System* MolecularFileDialog::openFile_(String type)
{
QStringList files = QFileDialog::getOpenFileNames(
0,
tr("Choose a molecular file to open"),
getWorkingDir().c_str(),
"*.*");
System* system = 0;
for (QStringList::Iterator it = files.begin(); it != files.end(); ++it)
{
vector<String> fields;
String seperators(FileSystem::PATH_SEPARATOR);
// workaround on windows: QT returns the filename in linux style
// but I am not sure, if this will stay this way.
#ifdef BALL_OS_WINDOWS
seperators += "/";
#endif
String file = ascii(*it);
Position p = file.split(fields, seperators.c_str()) -1;
String filename = fields[p];
setWorkingDirFromFilename_(file);
// construct a name for the system(the filename without the dir path)
system = openMolecularFile(file, type, filename);
}
return system;
}
// by default the confReader will look for a number like "cylinder5" and see the corresponding number.
//The number may be in decimals.
static double getCylinderSize(int num, std::string propertiesPath = "properties.conf") {
std::ifstream stream; // input stream
std::string buffer;
std::string temp;
std::string number;
int cylinderNum;
double cylinderSize;
stream.open(propertiesPath.c_str()); // open the file
size_t location(0);
while (std::getline(stream, buffer)) // while there is still stuff in the file, get a line from it and put it in buffer
{
removeCarrageReturn(buffer); // find and kill any '\r'
boost::char_separator<char> seperators(",\t()| &^%!@$="); // all of these chars will be ignored and used a tokenizers
tokenizer tokens(buffer, seperators); // tokenize
tokenizer::iterator tok = tokens.begin(); // there is a list of tokens made, it is accessible via iterator
if (tok == tokens.end()) // if there is nothing in the line
continue; // skip the line
temp = *tok; // string temp = dereference to tok (tok was pointing to a string)
if (temp[0] == '#') // this is a comment mark, if found, then ignore the line,
continue; // skip the line
// ++tok; // go to next token
temp = *tok; // string temp = dereference to token
(toLower(temp)); // turn to all lower case
if ((location = (temp).find("cylinder"))== std::string::npos){ // if that doesnt exist
return DEFAULT_CYLINDER_VAL;
}
number = (temp).substr(location+8); // everything after cylinder
if (number.find_first_not_of("1234567890") != std::string::npos) // if anything that isnt those exists
{
return DEFAULT_CYLINDER_VAL;
}
cylinderNum = boost::lexical_cast<int>(number);
if (num != cylinderNum)
continue;
++tok;
number = *tok;
if (number.find_first_not_of("1234567890.") != std::string::npos) // if anything that isnt those exists
{
return DEFAULT_CYLINDER_VAL;
}
cylinderSize = boost::lexical_cast<double>(number); // convert string to double
return cylinderSize;
}
// if all else fails, return the default val
return 15.0;
};
System* MolecularFileDialog::openMolecularFile(const String& file)
{
vector<String> fields;
String seperators(FileSystem::PATH_SEPARATOR);
// workaround on windows: QT returns the filename in linux style
// but I am not sure, if this will stay this way.
#ifdef BALL_OS_WINDOWS
seperators += "/";
#endif
Position p = file.split(fields, seperators.c_str()) -1;
String filename = fields[p];
setWorkingDirFromFilename_(file);
String extension = fields[filename.split(fields, ".") -1];
filename = filename.getSubstring(0, filename.size() - (extension.size() + 1));
return openMolecularFile(file, extension, filename);
}
paint::paint(const std::string& s)
: color_attrib_(ColorAttrib::VALUE),
backup_color_attrib_(ColorAttrib::NONE),
opacity_(1.0)
{
if(s == "none") {
color_attrib_ = ColorAttrib::NONE;
} else if(s == "currentColor") {
color_attrib_ = ColorAttrib::CURRENT_COLOR;
} else if(s.length() > 1 && s[0] == '#') {
ASSERT_LOG(s.length() == 4 || s.length() == 7, "Expected length of color definition to be 3 or 6 characters long, found: " << s.substr(1));
if(s.length() == 4) {
int r_hex = convert_hex_digit(s[1]);
int g_hex = convert_hex_digit(s[2]);
int b_hex = convert_hex_digit(s[3]);
color_value_ = color((r_hex << 4) | r_hex, (g_hex << 4) | g_hex, (b_hex << 4) | b_hex);
} else {
color_value_ = color((convert_hex_digit(s[1]) << 4) | convert_hex_digit(s[2]),
(convert_hex_digit(s[3]) << 4) | convert_hex_digit(s[4]),
(convert_hex_digit(s[5]) << 4) | convert_hex_digit(s[6]));
}
} else if(s.length() > 3 && s.substr(0,3) == "rgb") {
boost::char_separator<char> seperators(" \n\t\r,()");
boost::tokenizer<boost::char_separator<char>> tok(s.substr(3), seperators);
int count = 0;
int cv[3];
for(auto it = tok.begin(); it != tok.end(); ++it) {
char* end = NULL;
long value = strtol(it->c_str(), &end, 10);
uint8_t col_val = 0;
if(value == 0 && end == it->c_str()) {
ASSERT_LOG(false, "Unable to parse string as an integer: " << *it);
}
if(end != NULL && *end == '%') {
ASSERT_LOG(value >= 0 && value <= 100, "Percentage values range from 0-100: " << value);
col_val = uint8_t(value / 100.0 * 255);
} else {
ASSERT_LOG(value >= 0 && value <= 255, "Percentage values range from 0-255: " << value);
col_val = uint8_t(value);
}
ASSERT_LOG(count < 3, "Too many numbers in color value");
cv[count] = col_val;
}
color_value_ = color(cv[0],cv[1],cv[2]);
} else if(s.length() > 4 && s.substr(0, 4) == "url(") {
auto st_it = std::find(s.begin(), s.end(), '(');
auto ed_it = std::find(s.begin(), s.end(), '0');
color_ref_ = uri::uri::parse(std::string(st_it, ed_it));
color_attrib_ = ColorAttrib::FUNC_IRI;
std::string backup(ed_it, s.end());
if(!backup.empty()) {
// XXX parse stuff
}
} else if(s.length() > 9 && s.substr(0,9) == "icc-color") {
boost::char_separator<char> seperators(" \n\t\r,()");
boost::tokenizer<boost::char_separator<char>> tok(s.substr(9), seperators);
auto it = tok.begin();
icc_color_name_ = *it;
for(; it != tok.end(); ++it) {
try {
double value = boost::lexical_cast<double>(*it);
icc_color_values_.emplace_back(value);
} catch(boost::bad_lexical_cast&) {
ASSERT_LOG(false, "Unable to convert icc-color value from string to numeric: " << *it << " : " << s);
}
}
color_attrib_ = ColorAttrib::ICC_COLOR;
} else {
color_value_ = color::from_name(s);
}
}
std::vector<transform_ptr> transform::factory(const std::string& s)
{
std::vector<transform_ptr> results;
enum {
STATE_TYPE,
STATE_NUMBER,
} state = STATE_TYPE;
std::vector<double> parameters;
TransformType type = TransformType::ERROR;
boost::char_separator<char> seperators(" \n\t\r,", "()");
boost::tokenizer<boost::char_separator<char>> tok(s, seperators);
for(auto it = tok.begin(); it != tok.end(); ++it) {
if(state == STATE_TYPE) {
if(*it == "matrix") {
type = TransformType::MATRIX;
} else if(*it == "translate") {
type = TransformType::TRANSLATE;
} else if(*it == "scale") {
type = TransformType::SCALE;
} else if(*it == "rotate") {
type = TransformType::ROTATE;
} else if(*it == "skewX") {
type = TransformType::SKEW_X;
} else if(*it == "skewY") {
type = TransformType::SKEW_Y;
} else if(*it == "(") {
parameters.clear();
state = STATE_NUMBER;
} else {
ASSERT_LOG(false, "Unexpected token while looking for a type: " << *it << " : " << s);
}
} else if(state == STATE_NUMBER) {
if(*it == ")") {
ASSERT_LOG(type != TransformType::ERROR, "svg transform type was not initialized");
switch(type) {
case TransformType::MATRIX: {
matrix_transform* mtrf = new matrix_transform(parameters);
results.emplace_back(mtrf);
break;
}
case TransformType::TRANSLATE: {
ASSERT_LOG(parameters.size() == 1 || parameters.size() == 2, "Parsing transform:translate found " << parameters.size() << " parameter(s), expected 1 or 2");
double tx = parameters[0];
double ty = parameters.size() == 2 ? parameters[1] : 0.0f;
translate_transform * ttrf = new translate_transform(tx, ty);
results.emplace_back(ttrf);
break;
}
case TransformType::SCALE: {
ASSERT_LOG(parameters.size() == 1 || parameters.size() == 2, "Parsing transform:scale found " << parameters.size() << " parameter(s), expected 1 or 2");
double sx = parameters[0];
double sy = parameters.size() == 2 ? parameters[1] : sx;
scale_transform * strf = new scale_transform(sx, sy);
results.emplace_back(strf);
break;
}
case TransformType::ROTATE: {
ASSERT_LOG(parameters.size() == 1 || parameters.size() == 3, "Parsing transform:rotate found " << parameters.size() << " parameter(s), expected 1 or 3");
double angle = parameters[0] / 180.0 * M_PI;
double cx = parameters.size() == 3 ? parameters[1] : 0;
double cy = parameters.size() == 3 ? parameters[2] : 0;
rotation_transform* rtrf = new rotation_transform(angle, cx, cy);
results.emplace_back(rtrf);
break;
}
case TransformType::SKEW_X: {
ASSERT_LOG(parameters.size() == 1, "Parsing transform:skewX found " << parameters.size() << " parameter(s), expected 1");
double sa = tan(parameters[0]);
skew_x_transform* sxtrf = new skew_x_transform(sa);
results.emplace_back(sxtrf);
break;
}
case TransformType::SKEW_Y: {
ASSERT_LOG(parameters.size() == 1, "Parsing transform:skewY found " << parameters.size() << " parameter(s), expected 1");
double sa = tan(parameters[0]);
skew_y_transform* sxtrf = new skew_y_transform(sa);
results.emplace_back(sxtrf);
break;
}
case TransformType::ERROR:
assert(false);
break;
}
state = STATE_TYPE;
} else {
char* end = nullptr;
double value = strtod(it->c_str(), &end);
if(value == 0 && it->c_str() == end) {
ASSERT_LOG(false, "Invalid number value: " << *it);
}
ASSERT_LOG(errno != ERANGE, "parsed numeric value out-of-range: " << *it);
parameters.push_back(value);
}
}
}
return results;
}