PopulationParams::PopulationParams(nat id, nat numberOfGenerations, popSize_t initSize, const ProgramOptions &progOpt)
: initSize(initSize)
, correction(1)
// , correction(progOpt.get<nat>("ploidy") - 1 )
, isNeutral(false)
{
vector<string> stringEvents;
if(progOpt.hasOption("popEvent"))
stringEvents = progOpt.get<vector<string> >("popEvent");
// parse rates
recombinationRate = parseRate(progOpt.get<vector<string> >("recRate"),id);
// geneConversionRate = parseRate(progOpt.get<vector<string> >("mutRate"), id);
mutationRate = parseRate(progOpt.get<vector<string> >("mutRate"), id);
if(NOT stringEvents.empty())
{
parseEvents(stringEvents,id);
nat lastPopSize = initSize;
// for(auto event : events)
for(auto eventI = events.begin(); eventI != events.end(); ++eventI)
{
(*eventI)->init(lastPopSize);
if(eventI+1 != events.end())
{
nat whenIsNext = (*(eventI+1))->getWhen();
lastPopSize = (*eventI)->getByTime(whenIsNext-1);
}
}
}
}
void PropertyManager::parseBlock(BlockProperties& properties)
{
parseMethods(properties);
if (!properties.luaRef["perBlock"].isNil())
parsePerBlockProperties(properties);
if (!properties.luaRef["events"].isNil())
parseEvents(properties);
}
prvreader::PrvEvent* prvreader::PrvParser::parseLine()
{
string line;
PrvEvent* prvEvent;
if (prvStream){
if(getline(*prvStream,line)){
lineNumber++;
if (lineNumber%10000==0){
Message::Debug(to_string(lineNumber)+ " lines processed");
}
replace(line.begin(), line.end(), '\t', ' ');
std::size_t found = line.find_first_of("(");
if ((found!=std::string::npos)&&(found+1<line.length())){
found = line.find_first_of("a", found+1);
}
if ((found!=std::string::npos)&&(line[found+1]=='t')&&(found+5<line.length())&&(line[found+5]==PRV_HEADER_SEP_MAIN_CHAR)){
line[found+5]='*';
}
replace(line.begin(), line.end(), PRV_HEADER_QUOTE_IN_CHAR, GENERIC_SEP_CHAR);
replace(line.begin(), line.end(), PRV_HEADER_QUOTE_OUT_CHAR, GENERIC_SEP_CHAR);
trim_all(line);
if (!line.empty()){
escaped_list_separator<char> sep(GENERIC_ESCAPE_CHAR, PRV_HEADER_SEP_MAIN_CHAR, GENERIC_QUOTE_CHAR);
tokenizer<escaped_list_separator<char> > *tokens = new tokenizer<escaped_list_separator<char> >(line, sep);
tokenizer<escaped_list_separator<char> >::iterator tokensIterator=tokens->begin();
if (mode==Header){
prvEvent=parseHeader(tokens);
mode=Body;
}else{
string eventType=*tokensIterator;
tokensIterator++;
//communicator
if (eventType.compare(PRV_BODY_COMMUNICATOR)==0){
prvEvent= new PrvOther(lineNumber, prveventtype::Skip);
//communications
}else if (eventType.compare(PRV_BODY_COMMUNICATION)==0){
prvEvent=parseCommunications(tokens, lineNumber);
}else if (eventType.compare(PRV_BODY_EVENTS)==0){
prvEvent=parseEvents(tokens, lineNumber);
}else if (eventType.compare(PRV_BODY_STATE)==0){
prvEvent=parseState(tokens, lineNumber);
}else{
prvEvent= new PrvOther(lineNumber, prveventtype::Skip);
}
}
delete tokens;
}
}else{
prvEvent=new PrvOther(lineNumber, prveventtype::End);
}
}
return prvEvent;
}
void Testsuite::execute() {
// Main Loop for a testsuite
uint count = 0;
Common::Point pt = getDisplayRegionCoordinates();
pt.y += getLineSeparation();
int numEnabledTests = getNumTestsEnabled();
for (Common::Array<Test *>::iterator i = _testsToExecute.begin(); i != _testsToExecute.end(); ++i) {
if (!(*i)->enabled) {
logPrintf("Info! Skipping Test: %s, Skipped by configuration.\n", ((*i)->featureName).c_str());
_numTestsSkipped++;
continue;
}
if((*i)->isInteractive && !ConfParams.isSessionInteractive()) {
logPrintf("Info! Skipping Test: %s, non-interactive environment is selected\n", ((*i)->featureName).c_str());
_numTestsSkipped++;
continue;
}
logPrintf("Info! Executing Test: %s\n", ((*i)->featureName).c_str());
updateStats("Test", ((*i)->featureName).c_str(), count++, numEnabledTests, pt);
// Run the test and capture exit status.
TestExitStatus eStatus = (*i)->driver();
if (kTestPassed == eStatus) {
logPrintf("Result: Passed\n");
_numTestsExecuted++;
_numTestsPassed++;
} else if (kTestSkipped == eStatus){
logPrintf("Result: Skipped\n");
_numTestsSkipped++;
} else {
_numTestsExecuted++;
logPrintf("Result: Failed\n");
}
updateStats("Test", ((*i)->featureName).c_str(), count, numEnabledTests, pt);
// TODO: Display a screen here to user with details of upcoming test, he can skip it or Quit or RTL
// Check if user wants to quit/RTL/Skip next test by parsing events.
// Quit directly if explicitly requested
if (Engine::shouldQuit()) {
_toQuit = kEngineQuit;
genReport();
return;
}
_toQuit = parseEvents();
}
genReport();
}
int main(int argc, char ** argv)
{
if(argc != 2)
{
printf("Usage is midiParse <file>\n");
exit(1);
}
//now lets open it up
FILE * mFile;
mFile = fopen(argv[1], "r");
if(!mFile)
{
//printf("Opening file \"%s\" failed. Aborting.\n", argv[1]);
exit(1);
}
//get the file size
// obtain file size:
fseek (mFile , 0 , SEEK_END);
uint32_t lSize = ftell(mFile);
rewind (mFile);
printf("Size = %d\n", lSize);
//read the first header
fread(&hChunk, 14, 1, mFile);
/*printf("Header is [ ");
printf("%s %08X %04X %04X %04X]\n",
&hChunk.type,
hChunk.length,
hChunk.format,
hChunk.numtrk,
hChunk.div
);*/
//hChunk.type[4] = 0;
//printf("Type is %s\n", &hChunk.type);
//printf("Length is %d\n", endianSwap32(hChunk.length));
//printf("Format is %d\n", endianSwap16(hChunk.format));
//printf("Format is %d\n", endianSwap16(hChunk.numtrk));
//printf("Format is %d\n", endianSwap16(hChunk.div));
//TODO: allow for reading of any len > 5 headers
if((endianSwap32(hChunk.length) != 6) || (endianSwap16(hChunk.format) == 2))
{
printf("Length of header corrupt or format unknown! Aborting.\n");
exit(1);
}
fseek(mFile, 8 + endianSwap32(hChunk.length), SEEK_SET);
//loop through the rest of the file
while(ftell(mFile) < lSize)
{
char type[5];
type[4] = 0;
struct t_chunk * chunk = (struct t_chunk *)malloc(sizeof(struct t_chunk));
printf("Reading chunk...\n");
fread(&type, 1, 4, mFile);
fread(&((*chunk).size), 4, 1, mFile);
(*chunk).size = endianSwap32((*chunk).size);
(*chunk).data = (uint8_t *)malloc((*chunk).size);
fread((*chunk).data, 1, (*chunk).size, mFile);
printf("Type %s, Length = %d bytes\n", type, (*chunk).size);
//link them up
if(TCs)
{
//find the last one in the list
struct t_chunk * tmpTC = TCs;
while((*tmpTC).next)
{
tmpTC = (*tmpTC).next;
numTCs++;
}
//add our latest node
(*tmpTC).next = chunk;
numTCs++;
}
else
{
TCs = chunk;
numTCs++;
}
//break;
printf("at pos %d\n", ftell(mFile));
}
printf("Parsed %d Track Chunks.\n", numTCs);
//parse events
struct t_chunk * node = TCs;
while(node)
{
parseEvents((*node).data, (*node).size);
node = (*node).next;
}
return 0;
}
