void FileReaderEditor::setFile(String file)
{
File fileToRead(file);
lastFilePath = fileToRead.getParentDirectory();
fileReader->setFile(fileToRead.getFullPathName());
fileNameLabel->setText(fileToRead.getFileName(), dontSendNotification);
setEnabledState(true);
repaint();
}
void JuliaProcessorEditor::setFile(String file)
{
File fileToRead(file);
lastFilePath = fileToRead.getParentDirectory();
juliaProcessor->setFile(fileToRead.getFullPathName());
fileNameLabel->setText(fileToRead.getFileName(), dontSendNotification);
//setEnabledState(true);
//icon->setOpacity(1.0f); // tie this to hasJuliaInstance instead of just setting it!
repaint();
}
void funcInputData()
{
/* Example of Input files :
* numberofInputs (not existing now)
* NameofRNA
* ProteinSequence
* ... * numberofInputs
*
* CDSforA
* 455 1000
* (string of sequences~)
* ... * numberofInputs
*/
pFONTElementRef->ToElement()->SetAttribute("face", "consolas");
structRna xRna[4]; // Assume there is only 4 input.
int iNumberofInput ; // Fix variable for now, but made for If there are more inputs
//Deal with Proteins
std::ifstream fileToRead("data.txt");
fileToRead >> iNumberofInput;
{
std::string tmpFlush;
getline(fileToRead, tmpFlush);
}
for(int xIterator = 0 ; xIterator < iNumberofInput ; ++xIterator )
{
getline( fileToRead, xRna[xIterator].sName );
getline( fileToRead, xRna[xIterator].sProteinSequence );
}
funcCompare(xRna, iNumberofInput);
//Deal with Sequences
for(int xIterator = 0 ; xIterator < iNumberofInput ; ++xIterator )
{
int tmpCDSstarts;
int tmpCDSends;
std::string tmpString;
fileToRead >> tmpCDSstarts >> tmpCDSends;
fileToRead >> tmpString;
for(int xCurrentPos = tmpCDSstarts-1 ; xCurrentPos < tmpCDSends ; ++xCurrentPos){
xRna[xIterator].sSequenceBetweenCDS.push_back(tmpString[xCurrentPos]);
} // inner for
} // outer for
funcSequenceCompare(xRna, iNumberofInput);
}
void LinkBackupThread::processDir(QDir& currentFromDir, QDir& currentToDir)
{
long numErrors = getLogger().errorCount();
if (numErrors > 1000)
{
QString errorMessage = QString("%1 errors found, quit?");
QMessageBox::StandardButton reply = QMessageBox::question(nullptr, "Test", errorMessage, QMessageBox::Yes|QMessageBox::No);
if (reply == QMessageBox::Yes) {
requestCancel();
} else {
getLogger().clearErrorCount();
}
}
TRACE_MSG(QString("Processing directory %1").arg(currentFromDir.canonicalPath()), 1);
// Process directories, then process files.
QList<QFileInfo> list = currentFromDir.entryInfoList(QDir::Dirs | QDir::NoDotAndDotDot | QDir::NoSymLinks | QDir::Hidden | QDir::Readable);
QFileInfo info;
foreach (info, list) {
if (isCancelRequested()) {
return;
}
TRACE_MSG(QString("Found Dir to processes %1").arg(info.canonicalFilePath()), 2);
if (passes(info))
{
DEBUG_MSG(QString("Dir Passes: %1").arg(info.canonicalFilePath()), 2);
if (!currentToDir.mkdir(info.fileName())) {
ERROR_MSG(QString("Failed to create directory %1/%2").arg(currentToDir.canonicalPath(), info.fileName()), 1);
} else if (!currentToDir.cd(info.fileName())) {
ERROR_MSG(QString("Failed to cd to directory %1/%2").arg(currentToDir.canonicalPath(), info.fileName()), 1);
} else if (!currentFromDir.cd(info.fileName())) {
ERROR_MSG(QString("Failed to cd to directory %1/%2").arg(currentFromDir.canonicalPath(), info.fileName()), 1);
if (!currentToDir.cdUp()) {
ERROR_MSG("Failed to cd up a directory for the to directory", 1);
requestCancel();
return;
}
} else {
processDir(currentFromDir, currentToDir);
if (!currentToDir.cdUp()) {
ERROR_MSG("Failed to cd up a directory for the to directory", 1);
requestCancel();
return;
}
if (!currentFromDir.cdUp()) {
ERROR_MSG("Failed to cd up a directory for the from directory", 1);
requestCancel();
return;
}
}
}
else
{
DEBUG_MSG(QString("Skipping Dir: %1").arg(info.canonicalFilePath()), 2);
}
}
// Now handle files
list = currentFromDir.entryInfoList(QDir::Files | QDir::NoSymLinks | QDir::Hidden | QDir::Readable);
foreach (info, list) {
if (isCancelRequested()) {
return;
}
QString fullPathFileToRead = info.canonicalFilePath();
//TRACE_MSG(QString("Found File to test %1").arg(fullPathFileToRead), 2);
if (passes(info))
{
//TRACE_MSG(QString("File passes %1").arg(fullPathFileToRead), 2);
QFile fileToRead(fullPathFileToRead);
// Just in case someone deleted the file.
if (fileToRead.exists())
{
DBFileEntry* currentEntry = new DBFileEntry(info, m_fromDirWithoutTopDirName);
const DBFileEntry* linkEntry = m_oldEntries->findEntry(m_backupSet.getCriteria(), currentEntry, m_fromDirWithoutTopDirName);
QString pathToLinkFile = m_previousDirRoot;
// If not in the old backup, search the current backup.
if (linkEntry == nullptr)
{
linkEntry = m_currentEntries->findEntry(m_backupSet.getCriteria(), currentEntry, m_fromDirWithoutTopDirName);
pathToLinkFile = m_toDirRoot;
}
if (linkEntry == nullptr)
{
bool failedToCopy = false;
QString fullFileNameToWrite = m_toDirRoot + "/" + currentEntry->getPath();
bool needHash = (currentEntry->getHash().length() == 0);
if (needHash)
{
failedToCopy = !::getCopyLinkUtil().copyFileGenerateHash(fullPathFileToRead, fullFileNameToWrite);
if (!failedToCopy)
{
currentEntry->setHash(getCopyLinkUtil().getLastHash());
}
}
else if (!getCopyLinkUtil().copyFile(fullPathFileToRead, fullFileNameToWrite))
{
failedToCopy = true;
}
if (failedToCopy)
{
ERROR_MSG(QString(tr("EC %1")).arg(currentEntry->getPath()), 1);
}
else
{
INFO_MSG(QString(tr("C %1")).arg(currentEntry->getPath()), 1);
currentEntry->setLinkTypeCopy();
m_currentEntries->addEntry(currentEntry);
currentEntry = nullptr;
}
}
else
{
if (getCopyLinkUtil().linkFile(pathToLinkFile + "/" + linkEntry->getPath(), m_toDirRoot + "/" + currentEntry->getPath()))
{
currentEntry->setLinkTypeLink();
currentEntry->setHash(linkEntry->getHash());
m_currentEntries->addEntry(currentEntry);
INFO_MSG(QString(tr("L %1")).arg(currentEntry->getPath()), 1);
currentEntry = nullptr;
}
else
{
ERROR_MSG(QString(tr("EL %1")).arg(currentEntry->getPath()), 1);
ERROR_MSG(QString(tr("(%1)(%2)(%3)")).arg(pathToLinkFile, linkEntry->getPath(), m_toDirRoot), 1);
}
}
if (currentEntry != nullptr)
{
delete currentEntry;
currentEntry= nullptr;
}
}
}
}
TRACE_MSG(QString("Finished with directory %1").arg(currentFromDir.canonicalPath()), 1);
}
