void LuaList::rename(const QString& oldName, const QString& newName)
{
QString luaFileNameOld, luaFileNameNew, settingsFileNameOld, settingsFileNameNew;
getFileNames(oldName, luaFileNameOld, settingsFileNameOld);
getFileNames(newName, luaFileNameNew, settingsFileNameNew);
QFile fCode(luaFileNameOld);
QFile fSettings(settingsFileNameOld);
if(fCode.exists())
fCode.rename(luaFileNameNew);
if(fSettings.exists())
fSettings.rename(settingsFileNameNew);
}
StringSet SourceHighlightUtils::getOutLangFileNames(const std::string _path) {
string path = _path;
if (path == "")
path = Settings::retrieveDataDir();
return getFileNames(path, "outlang");
}
void TOPPASOutputFileListVertex::paint(QPainter* painter, const QStyleOptionGraphicsItem* /*option*/, QWidget* /*widget*/)
{
QPen pen(pen_color_, 1, Qt::SolidLine, Qt::FlatCap, Qt::MiterJoin);
if (isSelected())
{
pen.setWidth(2);
painter->setBrush(brush_color_.darker(130));
pen.setColor(Qt::darkBlue);
}
else
{
painter->setBrush(brush_color_);
}
painter->setPen(pen);
QPainterPath path;
path.addRoundRect(-70.0, -40.0, 140.0, 80.0, 20, 20);
painter->drawPath(path);
pen.setColor(pen_color_);
painter->setPen(pen);
QString text = QString::number(files_written_) + "/"
+ QString::number(files_total_) + " output file" + (files_total_ == 1 ? "" : "s");
QRectF text_boundings = painter->boundingRect(QRectF(0, 0, 0, 0), Qt::AlignCenter, text);
painter->drawText(-(int)(text_boundings.width() / 2.0), (int)(text_boundings.height() / 4.0), text);
// display file type(s)
Map<QString, Size> suffices;
foreach(QString fn, getFileNames())
{
QStringList l = QFileInfo(fn).completeSuffix().split('.');
QString suf = ((l.size() > 1 && l[l.size() - 2].size() <= 4) ? l[l.size() - 2] + "." : QString()) + l.back(); // take up to two dots as suffix (the first only if its <=4 chars, e.g. we want ".prot.xml" or ".tar.gz", but not "stupid.filename.with.longdots.mzML")
++suffices[suf];
}
TemporaryColumnMapper::TemporaryColumnMapper(const char * _path, size_t _tableId, size_t _columnId, aq::ColumnType _itemType, size_t _itemSize, size_t _packetSize)
:
nbRemap(0),
path(_path),
tableId(_tableId),
columnId(_columnId),
itemSize(_itemSize),
itemType(_itemType),
packetSize(_packetSize),
currentPacket(0)
{
char prefix[128];
char type_str[128];
switch (itemType)
{
case COL_TYPE_VARCHAR: strcpy(type_str, "CHA"); break;
case COL_TYPE_INT: strcpy(type_str, "INT"); break;
case COL_TYPE_DOUBLE: strcpy(type_str, "DOU"); break;
case COL_TYPE_BIG_INT:
case COL_TYPE_DATE:
strcpy(type_str, "LON");
break;
}
sprintf( prefix, "B001TMP%.4uC%.4u%s%.4uP", tableId, columnId, type_str, itemSize );
getFileNames(path.c_str(), this->temporaryFiles, prefix );
assert(!this->temporaryFiles.empty());
this->tmpMapper.reset(new aq::FileMapper(this->temporaryFiles[this->currentPacket].c_str()));
tmpMappers.resize(temporaryFiles.size());
}
void CMainFrame::OnFileOpen(int id) {
TextView *view = getActiveTextView();
if(view == NULL) {
showWarning(_T("No active view"));
return;
}
CFileDialog dlg(TRUE);
dlg.m_ofn.lpstrFilter = getFileDialogExtension().cstr();
dlg.m_ofn.lpstrTitle = _T("Open files");
dlg.m_ofn.nFilterIndex = getOptions().m_defaultExtensionIndex;
dlg.m_ofn.Flags |= OFN_ALLOWMULTISELECT | OFN_FILEMUSTEXIST;
TCHAR fileNames[1024];
fileNames[0] = 0;
dlg.m_ofn.lpstrFile = fileNames;
dlg.m_ofn.nMaxFile = ARRAYSIZE(fileNames);
if((dlg.DoModal() != IDOK) || (_tcsclen(fileNames) == 0)) {
return;
}
getOptions().m_defaultExtensionIndex = dlg.m_ofn.nFilterIndex;
TCHAR *files[3];
getFileNames(files,fileNames);
CWinDiffDoc *doc = view->getDocument();
if(_tcsclen(files[1]) == 0) { // only one selected
doc->setDoc(id, DIFFDOC_FILE, files[0]);
} else {
const String f1 = FileNameSplitter::getChildName(files[0],files[1]);
const String f2 = FileNameSplitter::getChildName(files[0],files[2]);
doc->setDocs(f1, f2);
}
Invalidate(FALSE);
}
StringSet SourceHighlightUtils::getCssStyleFileNames(const std::string _path) {
string path = _path;
if (path == "")
path = Settings::retrieveDataDir();
return getFileNames(path, "css");
}
void TOPPASInputFileListVertex::showFilesDialog()
{
TOPPASInputFilesDialog tifd(getFileNames(), cwd_);
if (tifd.exec())
{
QStringList updated_filelist;
tifd.getFilenames(updated_filelist);
if (getFileNames() != updated_filelist)
{ // files were changed
setFilenames(updated_filelist); // to correct filenames (separators etc)
qobject_cast<TOPPASScene *>(scene())->updateEdgeColors();
// update cwd
cwd_ = tifd.getCWD();
emit parameterChanged(true); // aborts the pipeline (if running) and resets downstream nodes
}
}
}
//remove files
void removeFiles(){
vector<string> fileNames;
getFileNames(&fileNames);
int size = fileNames.size();
for(int i=0; i<size; i++){
if(remove(fileNames[i].c_str())) {
printf("Could not delete the file");
}
}
}
bool LuaList::save(LuaContainer* container)
{
if(_filePath == "")
return false;
QString luaFileName, settingsFileName;
getFileNames(container->getName(), luaFileName, settingsFileName);
// save code
{
std::ofstream file;
file.open(luaFileName.toLocal8Bit().data(), std::ios::trunc);
if(!file.is_open())
{
std::cerr << "[Lua] can't open file " << luaFileName.toStdString() << std::endl;
return false;
}
std::string code;
#ifdef _WIN32
code = container->getCode().toLocal8Bit().constData();
#else
code = container->getCode().toUtf8().constData();
#endif
// rest = code
file << code;
file.flush();
file.close();
}
// save config
{
QSettings settings(settingsFileName, QSettings::IniFormat);
if(!settings.isWritable())
{
std::cerr << "[Lua] no write access for settings file " << settingsFileName.toStdString() << " -> aborting (code was saved)" << std::endl;
return false;
}
settings.clear();
container->getSettings(settings);
}
return true;
}
int chy(){
// get contents of file agent
getFileNames();
// rabin fingerprinting, SHA-1, extreme binning
rabinChunking();
// compare chunks
//comparePrints();
// remake new files from chunks
//remakeFiles();
return 0;
}
bool TrainSamplePage::serializeToStorage(QSettings& ini, const QString& directory) const
{
bool succ = true;
//copy files to target directory
QStringList fileNames = getFileNames();
foreach (const QString& fileName, fileNames) {
QString onlyName = fileName.mid(qMax(fileName.lastIndexOf("/"), fileName.lastIndexOf(QDir::separator())));
if (!QFile::copy(fileName, directory+QDir::separator()+onlyName)) {
kDebug() << "could not copy " << fileName << " to " << directory+QDir::separator()+onlyName;
fileNames.removeAll(fileName);
succ = false;
}
else {
if (!QFile::remove(fileName))
kWarning() << "Could not remove original input file!";
}
}
static void generalStreamReg(HRSstream_t s, void *tf)
{
s->type = HRS_GENERALSTREAM;
s->gs = (generalStream_s *) HRSmalloc(sizeof(generalStream_s),
"generalStreamReg");
s->bs = NULL;
s->ms = NULL;
if (strcmp(s->streamName, "sfstdin") == 0 ||
(strcmp(s->streamName, "stdin") == 0)) {
s->gs->numFileNames = 0;
s->gs->numFilesinStream = 1; /* count standard in stream as one file */
s->gs->fileNames = NULL;
s->gs->sio = 1; /* standard in stream */
}
else if (isDir(s->streamName)) {
s->gs->numFileNames = countFiles(s->streamName);
s->gs->fileNames = (char **) HRSmalloc(sizeof(char *)*s->gs->numFileNames,
"generalStreamReg");
getFileNames(s->streamName, s->gs->fileNames, 0);
s->gs->numFilesinStream = s->gs->numFileNames;
s->gs->sio = 0;
}
else { /* single file stream */
s->gs->numFileNames = 1;
s->gs->fileNames = (char **) HRSmalloc(sizeof(char *)*s->gs->numFileNames,
"generalStreamReg");
s->gs->fileNames[0] = (char *) HRSmalloc(strlen(s->streamName)+1,
"generalStreamReg");
strcpy(s->gs->fileNames[0], s->streamName);
checkStreamFile(s->gs->fileNames[0], 0);
s->gs->numFilesinStream = s->gs->numFileNames;
s->gs->sio = 0;
}
s->gs->count = 0;
s->gs->translate = (int (*)(char, void *, Sfio_t *, char *))tf;
s->gs->filter = NULL;
}
static void binaryStreamReg(HRSstream_t s,int physicalSize, void *tf)
{
s->type = HRS_BINARYSTREAM;
s->bs = (binaryStream_s *) HRSmalloc(sizeof(binaryStream_s),
"binaryStreamReg");
s->gs = NULL;
s->ms = NULL;
s->bs->physicalSize = physicalSize;
s->bs->temp = (char *) HRSmalloc(physicalSize, "binaryStreamReg");
if (strcmp(s->streamName, "sfstdin") == 0 ||
(strcmp(s->streamName, "stdin") == 0)) {
s->bs->numFileNames = 0;
s->bs->numFilesinStream = 1; /* count standard in stream as one file */
s->bs->fileNames = NULL;
s->bs->sio = 1; /* standard in stream */
}
else if (isDir(s->streamName)) {
s->bs->numFileNames = countFiles(s->streamName);
s->bs->fileNames = (char **) HRSmalloc(sizeof(char *)*s->bs->numFileNames,
"binaryStreamReg");
getFileNames(s->streamName, s->bs->fileNames, physicalSize);
s->bs->numFilesinStream = s->bs->numFileNames;
s->bs->sio = 0;
}
else { /* single file stream */
s->bs->numFileNames = 1;
s->bs->fileNames = (char **) HRSmalloc(sizeof(char *), "binaryStreamReg");
s->bs->fileNames[0] = (char *) HRSmalloc(strlen(s->streamName)+1,
"binaryStreamReg");
strcpy(s->bs->fileNames[0], s->streamName);
checkStreamFile(s->bs->fileNames[0], physicalSize);
s->bs->numFilesinStream = s->bs->numFileNames;
s->bs->sio = 0;
}
s->bs->count = 0;
s->bs->translate = (int (*)(char, void *, char *, char *))tf;
s->bs->filter = NULL;
}
void CMakeAviDlg::OnFileAddfFiles() {
CFileDialog dlg(TRUE);
dlg.m_ofn.lpstrFilter = fileDialogExtensions;
dlg.m_ofn.lpstrTitle = _T("Add files");
dlg.m_ofn.Flags |= OFN_ALLOWMULTISELECT | OFN_FILEMUSTEXIST;
#define NAMEBUFFERLENGTH 500000
TCHAR *nameBuffer = new TCHAR[NAMEBUFFERLENGTH];
nameBuffer[0] = 0;
dlg.m_ofn.lpstrFile = nameBuffer;
dlg.m_ofn.nMaxFile = NAMEBUFFERLENGTH;
if(dlg.DoModal() == IDOK) {
m_nameArray = getFileNames(nameBuffer);
m_nameArray.sort(stringCmp);
m_nameList.DeleteAllItems();
for(size_t i = 0; i < m_nameArray.size(); i++) {
addData(m_nameList, (int)i, 0, m_nameArray[i], true);
}
Invalidate();
}
delete[] nameBuffer;
}
KoResourceLoaderThread::KoResourceLoaderThread(KoResourceServerBase * server)
: QThread()
, m_server(server)
{
m_fileNames = getFileNames(m_server->extensions());
}
Args *getArgs(int argc, char *argv[]){
Args *args;
// char **r;
char c;
int arg;
// int numberOfFiles;
char list[256] = {0}; // options are not yet set
args = (Args *)emalloc(sizeof(Args));
args->i = NULL;
args->j = NULL;
args->o = NULL;
args->h = 0;
args->p = 0;
args->e = 0;
args->d = NULL;
args->n = NAMELENGTH;
args->D = DEFAULT_D;
args->w = DEFAULT_W;
args->c = 0;
args->q = 10000;
args->W = NULL;
args->P = 1-DEFAULT_P;
args->v = 0;
arg = 1;
args->m = DEFAULT_M;
args->t = 0;
args->r = 0;
args->s = 0;
args->f = -1;
// if none of the options is set as an argument, then take o1
args->o1 = 0;
args->o2 = 0;
args->I = NULL;
args->M = 0; // default min window sum to be considered relevant
while(arg < argc){
c = argv[arg][1];
switch (c){
case 'i': /* query file; if the option -d is included */
checkNullPointer(c, argv[arg]);
//args->i = argv[arg]; /* then search for the query file: (1) in the program's dir (2) in the directory specified with -d*/
// read one or more query files specified with an option -i
getFileNames(argc, argv, list, c, &args->i, &args->queryFileNumber, &arg);
break;
case 'j': /* subject files */
/* check that -d and -j option are used mutually exclusive! */
if (args->d) {
eprintf("Options -d and -j are mutually exclusive");
}
else {
getFileNames(argc, argv, list, c, &args->j, &args->subjectFileNumber, &arg);
break;
}
case 'd': /* directory where the subject files are saved and possibly the query file */
if (args->j) {
eprintf("Options -d and -j are mutually exclusive");
}
else {
args->d = argv[++arg];
checkNullPointer(c, args->d);
checkMultipleArgDef(list, c);
break;
}
case 'o': /* output file */
checkNullPointer(c, argv[++arg]);
args->o = argv[arg];
checkMultipleArgDef(list, c);
break;
case 'n': /* number of characters from header line printed */
checkNullPointer(c, argv[++arg]);
args->n = atoi(argv[arg]);
if(args->n < 0) {
args->n = INT_MAX;
}
checkMultipleArgDef(list, c);
break;
case 'D': /* maximum depth of suffix tree */
args->D = atoi(argv[++arg]);
checkNullPointer(c, argv[arg]);
checkMultipleArgDef(list, c);
break;
case 'w': /* window width and window increment */
checkNullPointer(c, argv[++arg]);
args->w = atoi(argv[arg]);
checkMultipleArgDef(list, c);
break;
case 'c': /* sliding window increment */
checkNullPointer(c, argv[++arg]);
args->c = atoi(argv[arg]);
checkMultipleArgDef(list, c);
break;
case 'v': /* print program version test */
args->v = 1;
break;
case 'h': /* print help */
args->h = 1;
break;
case 'W': /* output file where window analysis for all subjects are printed */
args->W = argv[++arg];
checkNullPointer(c, args->W);
checkMultipleArgDef(list, c);
break;
case 'P': /* fraction of random shustrings excluded from analysis */
args->P = atof(argv[++arg]);
if (args->P < 0) {
args->P = 0;
}
else if(args->P > 1) {
args->P = 1;
}
args->P = 1 - args->P;
break;
case 'q': /* fast search - size of mini list*/
args->q = atol(argv[++arg]);
if (args->q < 0) {
args->q = 1000;
}
break;
case 'm': /* multiplier for maxshulen by chance alone -- used for defining significant intervals */
args->m = atol(argv[++arg]);
if (args->m < 0) {
args->m = DEFAULT_M;
}
break;
case 't': /* print run-time information */
args->t = 1;
break;
case 'r': /* print runner(s)-up information */
args->r = 1;
break;
case 'f': /* minimal length of recombination fragment */
args->f = atoi(argv[++arg]);
//if (args->f < 0) {
// args->f = (int)args->w;
//}
break;
case 'o1': /* each annotation has the same subject set over all windows within annotation */
args->o1 = 1;
break;
case 'o2': /* subject set of an annotation is a subset of all windows within annotation */
args->o2 = 1;
break;
case 'M': /* minimal sum: max shulen by chance alone x window size */
args->M = 1;
break;
case 'I': /* name of input file that contains list of intervals; used for windows analysis based on precomputed intervals */
args->I = argv[++arg];
checkNullPointer(c, args->I);
checkMultipleArgDef(list, c);
break;
default:
printf("# unknown argument: %c\n", c);
args->e = 1;
return args;
} // end switch
arg++;
} // end while
// allowed stdin?
// if (!args->i) {
// printf("ERROR[gt]: Query file must be specified using -i option!\n");
// args->e = 1;
//}
if (args->c == 0) {
args->c = (int)((float)args->w/10. + 0.5);
}
if (args->f < 0) {
//args->f = (int)args->c;
args->f = (int)((float)args->w / 4. + 0.5);
}
if (args->w < args->c) {
printf("ERROR: Sliding window increment is greater than window size\n");
args->e = 1;
}
if (!args->o1 && !args->o2) {
args->o1 = 1; // when none of the options is set, set o1 as default
}
else if (args->o1 && args->o2) {
printf("ERROR: Options 1 and 2 are mutually exclusive\n");
args->e = 1;
}
if (args->o && args->I) {
printf("Interval analysis exists, so it won't be computed again (-o will be ignored)\n");
}
return args;
}
bool TrainSamplePage::cleanUp()
{
bool succ=true;
if (recorder->hasRecordingReady()) {
succ = recorder->deleteAll();
if (!succ)
KMessageBox::error(this, i18nc("%1 is file names", "Could not remove samples \"%1\".", getFileNames().join("\", \"")));
}
return succ;
}
static void removeFiles(std::vector<FileFragment> const & V)
{
std::vector<std::string> S = getFileNames(V);
for ( uint64_t i = 0; i < S.size(); ++i )
remove ( S[i].c_str() );
}
bool LuaList::load(const QString& name, LuaContainer* container, bool ignoreNoSettingsFile)
{
if(_filePath == "")
return false;
// set name
container->setName(name);
QString luaFileName, settingsFileName;
getFileNames(name, luaFileName, settingsFileName);
// load code
{
// check whether file exists
if(!QFile::exists(luaFileName))
{
std::cerr << "[Lua] can't find Lua file, checking templates" << luaFileName.toStdString() << std::endl;
QString templatename(_templateFilePath + name);
if(QFile::exists(templatename))
{
if(!QFile::copy(templatename, luaFileName))
{
return false;
}
}else{
std::cerr << "[Lua] can't find Lua file in templates" << templatename.toStdString() << std::endl;
return false;
}
}
std::ifstream file;
file.open(luaFileName.toLocal8Bit().data(), std::ios::in);
if(!file.good() || !file.is_open())
{
std::cerr << "[Lua] can't open file " << luaFileName.toStdString() << std::endl;
return false;
}
std::string line, c = "";
while(!file.eof())
{
std::getline(file, line);
c += line;
// don't add \n at the end of the file
if(!file.eof())
c += '\n';
}
container->setCode(c);
file.close();
}
// load config
{
// check whether file exists
if(!QFile::exists(settingsFileName))
{
if(ignoreNoSettingsFile)
{
std::cerr << "[Lua] can't find settings file " << settingsFileName.toStdString() << " -> continuing" << std::endl;
return true;
} else
{
std::cerr << "[Lua] can't find settings file " << settingsFileName.toStdString() << " -> aborting" << std::endl;
return false;
}
}
QSettings settings(settingsFileName, QSettings::IniFormat);
container->loadSettings(settings);
}
return true;
}
