ShellCommand * createShellCommand(char * commandLine){
int i;
ShellCommand * command = allocateMemory(getGlobalHeap() , sizeof(ShellCommand));
//parseamos el commandLine y creamos la matriz de symbolos
parseSequence(commandLine);
//seteamos la cantidad de argumentos
command->argsCount = getArgumentsCount();
//ponemos en 0 todos los caracteres del comando
memset(command->commandName , '\0' , CMD_MAX_LEN);
//ponemos en 0 todos los caracteres de todos los argumentos
for(i=0 ; i<CMD_MAX_ARG ; i++)
memset(command->args[i] , '\0' , CMD_MAX_LEN);
//seteamos el comando
strcpy(command->commandName , getCommandName());
//seteamos todos los argumentos
for( i=0 ; i<getArgumentsCount() ; i++){
strcpy(command->args[i] , getArgument(i));
}
return command;
}
// called by fmi2GetReal, fmi2GetInteger, fmi2GetBoolean, fmi2GetString, fmi2ExitInitialization
// if setStartValues or environment set new values through fmi2SetXXX.
// Lazy set values for all variable that are computed from other variables.
void calculateValues(ModelInstance *comp) {
if (comp->state == modelInitializationMode) {
eventQueue = malloc(sizeof(node_t));
eventQueue->next = NULL;
parseSequence(comp);
}
else {
if (!isEmpty()) {
double epsilon = 0.00000000001;
long t = getTime();
double v = getValue();
while (!isEmpty() && comp->time > t) {
getEvent();
t = getTime();
v = getValue();
i(i_) = 0;
}
if ( comp->time < t )
return;
if (comp->time == t && i(i_) == 0) {
if ( v < (r(input_) + epsilon) &&
v > (r(input_) - epsilon) ) {
b(output_) = fmi2True;
i(i_) = 1;
}
else {
b(output_) = fmi2False;
i(i_) = 1;
}
}
else if (comp->time == t && i(i_) == 1) {
if ( v < (r(input_) + epsilon) &&
v > (r(input_) - epsilon) ) {
b(output_) = fmi2True;
}
else {
if (getTime() == getNextTime()) {
getEvent();
t = getTime();
v = getValue();
if ( v < (r(input_) + epsilon) && v > (r(input_) - epsilon) ) {
b(output_) = fmi2True;
}
else {
b(output_) = fmi2False;
}
}
}
}
}
}
}
SgfTree * Parser::parseGameTree(QIODevice & in) {
SgfTree * tree = new SgfTree();
char c;
in.getChar(&c);
try {
if (c != '(') throw ParserException("'(' is expected but not present");
SgfSequence * sequence = parseSequence(in); // parsing in sequences
tree->setRoot(sequence);
in.getChar(&c);
while (c != ')') { // if we are not at the end of there is a game tree after the sequence
in.getChar(&c);
SgfTree * temp;
temp = parseGameTree();
tree->addNode(temp); // adding gametree to the tree
}
} catch ( ... ) {
delete tree;
delete sequence;
throw;
}
return tree;
}
void CodeGenerator::processRootState()
{
if (readAfterEOF && in!=&cin){
in->seekg (0, ios::end);
// output the last few lines or the complete file if not too big
if (in->tellg()>51200) {
in->seekg (-512, ios::end);
// output complete lines, ignore first line fragment
in->ignore(512, '\n');
} else {
in->seekg (0, ios::beg); // output complete file
}
}
string line;
size_t i=0;
bool tagOpen=false;
while (true)
{
if (!getline(*in, line))
{
// imitate tail bahaviour, continue to read after EOF
if (readAfterEOF)
{
out->flush();
in->clear();
#ifdef WIN32
Sleep(250);
#else
sleep(1);
#endif
}
else
{
//todo hier position merken, in der gui periodisch den dateizeiger auf diesen wert setzen und den neuen code einlesen
break;
}
}
else
{
i=0;
size_t seqEnd=string::npos;
while (i <line.length() )
{
if (line[i]==0x1b)
{
// fix grep --colour .[K (1b 5b 4b) sequences
if (line.length()>i+2 && line[i+2]==0x4b){
seqEnd=i+2;
} else {
seqEnd=line.find_first_of('m', i+1);
//TODO vor ; das hier anfangen xterm: ^[]0;~^G^M^M
// http://www.mit.edu/afs/athena/system/x11r4/src/mit/clients/xterm/ctlseq2.txt
if (seqEnd==string::npos) {
if (line[i+1]==']') seqEnd=line.find(0x07, i+1);
}
if (seqEnd==string::npos) seqEnd=line.find(';', i+1);
if (seqEnd==string::npos) seqEnd=line.find('h', i+1);
if (!ignoreFormatting && seqEnd!=string::npos)
{
if (!elementStyle.isReset()){
*out <<getCloseTag();
tagOpen=false;
}
parseSequence(line, i, seqEnd);
if (!elementStyle.isReset()) {
*out <<getOpenTag();
tagOpen=true;
}
}
}
i= 1+ ((seqEnd!=string::npos)?seqEnd:i);
}
else
{
*out << maskCharacter(line[i]);
++i;
}
}
*out << newLineTag;
}
}
if (tagOpen){
*out <<getCloseTag();
}
out->flush();
}
void PDBFormat::PDBParser::parseBioStruct3D(BioStruct3D& biostruct, U2OpStatus& ti) {
QByteArray readBuff(DocumentFormat::READ_BUFF_SIZE + 1, 0);
char* buf = readBuff.data();
qint64 len = 0;
bool firstCompndLine = true;
while (!ti.isCoR()) {
bool lineOk = true;
len = io->readUntil(buf, DocumentFormat::READ_BUFF_SIZE, TextUtils::LINE_BREAKS, IOAdapter::Term_Include, &lineOk);
if (len == 0) {
break;
}
// there could be no terminator if this is end of file, so we have to check for this
if (!lineOk && !io->isEof()) {
ti.setError(U2::PDBFormat::tr("Line is too long"));
return;
}
currentPDBLine = QString(QByteArray(buf, len));
ti.setProgress(io->getProgress() * 0.8);
if (currentPDBLine.startsWith("HEADER")) {
parseHeader(biostruct, ti);
continue;
}
if (currentPDBLine.startsWith("COMPND")) {
parseMacromolecularContent(firstCompndLine, ti);
firstCompndLine = false;
continue;
}
if (currentPDBLine.startsWith("SEQRES")) {
parseSequence(biostruct, ti);
continue;
}
if (currentPDBLine.startsWith("HELIX ") || currentPDBLine.startsWith("SHEET ")
|| currentPDBLine.startsWith("TURN ")) {
parseSecondaryStructure(biostruct, ti);
continue;
}
if (currentPDBLine.startsWith("ATOM ") || currentPDBLine.startsWith("HETATM")) {
parseAtom(biostruct, ti);
continue;
}
if (currentPDBLine.startsWith("TER")) {
++currentChainIndex;
continue;
}
if (currentPDBLine.startsWith("SPLIT ")) {
parseSplitSection(ti);
continue;
}
if (currentPDBLine.startsWith("MODEL")) {
currentChainIndex = 1;
parseModel(biostruct, ti);
continue;
}
if (currentPDBLine.startsWith("ENDMDL")) {
flagMultipleModels = true;
++currentModelIndex;
continue;
}
}
CHECK_OP(ti,);
if (!flagAtomRecordPresent) {
ti.setError(U2::PDBFormat::tr("Some mandatory records are absent"));
}
updateSecStructChainIndexes(biostruct);
}
