// Open a glf file for writing with the specified filename.
bool GlfFile::openForWrite(const char * filename, bool compressed)
{
// Reset for any previously operated on files.
resetFile();
if(compressed)
{
myFilePtr = ifopen(filename, "wb", InputFile::BGZF);
}
else
{
myFilePtr = ifopen(filename, "wb", InputFile::UNCOMPRESSED);
}
if (myFilePtr == NULL)
{
std::string errorMessage = "Failed to Open ";
errorMessage += filename;
errorMessage += " for writing";
myStatus.setStatus(GlfStatus::FAIL_IO, errorMessage.c_str());
throw(GlfException(myStatus));
return(false);
}
myIsOpenForWrite = true;
// Successfully opened the file.
myStatus = GlfStatus::SUCCESS;
return(true);
}
// Constructor, init variables and open the specified file based on the
// specified mode (READ/WRITE). Default is READ..
GlfFile::GlfFile(const char* filename, OpenType mode)
: myFilePtr(NULL),
myEndMarker()
{
resetFile();
bool openStatus = true;
if(mode == READ)
{
// open the file for read.
openStatus = openForRead(filename);
}
else
{
// open the file for write.
openStatus = openForWrite(filename);
}
if(!openStatus)
{
// Failed to open the file - print error and abort.
fprintf(stderr, "%s\n", getStatusMessage());
std::cerr << "FAILURE - EXITING!!!" << std::endl;
exit(-1);
}
}
void SamFile::init(const char* filename, OpenType mode, SamFileHeader* header)
{
init();
resetFile();
bool openStatus = true;
if(mode == READ)
{
// open the file for read.
openStatus = OpenForRead(filename, header);
}
else
{
// open the file for write.
openStatus = OpenForWrite(filename, header);
}
if(!openStatus)
{
// Failed to open the file - print error and abort.
fprintf(stderr, "%s\n", GetStatusMessage());
std::cerr << "FAILURE - EXITING!!!" << std::endl;
exit(-1);
}
}
SamFile::~SamFile()
{
resetFile();
if(myStatistics != NULL)
{
delete myStatistics;
}
}
void resetServer(){
for(int i=0;i<MAXSESSION;i++){
width[i] = height[i] = page[i] = -1;
zoom[i] = 0;
}
sessionCount = 0;
resetFile("list.txt");
return;
}
/*
Saída: Gera os arquivos temporários que serão utilizados pelo BucketSort
Custo : O(1) Todas as variáveis são constantes
*/
void createTemporaryFiles()
{
int i;
char * path = (char *) malloc(strlen(DIR)*sizeof(char));
for(i=0; i < TOTAL_INTERVAL/BUCKET_INTERVAL ; i++)
{
strcat(strcpy(path,DIR),itoa_lock(i,LOCK));
resetFile(path);
}
}
void VcfFile::reset()
{
// Reset the child class.
resetFile();
// Close the file.
if (myFilePtr != NULL)
{
// If we already have an open file, close it.
ifclose(myFilePtr);
myFilePtr = NULL;
}
myNumRecords = 0;
}
/*
Entrada: Caminho do arquivo a ser gerado com os arquivos concatenados
Saída: Gera o arquivo final ordenado
Custo : O(n) Concatena os arquivos temporários, logo, n
*/
void concatTempFiles(char * path)
{
resetFile(path);
int i;
FILE * concatFile = fopen(path,"ab+"), *temp;
char * pathTemp = (char *) malloc(strlen(DIR)*sizeof(char));
for(i=0; i < TOTAL_INTERVAL/BUCKET_INTERVAL ; i++)
{
strcat(strcpy(pathTemp,DIR),itoa_lock(i,LOCK));
temp = fopen(pathTemp,"rb");
filecat(concatFile,temp);
fclose(temp);
}
fclose(concatFile);
}
int createSession(const char *file){
// creates and initiates a new session
if(sessionCount==MAXSESSION){
printf("\nCANT HAVE ANYMORE STATUS !!\n");
return 0;
}
if(isExist(file)!=1){
printf("\nCANT CREATE NEW SESSION : FILE {%s} NOT FOUND !!",file);
return 0;
}
int session = sessionCount;
sessionCount++;
addNewSession(session,file);
char statusFile[100];
sprintf(statusFile,"status_%i.txt",session);
resetFile(statusFile);
char line[1000];
// launch the session and store windowid in windowId
char windowID[100];
windowID[0] = '\0';
launchPdf(file,windowID);
// initialize the new openned session
initializeWindow(windowID);
sprintf(line,"%s",windowID);
addLine(statusFile,line);
sprintf(line,"%s",file);
addLine(statusFile,line);
sprintf(line,"%d",PAGE_DEFAULT);
addLine(statusFile,line);
sprintf(line,"%d",ZOOM_DEFAULT);
addLine(statusFile,line);
sprintf(line,"%d",WIDTH_DEFAULT);
addLine(statusFile,line);
sprintf(line,"%d",HEIGHT_DEFAULT);
addLine(statusFile,line);
page[session] = PAGE_DEFAULT;
zoom[session] = ZOOM_DEFAULT;
width[session] = WIDTH_DEFAULT;
height[session] = HEIGHT_DEFAULT;
return 1;
}
// Open a glf file for reading with the specified filename.
bool GlfFile::openForRead(const char * filename)
{
// Reset for any previously operated on files.
resetFile();
myFilePtr = ifopen(filename, "rb");
if (myFilePtr == NULL)
{
std::string errorMessage = "Failed to Open ";
errorMessage += filename;
errorMessage += " for reading";
myStatus.setStatus(GlfStatus::FAIL_IO, errorMessage.c_str());
throw(GlfException(myStatus));
return(false);
}
myIsOpenForRead = true;
// Successfully opened the file.
myStatus = GlfStatus::SUCCESS;
return(true);
}
FileEditionWidget::FileEditionWidget(QWidget *parent) :
QWidget(parent),
ui(new Ui::FileEditionWidget), _askFileContext(None), _gridEditor(nullptr), _propertiesBrowser(nullptr),
_propertyDialog(nullptr), _plainTextEditor(nullptr), _textDialog(nullptr),
_nsEditor(nullptr), _nsDialog(nullptr)
{
ui->setupUi(this);
_editMapper = new QSignalMapper(this);
connect(_editMapper, SIGNAL(mapped(QString)), this, SLOT(editFile(QString)));
connect(ui->tableWidget, SIGNAL(cellDoubleClicked(int,int)), this, SLOT(rowDoubleClicked(int)));
_exportMapper = new QSignalMapper(this);
connect(_exportMapper, SIGNAL(mapped(QString)), this, SLOT(exportFile(QString)));
_importMapper = new QSignalMapper(this);
connect(_importMapper, SIGNAL(mapped(QString)), this, SLOT(importFile(QString)));
_resetMapper = new QSignalMapper(this);
connect(_resetMapper, SIGNAL(mapped(QString)), this, SLOT(resetFile(QString)));
connect(ui->btnImportFile, SIGNAL(clicked()), this, SLOT(importFromDisk()));
connect(ui->btnNewFile, SIGNAL(clicked()), this, SLOT(newFile()));
}
//====================================
int main(int argc, char *argv[])
//====================================
{
char syscom[120];
int ch,i,x;
currentStep = 1;
currentLoop = 0;
strcpy(gplFile,"gpl.txt");
inrpt[0] = IR0;
inrpt[1] = IR1;
inrpt[2] = IR2;
inrpt[3] = IR3;
inrpt[4] = IR4;
inrpt[5] = IR5;
sprintf(syscom,"ls *.conf > %s;",fileProjList);
x=system(syscom);
sprintf(syscom,"rm %s;touch %s;",fileTemp,fileTemp);
x=system(syscom);
sprintf(syscom,"rm %s;touch %s;",fileError,fileError);
x=system(syscom);
sprintf(syscom,"rm %s;touch %s;",fileServError,fileServError);
x=system(syscom);
sprintf(syscom,"rm %s;touch %s;",fileCopyError,fileCopyError);
x=system(syscom);
err = fopen(fileError,"w"); // Issue 15
readSetting();
readConfig(currentConf);
initSim();
resetSim();
readSimulation();
readSketchInfo();
setRange(confBoardType);
init(confWinMode);
unoInfo();
show(slog);
if(confLogFile == S_YES)resetFile("log.txt");
readMsg(gplFile);
openCommand();
delwin(uno);
delwin(ser);
delwin(slog);
delwin(msg);
endwin();
fclose(err);
}
GlfFile::~GlfFile()
{
resetFile();
}
// Constructor, init variables.
GlfFile::GlfFile()
: myFilePtr(NULL),
myEndMarker()
{
resetFile();
}
// Open a sam/bam file for reading with the specified filename.
bool SamFile::OpenForRead(const char * filename, SamFileHeader* header)
{
// Reset for any previously operated on files.
resetFile();
int lastchar = 0;
while (filename[lastchar] != 0) lastchar++;
// If at least one character, check for '-'.
if((lastchar >= 1) && (filename[0] == '-'))
{
// Read from stdin - determine type of file to read.
// Determine if compressed bam.
if(strcmp(filename, "-.bam") == 0)
{
// Compressed bam - open as bgzf.
// -.bam is the filename, read compressed bam from stdin
filename = "-";
myFilePtr = new InputFile;
// support recover mode - this switches in a reader
// capable of recovering from bad BGZF compression blocks.
myFilePtr->setAttemptRecovery(myAttemptRecovery);
myFilePtr->openFile(filename, "rb", InputFile::BGZF);
myInterfacePtr = new BamInterface;
// Read the magic string.
char magic[4];
ifread(myFilePtr, magic, 4);
}
else if(strcmp(filename, "-.ubam") == 0)
{
// uncompressed BAM File.
// -.ubam is the filename, read uncompressed bam from stdin.
// uncompressed BAM is still compressed with BGZF, but using
// compression level 0, so still open as BGZF since it has a
// BGZF header.
filename = "-";
// Uncompressed, so do not require the eof block.
#ifdef __ZLIB_AVAILABLE__
BgzfFileType::setRequireEofBlock(false);
#endif
myFilePtr = ifopen(filename, "rb", InputFile::BGZF);
myInterfacePtr = new BamInterface;
// Read the magic string.
char magic[4];
ifread(myFilePtr, magic, 4);
}
else if((strcmp(filename, "-") == 0) || (strcmp(filename, "-.sam") == 0))
{
// SAM File.
// read sam from stdin
filename = "-";
myFilePtr = ifopen(filename, "rb", InputFile::UNCOMPRESSED);
myInterfacePtr = new SamInterface;
}
else
{
std::string errorMessage = "Invalid SAM/BAM filename, ";
errorMessage += filename;
errorMessage += ". From stdin, can only be '-', '-.sam', '-.bam', or '-.ubam'";
myStatus.setStatus(SamStatus::FAIL_IO, errorMessage.c_str());
delete myFilePtr;
myFilePtr = NULL;
return(false);
}
}
else
{
// Not from stdin. Read the file to determine the type.
myFilePtr = new InputFile;
// support recovery mode - this conditionally enables a reader
// capable of recovering from bad BGZF compression blocks.
myFilePtr->setAttemptRecovery(myAttemptRecovery);
bool rc = myFilePtr->openFile(filename, "rb", InputFile::DEFAULT);
if (rc == false)
{
std::string errorMessage = "Failed to Open ";
errorMessage += filename;
errorMessage += " for reading";
myStatus.setStatus(SamStatus::FAIL_IO, errorMessage.c_str());
delete myFilePtr;
myFilePtr = NULL;
return(false);
}
char magic[4];
ifread(myFilePtr, magic, 4);
if (magic[0] == 'B' && magic[1] == 'A' && magic[2] == 'M' &&
magic[3] == 1)
{
myInterfacePtr = new BamInterface;
// Set that it is a bam file open for reading. This is needed to
// determine if an index file can be used.
myIsBamOpenForRead = true;
}
else
{
// Not a bam, so rewind to the beginning of the file so it
// can be read.
ifrewind(myFilePtr);
myInterfacePtr = new SamInterface;
}
}
// File is open for reading.
myIsOpenForRead = true;
// Read the header if one was passed in.
if(header != NULL)
{
return(ReadHeader(*header));
}
// Successfully opened the file.
myStatus = SamStatus::SUCCESS;
return(true);
}
VcfFileReader::~VcfFileReader()
{
resetFile();
}
// Close the file if there is one open.
void SamFile::Close()
{
// Resetting the file will close it if it is open, and
// will reset all other variables.
resetFile();
}
int main(int argc, char* argv[])
{
int a;
int anyargs = 0;
char Mode = MODE_IQ; // By default
int SampleRate=48000;
float SetFrequency=1e6;//1MHZ
float ppmpll=0.0;
char NoUsePwmFrequency=0;
while(1)
{
a = getopt(argc, argv, "i:f:m:s:p:hld:w:c:");
if(a == -1)
{
if(anyargs) break;
else a='h'; //print usage and exit
}
anyargs = 1;
switch(a)
{
case 'i': // File name
FileName = optarg;
break;
case 'f': // Frequency
SetFrequency = atof(optarg);
break;
case 'm': // Mode (IQ,IQFLOAT,RF,RFA)
if(strcmp("IQ",optarg)==0) Mode=MODE_IQ;
if(strcmp("RF",optarg)==0) Mode=MODE_RF;
if(strcmp("RFA",optarg)==0) Mode=MODE_RFA;
if(strcmp("IQFLOAT",optarg)==0) Mode=MODE_IQ_FLOAT;
if(strcmp("VFO",optarg)==0) Mode=MODE_VFO;
break;
case 's': // SampleRate (Only needeed in IQ mode)
SampleRate = atoi(optarg);
break;
case 'p': // ppmcorrection
ppmpll = atof(optarg);
break;
case 'h': // help
print_usage();
exit(1);
break;
case 'l': // loop mode
loop_mode_flag = 1;
break;
case 'd': // loop mode
DmaSampleBurstSize = atoi(optarg);
NUM_SAMPLES=4*DmaSampleBurstSize;
break;
case 'c': // Use clock instead of PWM pin
UsePCMClk = atoi(optarg);
if(UsePCMClk==1) printf("Use GPCLK Pin instead of PWM\n");
break;
case 'w': // No use pwmfrequency
NoUsePwmFrequency = atoi(optarg);
break;
case -1:
break;
case '?':
if (isprint(optopt) )
{
fprintf(stderr, "rpitx: unknown option `-%c'.\n", optopt);
}
else
{
fprintf(stderr, "rpitx: unknown option character `\\x%x'.\n", optopt);
}
print_usage();
exit(1);
break;
default:
print_usage();
exit(1);
break;
}/* end switch a */
}/* end while getopt() */
//Open File Input for modes which need it
if((Mode==MODE_IQ)||(Mode==MODE_IQ_FLOAT)||(Mode==MODE_RF)||(Mode==MODE_RFA))
{
if(FileName && strcmp(FileName,"-")==0)
{
FileInHandle = STDIN_FILENO;
useStdin = 1;
}
else FileInHandle = open(FileName, O_RDONLY);
if (FileInHandle < 0)
{
fatal("Failed to read Filein %s\n",FileName);
}
}
resetFile();
return pitx_run(Mode, SampleRate, SetFrequency, ppmpll, NoUsePwmFrequency, readFile, resetFile, NULL);
}
// Constructor, init variables.
SamFile::SamFile(ErrorHandler::HandlingType errorHandlingType)
: myStatus(errorHandlingType)
{
init();
resetFile();
}
// Constructor, init variables.
SamFile::SamFile()
: myStatus()
{
init();
resetFile();
}
// Open a sam/bam file for writing with the specified filename.
bool SamFile::OpenForWrite(const char * filename, SamFileHeader* header)
{
// Reset for any previously operated on files.
resetFile();
int lastchar = 0;
while (filename[lastchar] != 0) lastchar++;
if (lastchar >= 4 &&
filename[lastchar - 4] == 'u' &&
filename[lastchar - 3] == 'b' &&
filename[lastchar - 2] == 'a' &&
filename[lastchar - 1] == 'm')
{
// BAM File.
// if -.ubam is the filename, write uncompressed bam to stdout
if((lastchar == 6) && (filename[0] == '-') && (filename[1] == '.'))
{
filename = "-";
}
myFilePtr = ifopen(filename, "wb0", InputFile::BGZF);
myInterfacePtr = new BamInterface;
}
else if (lastchar >= 3 &&
filename[lastchar - 3] == 'b' &&
filename[lastchar - 2] == 'a' &&
filename[lastchar - 1] == 'm')
{
// BAM File.
// if -.bam is the filename, write compressed bam to stdout
if((lastchar == 5) && (filename[0] == '-') && (filename[1] == '.'))
{
filename = "-";
}
myFilePtr = ifopen(filename, "wb", InputFile::BGZF);
myInterfacePtr = new BamInterface;
}
else
{
// SAM File
// if - (followed by anything is the filename,
// write uncompressed sam to stdout
if((lastchar >= 1) && (filename[0] == '-'))
{
filename = "-";
}
myFilePtr = ifopen(filename, "wb", InputFile::UNCOMPRESSED);
myInterfacePtr = new SamInterface;
}
if (myFilePtr == NULL)
{
std::string errorMessage = "Failed to Open ";
errorMessage += filename;
errorMessage += " for writing";
myStatus.setStatus(SamStatus::FAIL_IO, errorMessage.c_str());
return(false);
}
myIsOpenForWrite = true;
// Write the header if one was passed in.
if(header != NULL)
{
return(WriteHeader(*header));
}
// Successfully opened the file.
myStatus = SamStatus::SUCCESS;
return(true);
}
void ExperimentReport::generateQualityIndicators() {
if ((!isSingleObjective_) && (paretoFrontDirectory_.empty())) {
generateReferenceFronts();
}
// TODO: Check if it is possible to use QualityIndicator class instead each independent class.
// Problem: knowing number of objectives of each problem
if (indicatorList_.size() > 0) {
cout << "PF file: " << paretoFrontDirectory_ << endl;
for (int algorithmIndex=0; algorithmIndex<algorithmNameList_.size(); algorithmIndex++) {
string algorithmDirectory;
algorithmDirectory = experimentBaseDirectory_ + "/data/" + algorithmNameList_[algorithmIndex] + "/";
for (int problemIndex=0; problemIndex<problemList_.size(); problemIndex++) {
string problemDirectory = algorithmDirectory + problemList_[problemIndex];
string paretoFrontPath;
if (!isSingleObjective_) {
if (paretoFrontDirectory_.empty()) {
string referenceFrontDirectory = experimentBaseDirectory_ + "/referenceFronts";
paretoFrontPath = referenceFrontDirectory + "/" + problemList_[problemIndex] + ".rf";
} else {
paretoFrontPath = paretoFrontDirectory_ + "/" + paretoFrontFile_[problemIndex];
} // if
} // if
for (int indicatorIndex = 0; indicatorIndex < indicatorList_.size(); indicatorIndex++) {
resetFile(problemDirectory + "/" + indicatorList_[indicatorIndex]);
if (indicatorList_[indicatorIndex].compare("FIT")==0) {
string solutionFrontFile = problemDirectory + "/FUN";
string qualityIndicatorFile = problemDirectory;
Fitness * indicators = new Fitness();
vector< vector<double> > solutionFront =
indicators->utils_->readFront(solutionFrontFile);
qualityIndicatorFile = qualityIndicatorFile + "/FIT";
indicators->fitness(solutionFront, qualityIndicatorFile);
delete indicators;
} else {
for (int numRun=0; numRun<independentRuns_; numRun++) {
stringstream outputParetoFrontFilePath;
outputParetoFrontFilePath << problemDirectory << "/FUN_" << numRun;
string solutionFrontFile = outputParetoFrontFilePath.str();
string qualityIndicatorFile = problemDirectory;
double value;
cout << "ExperimentReport: Quality indicator: " << indicatorList_[indicatorIndex] << endl;
if (indicatorList_[indicatorIndex].compare("HV")==0) {
Hypervolume * indicators = new Hypervolume();
vector< vector<double> > solutionFront =
indicators->utils_->readFront(solutionFrontFile);
vector< vector<double> > trueFront =
indicators->utils_->readFront(paretoFrontPath);
value = indicators->hypervolume(solutionFront, trueFront, trueFront[0].size());
delete indicators;
qualityIndicatorFile = qualityIndicatorFile + "/HV";
}
if (indicatorList_[indicatorIndex].compare("SPREAD")==0) {
Spread * indicators = new Spread();
vector< vector<double> > solutionFront =
indicators->utils_->readFront(solutionFrontFile);
vector< vector<double> > trueFront =
indicators->utils_->readFront(paretoFrontPath);
value = indicators->spread(solutionFront, trueFront, trueFront[0].size());
delete indicators;
qualityIndicatorFile = qualityIndicatorFile + "/SPREAD";
}
if (indicatorList_[indicatorIndex].compare("IGD")==0) {
InvertedGenerationalDistance * indicators = new InvertedGenerationalDistance();
vector< vector<double> > solutionFront =
indicators->utils_->readFront(solutionFrontFile);
vector< vector<double> > trueFront =
indicators->utils_->readFront(paretoFrontPath);
value = indicators->invertedGenerationalDistance(solutionFront, trueFront, trueFront[0].size());
delete indicators;
qualityIndicatorFile = qualityIndicatorFile + "/IGD";
}
if (indicatorList_[indicatorIndex].compare("EPSILON")==0) {
Epsilon * indicators = new Epsilon();
vector< vector<double> > solutionFront =
indicators->utils_->readFront(solutionFrontFile);
vector< vector<double> > trueFront =
indicators->utils_->readFront(paretoFrontPath);
value = indicators->epsilon(solutionFront, trueFront, trueFront[0].size());
delete indicators;
qualityIndicatorFile = qualityIndicatorFile + "/EPSILON";
}
cout << "ExperimentReport: Quality indicator file: " << qualityIndicatorFile << endl;
if (qualityIndicatorFile.compare(problemDirectory)!=0) {
std::fstream out(qualityIndicatorFile.c_str(),
std::ios::out | std::ios::app);
out << value << endl;
out.close();
} // if
} // for
} // if
} // for
} // for
} // for
} // if
} // generateQualityIndicators
Loader::Impl::~Impl()
{
resetFile(FileName());
}