//Fileoutput
int Gene::SaveGene(string InFilename) {
if (InFilename.length() == 0) {
InFilename = GetData("FILENAME",STRING);
if (InFilename.length() == 0) {
InFilename = GetData("DATABASE",STRING);
if (InFilename.length() == 0) {
return FAIL;
}
}
}
if (InFilename.substr(1,1).compare(":") != 0 && InFilename.substr(0,1).compare("/") != 0) {
InFilename = GetDatabaseDirectory(GetParameter("database"),"new gene directory")+InFilename;
}
ofstream Output;
if (!OpenOutput(Output,InFilename)) {
return FAIL;
}
//First I check to see if the user specified that the input headers be printed in the output file
vector<string>* FileHeader = StringToStrings(GetParameter("gene data to print"),";");
vector<string> InputHeaders;
for (int i=0; i < int(FileHeader->size()); i++) {
if ((*FileHeader)[i].compare("INPUT_HEADER") == 0) {
InputHeaders = GetAllData("INPUT_HEADER",STRING);
break;
}
}
for (int i=0; i < int(InputHeaders.size()); i++) {
string Data;
Interpreter(InputHeaders[i],Data,false);
Output << InputHeaders[i] << "\t" << Data << endl;
}
for (int i=0; i < int(FileHeader->size()); i++) {
//I check to see if the current file header has already been printed to file
if ((*FileHeader)[i].compare("INPUT_HEADER") != 0) {
int j =0;
for (j=0; j < int(InputHeaders.size()); j++) {
if (InputHeaders[j].compare((*FileHeader)[i]) == 0) {
break;
}
}
if (j == int(InputHeaders.size())) {
//If the current file header has not already been printed to file, it is printed now
string Data;
Interpreter((*FileHeader)[i],Data,false);
if (Data.length() > 0) {
Output << (*FileHeader)[i] << "\t" << Data << endl;
}
}
}
}
Output.close();
return SUCCESS;
}
ValuePtr UserFunction::exec (AgentPtr agent, TablePtr params) {
switch (agent->getType()) {
case Type::TURTLE:
return TurtleInterpreter().interpret(*manager, agent, tree, params);
case Type::WORLD:
return WorldInterpreter().interpret(*manager, agent, tree, params);
default:
return Interpreter().interpret(*manager, agent, tree, params);
}
}
int Gene::LoadGene(string InFilename) {
if (InFilename.length() == 0) {
InFilename = GetData("FILENAME",STRING);
if (InFilename.length() == 0) {
InFilename = GetData("DATABASE",STRING);
if (InFilename.length() == 0) {
return FAIL;
}
}
}
if (InFilename.length() == 0) {
return FAIL;
}
SetData("FILENAME",InFilename.data(),STRING);
if (!FileExists(InFilename)) {
InFilename = GetDatabaseDirectory(GetParameter("database"),"gene directory")+InFilename;
if (!FileExists(InFilename)) {
return FAIL;
}
}
ifstream Input;
if (!OpenInput(Input,InFilename)) {
SetKill(true);
return FAIL;
}
do {
vector<string>* Strings = GetStringsFileline(Input,"\t");
if (Strings->size() >= 2) {
//I save the input headings so I can print out the same headings when it's time to save the file
AddData("INPUT_HEADER",(*Strings)[0].data(),STRING);
for (int i=1; i < int(Strings->size()); i++) {
Interpreter((*Strings)[0],(*Strings)[i],true);
}
}
delete Strings;
} while(!Input.eof());
if (GetData("DATABASE",STRING).length() == 0) {
AddData("DATABASE",InFilename.data(),STRING);
}
if (MainData != NULL && MainData->GetData("DATABASE",STRING).length() > 0 && GetData("DATABASE",STRING).length() > 0) {
AddData(MainData->GetData("DATABASE",STRING).data(),GetData("DATABASE",STRING).data(),DATABASE_LINK);
}
Input.close();
return SUCCESS;
}
Data DebugSession::debugPrepare(const Data& data) {
Data replyData;
if (!data.hasKey("xml") && !data.hasKey("url")) {
replyData.compound["status"] = Data("failure", Data::VERBATIM);
replyData.compound["reason"] = Data("No XML or URL given", Data::VERBATIM);
return replyData;
}
debugStop(data);
_isAttached = false;
try {
if (data.hasKey("xml")) {
_interpreter = Interpreter::fromXML(data.at("xml").atom, (data.hasKey("url") ? data.at("url").atom : ""));
} else if (data.hasKey("url")) {
_interpreter = Interpreter::fromURL(data.at("url").atom);
} else {
_interpreter = Interpreter();
}
} catch(ErrorEvent e) {
std::cerr << e;
} catch(...) {}
if (_interpreter) {
// register ourself as a monitor
_interpreter.addMonitor(_debugger);
_debugger->attachSession(_interpreter.getImpl().get(), shared_from_this());
replyData.compound["status"] = Data("success", Data::VERBATIM);
} else {
replyData.compound["status"] = Data("failure", Data::VERBATIM);
}
return replyData;
}
Data DebugSession::debugStop(const Data& data) {
Data replyData;
if (_interpreter) {
// detach from old intepreter
_debugger->detachSession(_interpreter.getImpl().get());
}
if (_isRunning && _interpreterThread != NULL) {
_isRunning = false;
_interpreterThread->join();
delete(_interpreterThread);
}
// unblock
_resumeCond.notify_all();
_skipTo = Breakpoint();
replyData.compound["status"] = Data("success", Data::VERBATIM);
// calls destructor
_interpreter = Interpreter();
return replyData;
}
