Caller::Caller( const double poissonLambda, const int minDepth, const double leftStrandBias, const double rightStrandBias, const double readEndFraction, const int qCutoff, const char* tumorDirectoryPath, const char* benignDirectoryPath, const char* outputDirectoryPath, const int usePoissonGermline, const int disableLvl5Filter)
{
this->poissonLambda = poissonLambda;
this->minDepth = minDepth;
this->strandBiasLeft = leftStrandBias;
this->strandBiasRight = rightStrandBias;
this->minQScore = qCutoff;
this->readEndFraction = readEndFraction;
this->usePoissonGermline = usePoissonGermline;
this->disableLvl5Filter = disableLvl5Filter;
( this->tumorDirectoryPath).assign( tumorDirectoryPath);
( this->benignDirectoryPath).assign( benignDirectoryPath);
( this->outputDirectoryPath).assign( outputDirectoryPath);
Common::getFilesInDir( this->tumorDirectoryPath, tumorPaths);
std::sort( tumorPaths.begin(), tumorPaths.end());
Common::getFilesInDir( this->benignDirectoryPath, benignPaths);
std::sort( benignPaths.begin(), benignPaths.end());
for( int i = 0; i < tumorPaths.size(); i++)
{
std::string nextTumorSamplePath = this->tumorDirectoryPath + "/" + tumorPaths[i];
std::string nextBenignSamplePath = this->benignDirectoryPath + "/" + benignPaths[i];
loadEntries( nextTumorSamplePath);
loadEntries( nextBenignSamplePath);
}
}
void MainWindow::on_actionAdd_New_Entry_triggered()
{
NewEntryChooser entryChooser(this, xdbf);
entryChooser.exec();
loadEntries();
}
void MainWindow::on_actionOpen_triggered()
{
QString file_name = QFileDialog::getOpenFileName(this, tr("Open File"), desktop_location, "*.gpd");
if(file_name == NULL)
return;
if(xdbf != NULL)
{
xdbf->close();
xdbf = NULL;
}
QByteArray ba = file_name.toAscii();
name = ba.data();
try
{
xdbf = new XDBF(name);
loadEntries();
}
catch (...)
{
QMessageBox::critical(this, "Error", "An unknown error occured while opening the GPD!");
return;
}
ui->actionAdd_New_Entry->setEnabled(true);
ui->actionExtract_All->setEnabled(true);
ui->actionClean_GPD->setEnabled(true);
ui->actionAddress_Converter->setEnabled(true);
ui->actionClose->setEnabled(true);
return;
}
Caller::Caller( const double poissonLambda, const int minDepth, const double leftStrandBias, const double rightStrandBias, const double readEndFraction, const int qCutoff, const char* tumorDirectoryPath, const char* outputDirectoryPath, const int usePoissonGermline, const int disableLvl5Filter)
{
this->poissonLambda = poissonLambda;
this->minDepth = minDepth;
this->strandBiasLeft = leftStrandBias;
this->strandBiasRight = rightStrandBias;
this->minQScore = qCutoff;
this->readEndFraction = readEndFraction;
this->usePoissonGermline = usePoissonGermline;
this->disableLvl5Filter = disableLvl5Filter;
( this->tumorDirectoryPath).assign( tumorDirectoryPath);
( this->outputDirectoryPath).assign( outputDirectoryPath);
// Setup output files
( this->outputPaths).push_back( this->outputDirectoryPath + "/calls_level1.sinvict");
( this->outputPaths).push_back( this->outputDirectoryPath + "/calls_level2.sinvict");
( this->outputPaths).push_back( this->outputDirectoryPath + "/calls_level3.sinvict");
( this->outputPaths).push_back( this->outputDirectoryPath + "/calls_level4.sinvict");
( this->outputPaths).push_back( this->outputDirectoryPath + "/calls_level5.sinvict");
( this->outputPaths).push_back( this->outputDirectoryPath + "/calls_level6.sinvict");
Common::getFilesInDir( this->tumorDirectoryPath, tumorPaths);
std::sort( tumorPaths.begin(), tumorPaths.end());
for( int i = 0; i < tumorPaths.size(); i++)
{
std::string nextTumorSamplePath = this->tumorDirectoryPath + "/" + tumorPaths[i];
loadEntries( nextTumorSamplePath);
}
calculateStatistics();
}
Private()
{
KConfigGroup grp(KGlobal::config(), "RecentFiles");
maxItems = grp.readEntry("maxRecentFileItems", 100);
loadEntries(grp);
}
void Serializer::saveOrLoadEntries(Entry *entry) {
debug(DBG_SER, "Serializer::saveOrLoadEntries() _mode=%d", _mode);
_bytesCount = 0;
switch (_mode) {
case SM_SAVE:
saveEntries(entry);
break;
case SM_LOAD:
loadEntries(entry);
break;
}
debug(DBG_SER, "Serializer::saveOrLoadEntries() _bytesCount=%d", _bytesCount);
}
activityLogger::activityLogger(QWidget *parent) : QMainWindow(parent), ui(new Ui::activityLogger){
QTimer *timer = new QTimer(this);
connect(timer, SIGNAL(timeout()), this, SLOT(onUpdate()));
timer->start(10);
this->setWindowIcon(QIcon(":/icon/icon.ico"));
ui->setupUi(this);
pause_offset=0;
epoch=-1;
loadActivities();
loadEntries();
foreach(QListWidgetItem item,activities){
ui->activityList->addItem(new QListWidgetItem(item.text()));
}
FAT16Analyzer::FAT16Analyzer(char *fname)
{
this->fs = fopen(fname, "rb+");
if (fs == NULL)
{
printf("Erro ao abrir o arquivo com o sistema de arquivo.\n\n");
exit(1);
}
fat1 = NULL;
fat2 = NULL;
loadEntries();
}
void MainWindow::on_actionNew_triggered()
{
bool a = false;
NewGpdDialog dialog(this, &xdbf, &a);
dialog.exec();
if (!a)
return;
loadEntries();
ui->actionAdd_New_Entry->setEnabled(true);
ui->actionExtract_All->setEnabled(true);
ui->actionClean_GPD->setEnabled(true);
ui->actionAddress_Converter->setEnabled(true);
ui->actionClose->setEnabled(true);
}
MainWindow::MainWindow(QWidget *parent, string filePath) : QMainWindow(parent), ui(new Ui::MainWindow)
{
desktop_location = QDesktopServices::storageLocation(QDesktopServices::DesktopLocation);
ObjectRole = Qt::UserRole;
ui->setupUi(this);
friendlyNames[0] = "Achievement";
friendlyNames[1] = "Image";
friendlyNames[2] = "Setting";
friendlyNames[3] = "Title";
friendlyNames[4] = "String";
friendlyNames[5] = "Avatar Award";
QStringList columnHeaders;
columnHeaders.push_back("ID");
columnHeaders.push_back("Size");
columnHeaders.push_back("Offset");
columnHeaders.push_back("Type");
ui->tableWidget->setColumnCount(columnHeaders.length());
ui->tableWidget->setHorizontalHeaderLabels(columnHeaders);
xdbf = NULL;
ui->tableWidget->setContextMenuPolicy(Qt::CustomContextMenu);
connect(ui->tableWidget, SIGNAL(customContextMenuRequested(QPoint)), this, SLOT(showRemoveContextMenu(QPoint)));
if (filePath != "")
{
try
{
xdbf = new XDBF(filePath);
loadEntries();
ui->actionAdd_New_Entry->setEnabled(true);
ui->actionExtract_All->setEnabled(true);
ui->actionClean_GPD->setEnabled(true);
ui->actionAddress_Converter->setEnabled(true);
ui->actionClose->setEnabled(true);
}
catch (...)
{
QMessageBox::critical(this, "Error", "An unknown error occured while opening the GPD!");
return;
}
}
}
XdbfDialog::XdbfDialog(QStatusBar *statusBar, GpdBase *gpd, bool *modified, QWidget *parent) :
QDialog(parent), ui(new Ui::XdbfDialog), gpd(gpd), modified(modified), statusBar(statusBar)
{
ui->setupUi(this);
setWindowFlags(windowFlags() & ~Qt::WindowContextHelpButtonHint);
ui->treeWidget->header()->resizeSection(0, 260);
loadEntries();
// display the gpd name
for (DWORD i = 0; i < gpd->strings.size(); i++)
if (gpd->strings.at(i).entry.id == TitleInformation)
{
if (gpd->strings.at(i).ws != L"")
setWindowTitle("Xdbf Viewer - " + QString::fromStdWString(gpd->strings.at(i).ws));
break;
}
ui->treeWidget->setContextMenuPolicy(Qt::CustomContextMenu);
connect(ui->treeWidget, SIGNAL(customContextMenuRequested(QPoint)), this, SLOT(showContextMenu(QPoint)));
}
void XdbfDialog::showContextMenu(QPoint p)
{
if (ui->treeWidget->selectedItems().count() < 1)
return;
QPoint globalPos = ui->treeWidget->mapToGlobal(p);
QMenu contextMenu;
contextMenu.addAction(QPixmap(":/Images/extract.png"), "Extract Selected");
if (ui->treeWidget->selectedItems().count() == 1)
contextMenu.addAction(QPixmap(":/Images/replace.png"), "Replace Entry");
contextMenu.addSeparator();
contextMenu.addAction(QPixmap(":/Images/convert.png"), "Address Converter");
contextMenu.addSeparator();
contextMenu.addAction(QPixmap(":/Images/clean.png"), "Clean");
QAction *selectedItem = contextMenu.exec(globalPos);
if (selectedItem == NULL)
return;
else if (selectedItem->text() == "Extract Selected")
{
QList<QTreeWidgetItem*> items = ui->treeWidget->selectedItems();
// get the out path
QString path;
if (items.count() > 1)
path = QFileDialog::getExistingDirectory(this, "Extract Directory", QtHelpers::DesktopLocation()) + "/";
else
path = QFileDialog::getSaveFileName(this, "Choose a place to extract the entry", QtHelpers::DesktopLocation() + "/" + ui->treeWidget->currentItem()->text(0));
if (path == "" || path == "\\")
return;
try
{
for (int i = 0; i < items.count(); i++)
{
int index = -1;
for (int x = 0; x < ui->treeWidget->topLevelItemCount(); x++)
if (ui->treeWidget->topLevelItem(x) == items.at(i))
{
index = x;
break;
}
Entry e = indexToEntry(index);
XdbfEntry xentry;
// get the xdbf entry
if (e.type == Achievement)
xentry = gpd->xdbf->achievements.entries.at(e.index);
else if (e.type == Image)
xentry = gpd->xdbf->images.at(e.index);
else if (e.type == Setting)
xentry = gpd->xdbf->settings.entries.at(e.index);
else if (e.type == Title)
xentry = gpd->xdbf->titlesPlayed.entries.at(e.index);
else if (e.type == String)
xentry = gpd->xdbf->strings.at(e.index);
else if (e.type == AvatarAward)
xentry = gpd->xdbf->avatarAwards.entries.at(e.index);
// extract the entry into memory
BYTE *entryBuff = new BYTE[xentry.length];
gpd->xdbf->ExtractEntry(xentry, entryBuff);
QString outPath = path;
if (items.count() > 1)
outPath += items.at(i)->text(0);
// Write the data to a file
FileIO io(outPath.toStdString(), true);
io.Write(entryBuff, xentry.length);
io.Close();
// free the temporary memory
delete[] entryBuff;
}
statusBar->showMessage("Selected entries extracted successfully", 3000);
}
catch (string error)
{
QMessageBox::critical(this, "Error", "An error occurred while extracting.\n\n" + QString::fromStdString(error));
}
}
else if (selectedItem->text() == "Replace Entry")
{
QString entryPath = QFileDialog::getOpenFileName(this, "Open the entry to replace the current with", QtHelpers::DesktopLocation() + "/" + ui->treeWidget->currentItem()->text(0));
if (entryPath == "")
return;
try
{
Entry e = indexToEntry(ui->treeWidget->currentIndex().row());
XdbfEntry xentry;
// get the xdbf entry
if (e.type == Achievement)
xentry = gpd->xdbf->achievements.entries.at(e.index);
else if (e.type == Image)
xentry = gpd->xdbf->images.at(e.index);
else if (e.type == Setting)
xentry = gpd->xdbf->settings.entries.at(e.index);
else if (e.type == Title)
xentry = gpd->xdbf->titlesPlayed.entries.at(e.index);
else if (e.type == String)
xentry = gpd->xdbf->strings.at(e.index);
else if (e.type == AvatarAward)
xentry = gpd->xdbf->avatarAwards.entries.at(e.index);
// open the file and get the length
FileIO io(entryPath.toStdString());
io.SetPosition(0, ios_base::end);
DWORD fileLen = io.GetPosition();
// allocate enough memory for the buffer
BYTE *entryBuff = new BYTE[fileLen];
// read in the file
io.SetPosition(0);
io.ReadBytes(entryBuff, fileLen);
xentry.length = fileLen;
gpd->xdbf->ReWriteEntry(xentry, entryBuff);
// cleanup
delete[] entryBuff;
io.Close();
if (modified != NULL)
*modified = true;
// get the xdbf entry again so we can update the UI
if (e.type == Achievement)
xentry = gpd->xdbf->achievements.entries.at(e.index);
else if (e.type == Image)
xentry = gpd->xdbf->images.at(e.index);
else if (e.type == Setting)
xentry = gpd->xdbf->settings.entries.at(e.index);
else if (e.type == Title)
xentry = gpd->xdbf->titlesPlayed.entries.at(e.index);
else if (e.type == String)
xentry = gpd->xdbf->strings.at(e.index);
else if (e.type == AvatarAward)
xentry = gpd->xdbf->avatarAwards.entries.at(e.index);
// update the entry in the UI
QTreeWidgetItem *item = ui->treeWidget->selectedItems().at(0);
item->setText(1, "0x" + QString::number(gpd->xdbf->GetRealAddress(xentry.addressSpecifier), 16).toUpper());
item->setText(2, "0x" + QString::number(xentry.length, 16).toUpper());
statusBar->showMessage("Entry replaced successfully", 3000);
}
catch (string error)
{
QMessageBox::critical(this, "Error", "An error occurred while replacing.\n\n" + QString::fromStdString(error));
}
}
else if (selectedItem->text() == "Address Converter")
{
AddressConverterDialog dialog(gpd->xdbf, this);
dialog.exec();
}
else if (selectedItem->text() == "Clean")
{
int btn = QMessageBox::question(this, "Continue?", "Cleaning the Gpd will remove all of the unused memory that is in the file. This could potentially reduce the size of the Gpd.\n\nDo you want to continue?", QMessageBox::Yes, QMessageBox::No);
if (btn != QMessageBox::Yes)
return;
// clean the Gpd
try
{
gpd->xdbf->Clean();
}
catch (std::string error)
{
QMessageBox::critical(this, "Clean Error", "An error occured while cleaning the Gpd.\n\n" + QString::fromStdString(error));
return;
}
// reload the listing
ui->treeWidget->clear();
loadEntries();
if (modified != NULL)
*modified = true;
statusBar->showMessage("Cleaned Gpd successfully", 3000);
}
}
Wad::Wad(const Path& path) :
m_file(Disk::openFile(path)) {
if (m_file == NULL)
throw AssetException("Cannot open wad file " + path.asString());
loadEntries();
}
