
s.beginGroup("VLayer");
_anodelayers['V'].loadSettings(s);
s.endGroup();
s.beginGroup("WLayer");
_anodelayers['W'].loadSettings(s);
s.endGroup();
break;
case Quad:
s.beginGroup("XLayer");
_anodelayers['X'].loadSettings(s);
s.endGroup();
s.beginGroup("YLayer");
_anodelayers['Y'].loadSettings(s);
s.endGroup();
break;
default:
throw invalid_argument("DelaylineDetector::loadSettings(): delayline type '" +
toString(delaylinetype) + "' does not exist");
break;
}
_analyzer =
DetectorAnalyzerBackend::instance(static_cast<DetectorAnalyzerType>(s.value("AnalysisMethod",DelaylineSimple).toInt()));
_analyzer->loadSettings(s, *this);
s.beginGroup("Particles");
_particles.clear();
QStringList particlesNameList(s.childGroups());
QStringList::const_iterator pNamesIt (particlesNameList.begin());
for (; pNamesIt != particlesNameList.end();++pNamesIt)
{
s.beginGroup(*pNamesIt);
string particleName (pNamesIt->toStdString());
_particles[particleName].loadSettings(s);
s.endGroup();
}
s.endGroup();
s.endGroup();
}
void NRemoteFSBrowser::send_favorites(const QStringList &favs)
{
SignalFrame frame("set_favorites", uri(), SERVER_CORE_PATH);
QStringList::const_iterator it = favs.begin();
std::vector<std::string> vect( favs.count() );
for( int i = 0 ; it != favs.end() ; ++it, ++i )
vect[i] = it->toStdString();
frame.set_array("favorite_dirs", common::class_name<std::string>(), common::option_vector_to_str(vect, ";"), ";");
frame.options().flush();
NetworkQueue::global()->send( frame, NetworkQueue::IMMEDIATE );
}
/**Moves the entry in the line edit new2Add_edit to the
* listbox toAdd_List, expanding any run number lists
*/
void SANSAddFiles::add2Runs2Add() {
// split comma separated file names or run numbers into a list
ArrayProperty<std::string> commaSep(
"unusedName", m_SANSForm->new2Add_edit->text().toStdString());
const std::vector<std::string> nam = commaSep;
for (std::vector<std::string>::const_iterator i = nam.begin(); i != nam.end();
++i) { // each comma separated item could be a range of run numbers
// specified with a ':' or '-'
QStringList ranges;
std::vector<int> runNumRanges;
try { // if the entry is in the form 454:456, runNumRanges will be filled
// with the integers ({454, 455, 456}) otherwise it will throw
appendValue(*i, runNumRanges);
std::vector<int>::const_iterator num = runNumRanges.begin();
for (; num != runNumRanges.end(); ++num) {
ranges.append(QString::number(*num));
}
} catch (boost::bad_lexical_cast &) { // this means that we don't have a
// list of integers, treat it as full
// (and valid) filename
ranges.append(QString::fromStdString(*i));
}
for (QStringList::const_iterator k = ranges.begin(); k != ranges.end();
++k) {
// Don't display the full file path in the box, it's too long
QListWidgetItem *newL = insertListFront(QFileInfo(*k).fileName());
newL->setData(Qt::WhatsThisRole, QVariant(*k));
// Put the full path in the tooltip so people can see it if they want to
// do this with the file finding functionality of the FileProperty
FileProperty search("dummy", k->toStdString(), FileProperty::Load,
std::vector<std::string>(), Direction::Input);
if (search.isValid() == "") { // this means the file was found
newL->setToolTip(QString::fromStdString(search.value()));
// If we don't have an event workspace data set, then we disable the
// event options
if (!isEventWorkspace(QString::fromStdString(search.value()))) {
setBinningOptions(false);
}
}
}
}
m_SANSForm->new2Add_edit->clear();
}
void SQLiteDatabaseConnection::open(QString dbConnectionString)
{
int rc; //return-Wert speichern
QFile file(dbConnectionString);
bool dbExisted = file.exists();
rc = sqlite3_open_v2(dbConnectionString.toStdString().c_str(), &_db,
SQLITE_OPEN_READWRITE |
SQLITE_OPEN_CREATE |
SQLITE_OPEN_FULLMUTEX,
NULL);
if (rc != SQLITE_OK)
{ //Es gab einen Fehler beim Öffnen der Datenbank.
_dbOpen = false;
sqlite3_close(_db);
std::cerr << "Failed to open database file \"" << dbConnectionString.toStdString()
<< "\"" << std::endl;
return;
}
//Erstelle Tabellen nur, wenn die Datei vorher nicht existierte.
if (!dbExisted)
_dbOpen = createTables();
else
{
_dbOpen = true;
//Geschwindigkeit der DB erhöhen
QStringList statements;
statements << "PRAGMA page_size = 4096;";
statements << "PRAGMA max_page_count = 2147483646;";
statements << "PRAGMA cache_size=50000;";
statements << "PRAGMA synchronous=OFF;";
statements << "PRAGMA journal_mode=MEMORY;";
statements << "PRAGMA temp_store = MEMORY;";
QStringList::const_iterator it;
for (it = statements.constBegin(); it != statements.constEnd(); it++)
{
execCreateTableStatement(it->toStdString());
}
}
}
bool SQLiteDatabaseConnection::createIndexes()
{
bool retVal = true;
//Liste von auszuführenden Statements erstellen
QStringList statements;
statements << "CREATE INDEX IF NOT EXISTS EDGES_STARTNODE_INDEX ON EDGES(STARTNODE);";
statements << "CREATE INDEX IF NOT EXISTS EDGES_ENDNODE_INDEX ON EDGES(ENDNODE);";
//Alle Statements der Liste ausführen in einer Transaktion
retVal = this->beginTransaction();
QStringList::const_iterator it;
for (it = statements.constBegin(); it != statements.constEnd(); it++)
{
retVal &= execCreateTableStatement(it->toStdString());
}
retVal &= this->endTransaction();
return retVal;
}
const vector<string> &SymbolManager::getAvailableSymbolNames() const
{
static vector<string> symbolNames;
symbolNames.clear();
string annoPath;
const Filename* pSupportFilesPath = ConfigurationSettings::getSettingSupportFilesPath();
if (pSupportFilesPath != NULL)
{
annoPath = pSupportFilesPath->getFullPathAndName();
}
QDir dir(QString::fromStdString(annoPath + SLASH + "Annotation"), "*.cgm");
QStringList entryList = dir.entryList();
for (QStringList::const_iterator iter = entryList.begin();
iter != entryList.end(); ++iter)
{
symbolNames.push_back(iter->toStdString());
}
return symbolNames;
}
bool CEPasteDialog::acceptVaspFormat()
{
// Validate identities field
QStringList idents = ui.edit_identities->text().simplified()
.split(QRegExp("\\s+|,|;"));
if (static_cast<unsigned int>(idents.size()) != m_numAtomTypes) {
QMessageBox::critical
(this,
tr("Bad Compostion"),
tr("The identities field must contain the same number of "
"space delimited entries as line 6 of the POSCAR."));
return false;
}
bool ok;
QList<unsigned int> compAtomicNums;
QList<unsigned int> compCounts;
for (QStringList::const_iterator
it = idents.constBegin(),
it_end = idents.constEnd();
it != it_end; ++it) {
// Attempt to use the string as a uint
unsigned int atomicNum = it->toUInt(&ok);
// If this doesn't work, try passing the string to OB's translator
if (!ok) {
atomicNum = OpenBabel::etab.GetAtomicNum(it->toStdString().c_str());
}
compAtomicNums.append(atomicNum);
}
QStringList lines = m_text.split("\n");
unsigned int lineIndex = 0;
const QString *line;
QStringList lineList;
unsigned int numAtoms = 0;
QList<Eigen::Vector3d> positions;
QList<unsigned int> atomicNums;
Eigen::Matrix3d cellMatrix;
// First line is comment
line = &lines[lineIndex++];
// Next is a scale factor, single float
line = &lines[lineIndex++];
double scale = line->toDouble(&ok);
if (!ok) {
return false;
}
// Next three lines are cell vectors, three floats
for (int vecInd = 0; vecInd < 3; ++vecInd) {
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
if (lineList.size() != 3) {
return false;
}
for (int i = 0; i < 3; ++i) {
double v = lineList.at(i).toDouble(&ok);
if (!ok) {
return false;
}
cellMatrix(vecInd, i) = v * scale;
}
}
// Next line is a list of unsigned integers (composition)
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
// If vasp >= 5.x, this may be a list of atomic symbols. Skip it if so,
// since the user should have already specified/verified the composition
// in the GUI by this point.
if (lineList.isEmpty()) {
return false;
}
bool vaspVersionLessThan5;
lineList.first().toUInt(&vaspVersionLessThan5);
if (!vaspVersionLessThan5) {
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
}
for (QStringList::const_iterator it = lineList.constBegin(),
it_end = lineList.constEnd(); it != it_end; ++it) {
unsigned int v = it->toUInt(&ok);
if (!ok) {
return false;
}
numAtoms += v;
compCounts.append(v);
}
// Next line is a string. First character is important:
line = &lines[lineIndex++];
if (line->size() && line->at(0).toLower() == QChar('s')){
// If first letter is s (selective dynamics), skip one more line
line = &lines[lineIndex++];
}
// Current line is a string. If it starts with K, k, C, or c,
// positions are in cartesian units. Otherwise, reciprocal units.
bool isCartesian = false;
if (line->size() &&
(line->at(0).toLower() == QChar('k') ||
line->at(0).toLower() == QChar('c') ) ) {
isCartesian = true;
}
// Next [numAtoms] lines are vectors. So long as they're ok, we
// have a POSCAR or CONTCAR!
for (unsigned int i = 0; i < numAtoms; ++i) {
line = &lines[lineIndex++];
lineList = line->simplified().split(QRegExp("\\s+|,|;"));
if (lineList.size() != 3) {
return false;
}
Eigen::Vector3d vec;
for (int i = 0; i < 3; ++i) {
double v = lineList.at(i).toDouble(&ok);
if (!ok) {
return false;
}
vec(i) = v;
}
positions.append(vec);
}
// Build list of atomic numbers
Q_ASSERT(compAtomicNums.size() == compCounts.size());
for (int i = 0; i < compCounts.size(); ++i) {
for (unsigned int j = 0; j < compCounts.at(i); ++j) {
atomicNums.append(compAtomicNums.at(i));
}
}
Q_ASSERT(atomicNums.size() == positions.size());
// Set unit cell
QWriteLocker locker (m_molecule->lock());
OpenBabel::OBUnitCell *cell = m_molecule->OBUnitCell();
cell->SetData(Eigen2OB(cellMatrix));
// Convert to cartesian coords if necessary:
if (!isCartesian) {
for (QList<Eigen::Vector3d>::iterator
it = positions.begin(),
it_end = positions.end();
it != it_end; ++it) {
*it = OB2Eigen(cell->FractionalToCartesian
(Eigen2OB(*it)));
}
}
// Remove old atoms
QList<Avogadro::Atom*> oldAtoms = m_molecule->atoms();
for (QList<Avogadro::Atom*>::iterator
it = oldAtoms.begin(),
it_end = oldAtoms.end();
it != it_end;
++it) {
m_molecule->removeAtom(*it);
}
// Add new atoms
for (int i = 0; i < positions.size(); ++i) {
Atom *atom = m_molecule->addAtom();
atom->setAtomicNumber(atomicNums.at(i));
atom->setPos(positions.at(i));
}
return true;
}
ExitCodes main_(int, const char **) override
{
//-------------------------------------------------------------
// Parsing parameters
//-------------------------------------------------------------
String in = getStringOption_("in");
String out_sirius = getStringOption_("out_sirius");
String out_csifingerid = getStringOption_("out_fingerid");
// needed for counting
int number_compounds = getIntOption_("number");
// Parameter for Sirius3
QString executable = getStringOption_("executable").toQString();
const QString profile = getStringOption_("profile").toQString();
const QString elements = getStringOption_("elements").toQString();
const QString database = getStringOption_("database").toQString();
const QString isotope = getStringOption_("isotope").toQString();
const QString noise = QString::number(getIntOption_("noise"));
const QString ppm_max = QString::number(getIntOption_("ppm_max"));
const QString candidates = QString::number(getIntOption_("candidates"));
bool auto_charge = getFlag_("auto_charge");
bool no_recalibration = getFlag_("no_recalibration");
bool iontree = getFlag_("iontree");
//-------------------------------------------------------------
// Determination of the Executable
//-------------------------------------------------------------
// Parameter executable not provided
if (executable.isEmpty())
{
const QProcessEnvironment env;
const QString & qsiriuspathenv = env.systemEnvironment().value("SIRIUS_PATH");
if (qsiriuspathenv.isEmpty())
{
writeLog_( "FATAL: Executable of Sirius could not be found. Please either use SIRIUS_PATH env variable or provide with -executable");
return MISSING_PARAMETERS;
}
executable = qsiriuspathenv;
}
// Normalize file path
QFileInfo file_info(executable);
executable = file_info.canonicalFilePath();
writeLog_("Executable is: " + executable);
const QString & path_to_executable = File::path(executable).toQString();
//-------------------------------------------------------------
// Calculations
//-------------------------------------------------------------
PeakMap spectra;
MzMLFile f;
f.setLogType(log_type_);
f.load(in, spectra);
std::vector<String> subdirs;
QString tmp_base_dir = File::getTempDirectory().toQString();
QString tmp_dir = QDir(tmp_base_dir).filePath(File::getUniqueName().toQString());
String tmp_ms_file = QDir(tmp_base_dir).filePath((File::getUniqueName() + ".ms").toQString());
String out_dir = QDir(tmp_dir).filePath("sirius_out");
//Write msfile
SiriusMSFile::store(spectra, tmp_ms_file);
// Assemble SIRIUS parameters
QStringList process_params;
process_params << "-p" << profile
<< "-e" << elements
<< "-d" << database
<< "-s" << isotope
<< "--noise" << noise
<< "--candidates" << candidates
<< "--ppm-max" << ppm_max
<< "--quiet"
<< "--output" << out_dir.toQString(); //internal output folder for temporary SIRIUS output file storage
// Add flags
if (no_recalibration)
{
process_params << "--no-recalibration";
}
if (!out_csifingerid.empty())
{
process_params << "--fingerid";
}
if (iontree)
{
process_params << "--iontree";
}
if (auto_charge)
{
process_params << "--auto-charge";
}
process_params << tmp_ms_file.toQString();
// The actual process
QProcess qp;
qp.setWorkingDirectory(path_to_executable); //since library paths are relative to sirius executable path
qp.start(executable, process_params); // does automatic escaping etc... start
std::stringstream ss;
ss << "COMMAND: " << executable.toStdString();
for (QStringList::const_iterator it = process_params.begin(); it != process_params.end(); ++it)
{
ss << " " << it->toStdString();
}
LOG_DEBUG << ss.str() << endl;
writeLog_("Executing: " + String(executable));
writeLog_("Working Dir is: " + path_to_executable);
const bool success = qp.waitForFinished(-1); // wait till job is finished
qp.close();
if (success == false || qp.exitStatus() != 0 || qp.exitCode() != 0)
{
writeLog_( "FATAL: External invocation of Sirius failed. Standard output and error were:");
const QString sirius_stdout(qp.readAllStandardOutput());
const QString sirius_stderr(qp.readAllStandardOutput());
writeLog_(sirius_stdout);
writeLog_(sirius_stderr);
writeLog_(String(qp.exitCode()));
return EXTERNAL_PROGRAM_ERROR;
}
//-------------------------------------------------------------
// writing output
//-------------------------------------------------------------
//Extract path to subfolders (sirius internal folder structure)
QDirIterator it(out_dir.toQString(), QDir::Dirs | QDir::NoDotAndDotDot, QDirIterator::NoIteratorFlags);
while (it.hasNext())
{
subdirs.push_back(it.next());
}
//sort vector path list
std::sort(subdirs.begin(), subdirs.end(), sortByScanIndex);
//Convert sirius_output to mztab and store file
MzTab sirius_result;
MzTabFile siriusfile;
SiriusMzTabWriter::read(subdirs, number_compounds, sirius_result);
siriusfile.store(out_sirius, sirius_result);
//Convert sirius_output to mztab and store file
if (out_csifingerid.empty() == false)
{
MzTab csi_result;
MzTabFile csifile;
CsiFingerIdMzTabWriter::read(subdirs, number_compounds, csi_result);
csifile.store(out_csifingerid, csi_result);
}
//clean tmp directory if debug level < 2
if (debug_level_ >= 2)
{
writeDebug_("Keeping temporary files in directory '" + String(tmp_dir) + " and msfile at this location "+ tmp_ms_file + ". Set debug level to 1 or lower to remove them.", 2);
}
else
{
if (tmp_dir.isEmpty() == false)
{
writeDebug_("Deleting temporary directory '" + String(tmp_dir) + "'. Set debug level to 2 or higher to keep it.", 0);
File::removeDir(tmp_dir);
}
if (tmp_ms_file.empty() == false)
{
writeDebug_("Deleting temporary msfile '" + tmp_ms_file + "'. Set debug level to 2 or higher to keep it.", 0);
File::remove(tmp_ms_file); // remove msfile
}
}
return EXECUTION_OK;
}
