//Checks validity of the file and also if the defaultNameSpace is declared or not.
bool TandemReader::checkValidity(const std::string &file)
{
bool isvalid;
std::ifstream fileIn(file.c_str(), std::ios::in);
if (!fileIn)
{
ostringstream temp;
temp << "Error : can not open file " << file << std::endl;
throw MyException(temp.str());
}
std::string line,line_xml,line_bioml;
if (!getline(fileIn, line))
{
ostringstream temp;
temp << "Error : can not read file " << file << std::endl;
throw MyException(temp.str());
}
if (line.find("<?xml") != std::string::npos)
{
getline(fileIn, line_xml);
getline(fileIn, line_bioml);
if (line_xml.find("tandem") == std::string::npos||line_bioml.find("<bioml") == std::string::npos)
{
std::cerr << "XML file not generated by X!tandem: " << file << std::endl;
isvalid = false;
}
else
{
isvalid=true;
}
}
else
{
isvalid = false;
}
fileIn.close();
return isvalid;
}
int main()
{
try
{
throw MyException();
}
catch (std::exception & ex)
{
std::cout << "Message: " << ex.what() << std::endl;
}
getchar();
}
void Sound::prepare(){
if(soundsLoaded){
al_reserve_samples(2);
soundsPrepared = true;
songInstance = al_create_sample_instance(backgroundSong);
al_set_sample_instance_playmode(songInstance, ALLEGRO_PLAYMODE_LOOP);
al_attach_sample_instance_to_mixer(songInstance, al_get_default_mixer());
}
else
throw MyException("Sounds was not attached.");
}
SymbolType *UnaryOpNode::getType(){
if(nodeType)
return nodeType;
SymbolType *type = operand->getType();
Values operation = token->value;
switch(operation){
case factor:
if(!dynamic_cast<PointerSymbol*>(type))
throw MyException("Type of unary operation is not a pointer", token);
nodeType = dynamic_cast<PointerSymbol*>(type)->pointer;
return nodeType;
case b_and:
if(!operand->isLvalue())
throw MyException("Expression must be a modifiable lvalue", token->line, token->start);
nodeType = new PointerSymbol(type);
return nodeType;
case b_not:
operand = makeTypeCoerce(operand, type, IntType);
break;
case l_not:
if(dynamic_cast<StructSymbol*>(type))
throw MyException("No operator \"!\" matches these operands operand types are: !" + type->name, token);
break;
case incr:
case decr:
if(!operand->isModifiableLvalue())
throw MyException("Expression must be a modifiable lvalue", token);
break;
case Values::minus:
if(!type->canConvertTo(FloatType))
throw MyException("Expression must have arithmetical type", token);
}
nodeType = type;
return type;
}
void *LibLoader::getSym(void *inputPoint, const std::string &symName)
{
void *symbol;
if (_libs.find(inputPoint) == _libs.end())
throw(MyException("No such lib loaded dude.."));
#ifdef __unix
symbol = dlsym(inputPoint, symName.c_str());
#elif _WIN32
symbol = GetProcAddress((HMODULE)inputPoint, symName.c_str());
#endif
return symbol;
}
/**
* \fn void MainWindow::saveWorkspaceAs()
* \brief Fontion de sauvegarde (Save As..)
* Slot faisant appelle à la fonction de sauvegarde du Workspace en passant en argument le chemin de sauvegarde choisi par l'utilisateur.
*/
void MainWindow::saveWorkspaceAs()
{
QString dossier = QFileDialog::getSaveFileName(ui->centralwidget, "Save workspace as...", QString(), "*.*");
QDir workFolder(dossier);
if(!workFolder.mkpath(dossier))
throw MyException("An error occured while creating the workspace directory");
else
{
NoteManager::getInstance().setPath(QString(dossier)+"/");
QMessageBox::information(ui->centralwidget,"Information","Le chemin est :"+NoteManager::getInstance().getPath());
Workspace::getInstance().saveInFile();
}
}
/**
* \fn QString MainWindow::getPath() const
* \brief Récupérer un chemin défini par l'utilisateur.
* \return Retourne le chemin choisi.
* Methode servant à recupérer le chemin de sauvegarde des fichiers par l'intermédiaire d'une boîte de dialogue.
*/
QString MainWindow::getPath() const
{
QString dossier = QFileDialog::getSaveFileName(ui->centralwidget, "Save a workspace", QString(), "*.*");
if(dossier=="")
return "";
QDir workFolder(dossier);
if(!workFolder.mkpath(dossier))
throw MyException("An error occured while creating the workspace directory");
else
{
return QString(dossier);
}
}
Node *Node::makeTypeCoerce(Node *expr, SymbolType *from, SymbolType *to){
if(!from->canConvertTo(to))
throw MyException("Cannot perform conversion", expr->token);
if(from == to || *from == to)
return expr;
if (!dynamic_cast<ScalarSymbol*>(from) || !dynamic_cast<ScalarSymbol*>(to))
return expr;
else {
if(typePriority[to] - typePriority[from] == 1)
return new CastNode(0, expr, to);
return new CastNode(0, makeTypeCoerce(expr, from, IntType), FloatType);
}
}
void handler(const std::string& msg, const char* file, int line) {
const int max_frames = 20;
void *frames[max_frames];
int num_frames = backtrace(frames, max_frames);
char** frame_strings = backtrace_symbols(frames, num_frames);
std::stringstream buffer;
buffer << msg << " at " << file << ":" << line << "\n";
buffer << "Stack trace below:\n";
for (int i = 1; i < num_frames; ++i)
buffer << frame_strings[i] << "\n";
free(frame_strings);
throw MyException(buffer.str());
}
void Params::set_input_dir(const std::string &input_dir_) throw (std::exception){
input_dir = input_dir_;
if( input_dir.at(input_dir.length()-1 )!='/' ) input_dir += "/";
clusters_old = input_dir + "clusters.dmp";
headers_old = input_dir + "headers.dmp";
aln_dir_old = input_dir + "alignments/";
dbsorted_old = input_dir + "db_sorted.fas";
if( !Params::exists( clusters_old.c_str() ) )
throw MyException("The clusters file '%s' in the input directory does not exist!", clusters_old.c_str());
if( !Params::exists( aln_dir_old.c_str() ) )
throw MyException("No directory with alignments '%s' exists in the input directory!", aln_dir_old.c_str());
if( !Params::exists( headers_old.c_str() ) )
throw MyException("The headers file '%s' in the input directory does not exist!", headers_old.c_str());
// if( !Params::exists( dbsorted_old.c_str() ) )
// throw MyException("The sorted db file '%s' in the input directory does not exist!", headers_old.c_str());
}
T List<T>::get(const int& index)
{
if(isEmpty())
{
throw MyException("Attempt to access element in an empty list");
}
else
{
// Check for index out of bounds
int count = 0;
Queue<T> temp1;
temp1 = *queue;
while(!(temp1.isEmpty()))
{
count++;
temp1.dequeue();
}
if((count-1) < index || index < 0 || index != static_cast<int>(index))
{
throw MyException("Index out of bounds or invalid");
}
// Get value
Queue<T> temp2;
temp2 = *queue;
int i = 0;
while(i < (index))
{
temp2.dequeue();
++i;
}
return temp2.dequeue();
}
}
// added by shenzhi for MSVC
void ModelDB::SearchDirectory(char *pathname)
{
long handle;
struct _finddata_t filestruct;
//info for the file(or directory)
char path_search[500];
// start the searching, find the first file or subdirectory under current path
// "*" represents "search for everything", filestruct keeps the searching results
handle = _findfirst("*", &filestruct);
// if handle == -1, the directory is empty, stop search and return
// ERROR MESSAGE 12
if((handle == -1))
throw MyException("Wrong model file or path value");
do{
// check whether the first object is a directory (filestruct.name is the pathname)
if(::GetFileAttributes(filestruct.name) & FILE_ATTRIBUTE_DIRECTORY) {
// if it is a directory, skip it;
// the code commented below is to read recursively under the directory.
/*
// if it is a directory, enter it and recursively call search_directory
// note: skip "." or ".." files
if(filestruct.name[0] != '.') {
_chdir(filestruct.name);
SearchDirectory(pathname);
// after searching, go back up a level
_chdir("..");
}
*/
}
// if it is a file, and not ending with ~
else if(filestruct.name[strlen(filestruct.name)-1]!='~') {
// get the full path
_getcwd(path_search, 500);
// then get the pathname for the file (including the filename)
strcat(path_search,"\\");
strcat(path_search,filestruct.name);
// parse the file
string modelID(filestruct.name);
parseSingleModelFile(path_search, modelID);
}
} while (_findnext(handle, &filestruct)==0);
_findclose(handle);
}
void ParsingArithmeticExpressions::Calculation()
{
while (*myPtr)
{
if (*myPtr == ')'){
stChar.Push(*myPtr);
--myPtr;
Calculation();
}
else if (*myPtr == '('){
--myPtr;
break;
}
else if (TokenTypeNumber(*myPtr)){
Number();
if (!TokenTypeOperator(*myPtr)){
if (stChar.Peek() == ')') throw MyException("Ошибка. Между открывающей и закрывающей скобкой отсутствует выражение.", myPtr, Expression + 1);
else throw MyException("Ошибка. Отсутствует выражение.", nullptr, Expression + 1);
}
}
else if (*myPtr == '+' || *myPtr == '-'){
MultiplicationDivision();
stChar.Push(*myPtr);
--myPtr;
Number();
}
else if (*myPtr == '*' || *myPtr == '/' || *myPtr == '^'){
stChar.Push(*myPtr);
--myPtr;
Number();
}
}
MultiplicationDivision();
AdditionSubtraction();
}
void *LibLoader::getFromPath(const std::string & path) const
{
std::map<void *, std::string>::const_iterator it = _libs.begin();
std::map<void *, std::string>::const_iterator ite = _libs.end();
std::cout << "get from path: " << path << "$" << std::endl;
while (it != ite)
{
if (it->second == path)
return (it->first);
else
std::cout << "val: " << it->second << std::endl;
++it;
}
throw(MyException("No such lib loaded dude.."));
}
size_t
Master::deHash(const std::string& str)
{
if (str.find_first_not_of(hash) != str.npos) {
throw MyException("Unsupported character in hash string(" + str + ")");
return 0;
}
size_t val(0);
for (int i(str.size()-1), n(hash.size()); i >= 0; --i) {
val *= n;
val += hash.find(str[i]);
}
return val;
}
std::string PSMDescription::removePTMs(const string& peptide) {
std::string peptideSequence = peptide;
peptideSequence = peptide.substr(2, peptide.size()- 4);
for (unsigned int ix = 0; ix < peptideSequence.size(); ++ix) {
if (peptideSequence[ix] == '[') {
size_t posEnd = peptideSequence.substr(ix).find_first_of(']');
if (posEnd == string::npos) {
ostringstream temp;
temp << "Error : Peptide sequence " << peptide << " contains an invalid modification" << endl;
throw MyException(temp.str());
} else {
peptideSequence.erase(ix--, posEnd + 1);
}
}
}
return peptide.substr(0,1) + std::string(".") + peptideSequence + std::string(".") + peptide.substr(peptide.size() - 1,1);
}
int init_conn(CURL* eh, StringHash url, Conn* conn) {
conn->easy = eh;
conn->url = url;
std::stringstream file_path;
file_path << DEFAULT_OUTPUT_DIR << "/" << m_file_id;
m_file_id += 1;
string tmp_file_path =file_path.str();
conn->file_path = m_psp->add_string(&tmp_file_path);
conn->output = fopen(tmp_file_path.c_str(), "w+");
if (NULL == conn->output) {
throw MyException("@init_easy_handler@ can't open file " + tmp_file_path);
}
return 0;
}
bool SpectrumFileList::initFromFile(const std::string& fileListFN) {
std::ifstream specListFN(fileListFN.c_str());
std::string line;
if (specListFN.is_open()) {
while (getline(specListFN, line)) {
std::string filePath;
std::istringstream iss(line);
iss >> filePath;
addFile(filePath);
}
if (fileIndexVector_.size() == 0) {
std::stringstream ss;
ss << "(SpectrumFileList.cpp) no input files detected in " << fileListFN << std::endl;
throw MyException(ss);
}
} else {
void ParsingArithmeticExpressions::Number()
{
if (TokenTypeNumber(*myPtr)){
double rez = 0.0;
int index = 0;
bool flag = false;
while (*myPtr && (TokenTypeNumber(*myPtr))){
if (*myPtr == ','){
if (flag) throw MyException("Ошибка. Некорректная запись десятичной дроби.", myPtr, Expression + 1); // Если две запятых
flag = true;
}
myPtr--;
}
rez = atof(myPtr + 1);
stDou.Push(rez);
}
}
int main() {
try
{
throw MyException();
}
catch (BaseException* e)
{
std::cout << "BaseException" << std::endl;
}
catch (std::exception& e)
{
std::cout << "exception" << std::endl;
}
catch (...)
{
std::cout << "catch all" << std::endl;
}
return 0;
}
Node* TernaryOpNode::calculate() {
if(*condition->token == T_INTEGER){
if(dynamic_cast<IntNumber*>(condition->token)->v2)
return left;
else return right;
} else
if(*condition->token == T_FLOAT){
if(dynamic_cast<FloatNumber*>(condition->token)->v2)
return left;
else
return right;
} else
if(*condition->token == T_CHAR){
if(dynamic_cast<Char*>(condition->token)->v2)
return left;
else
return right;
} else
throw MyException("Wrong call of high-level optimizer (const folding)", token);
}
void MsgfplusReader::searchEngineSpecificParsing(
const ::mzIdentML_ns::SpectrumIdentificationItemType & item, const int itemCount) {
// First, check whether addFeatures was set to 1, in MS-GF+
if (!additionalMsgfFeatures) {
BOOST_FOREACH (const ::mzIdentML_ns::UserParamType & up, item.userParam()) {
if (up.value().present()) {
std::string param_name(up.name().c_str());
// Check whether the mzid-file seem to include the additional features
if (param_name == "ExplainedIonCurrentRatio") { // If one additional feature is found
additionalMsgfFeatures = true;
}
}
}
if (!additionalMsgfFeatures) { // If no additional features were found in first PSM
ostringstream temp;
temp << "Error: No features for learning were found in the mzid-file."
<< " Run MS-GF+ with the addFeatures option set to 1." << std::endl;
throw MyException(temp.str());
}
}
void serialize(SF::Archive &ar)
{
RCF_ASSERT(ar.isRead() || ar.isWrite());
switch (mWhich)
{
case 0:
ar & a1 & a2;
break;
case 1:
ar & a1 & a2;
throw MyException();
ar & a3;
break;
case 2:
ar & a3;
break;
default:
RCF_ASSERT(0);
}
}
void PolygonDialog::getCoords(Coordinates& coords) const {
GtkTreeIter iter;
gboolean valid;
double x, y;
valid = gtk_tree_model_get_iter_first (m_model,
&iter);
if(!valid)
throw MyException("Adicione pelo menos uma coordenada.\n");
while(valid){
gtk_tree_model_get (m_model, &iter,
0, &x, 1, &y, -1);
coords.emplace_back(x, y);
valid = gtk_tree_model_iter_next (m_model,
&iter);
}
}
double mySqrt(double x) throw(MyException) {
if (x <= 0) {
throw MyException(-1, "input invalide: must be >=0 but input: " + to_string(x));
// return 0;
}
double result;
double delta;
result = x;
// do ten iterations
int i;
for (i = 0; i < 10; ++i) {
if (result <= 0) {
result = 0.1;
}
delta = x - (result * result);
result = result + 0.5 * delta / result;
}
LOGD("mysqrt(%g) = %g", x, result);
return result;
}
void Compute::divideCompute() //除法类除法计算方法成员定义
{
try
{
if(m_value2== 0) //如果除数为0，则抛出相应异常
{
throw MyException("divisor is 0!");
}
else //否则计算两数相除，并打印结果
{
cout<<"m_value1/m_value2:"<<(m_value1/m_value2)<<endl;
}
}catch(MyException&e) //捕获对应异常类型
{
string errorMessage = e.what(); //定义错误信息字符串对象，获取对应异常信息
cout<<errorMessage<<endl; //打印输出对应的异常信息
}catch(...) //捕获所有异常
{
string errorMessage = "Don’t knowerror!";//捕获所有异常处理信息
cout<<errorMessage<<endl;
}
}
void TatortTendencyParser::writeMapToFile(map<int, vector< pair<int, double> > > *data, string filename) {
ofstream ofile(filename);
if (!ofile.is_open())
throw MyException("EXCEPTION: file '" + filename + "' could not be opened for writing");
// DATAFILE format:
// key
// numberOfEntries
// int;double
map<int, vector< pair<int, double> > >::iterator iter = data->begin();
while (iter != data->end()) {
ofile << iter->first << endl;
ofile << iter->second.size() << endl;
for (unsigned int i = 0; i < iter->second.size(); i++) {
ofile << iter->second[i].first << ";" << iter->second[i].second << endl;
}
iter++;
}
}
void Params::set_working_dir(const std::string &dir) throw (std::exception){
working_dir = dir;
if( working_dir.at(working_dir.length()-1 )!='/' ) working_dir += "/";
if( !Params::is_directory( working_dir.c_str() ) ){
std::string cmd = "mkdir " + working_dir;
int i = system( cmd.c_str() );
if (i != 0) throw MyException("The working directory '%s' could not be created!", working_dir.c_str());
//throw MyException("The denoted working directory '%s' does not exist or is not a directory!", working_dir.c_str());
}
if (profile_query) dbsorted = working_dir + "db_cons_sorted.fas";
else dbsorted = working_dir + "db_sorted.fas";
if (profile_query) db = working_dir + "db_tmp.fas";
header_dmp_file = working_dir + "headers.dmp";
nodes_dmp_file = working_dir + "clusters.dmp";
refined_nodes_dmp_file = working_dir + "refined_clusters.dmp";
rep_db_file = working_dir + "representatives.fas";
if (cons_db_file == "") {
cons_db_file = working_dir + "consensus.fas";
}
set_tmp_dir(working_dir + "tmp" + "/");
}
void ParsingArithmeticExpressions::MultiplicationDivision()
{
double tmp1 = 0.0;
double tmp2 = 0.0;
while (stChar.Peek() == '*' || stChar.Peek() == '/' || stChar.Peek() == '^'){
switch (stChar.Pop()){
case'/':
tmp1 = stDou.Pop();
tmp2 = stDou.Pop();
if (tmp2 == 0) throw MyException("Ошибка. Деление на ноль.", myPtr + 1, Expression + 1);
stDou.Push(tmp1 / tmp2);
break;
case'*':
tmp1 = stDou.Pop();
tmp2 = stDou.Pop();
stDou.Push(tmp1 * tmp2);
break;
case '^':
Involution();
break;
}
}
}
Node* UnaryOpNode::calculate(){
Values value = token->value;
IntNumber *intToken = dynamic_cast<IntNumber*>(operand->token);
FloatNumber *floatToken = dynamic_cast<FloatNumber*>(operand->token);
Char *charToken = dynamic_cast<Char*>(operand->token);
if(!(intToken || floatToken || charToken))
throw MyException("Wrong call of the optimizer (constants folding)");
if(value == b_not){
int t = intToken ? intToken->v2 : charToken->v2;
return new IntNode(new IntNumber(token->start, 0, ~t));
}
float t = intToken ? intToken->v2 : floatToken ? floatToken->v2 : charToken->v2;
switch(value){
case l_not:
return new IntNode(new IntNumber(token->start, 0, !t));
case minus:
if(floatToken)
return new FloatNode(new FloatNumber(token->start, 0, -t), 0);
else
return new IntNode(new IntNumber(token->start, 0, -(int)t));
default:
return 0;
}
}
