void RefSeqManager::AddRef(std::string ref_fa_filename, std::string ref_name) {
std::ifstream file(ref_dir_ + "/" + ref_fa_filename);
if (file.is_open() == false) {
std::cerr << "Error: Could not open FASTA file " << ref_fa_filename << std::endl;
file.close();
return;
}
file.close();
// Check if fpga files are already built
bool all_files_present = true;
file.open(ref_dir_ + "/" + ref_name + ".meta");
all_files_present &= file.is_open();
file.close();
for (int i = 0; i < NUM_FPGAS; i++) {
file.open(ref_dir_ + "/" + ref_name + "." + std::to_string(i) + ".fpga2bit");
all_files_present &= file.is_open();
file.close();
}
// Build the fpga files if needed
if (all_files_present == false) {
BuildFpgaFiles(ref_fa_filename, ref_name);
}
// Load the fpga files
LoadRef(ref_fa_filename, ref_name);
// Initialize and add a mutex for ref seq file
pthread_mutex_t ref_mutex;
pthread_mutex_init(&ref_mutex, NULL);
ref_fd_mutex_.push_back(ref_mutex);
}
MainWindow::MainWindow( QWidget * parent)
: QMainWindow(parent)
{
setupUi(this);
version = "2015-08-28";
inimage = false;
x1drag = false;
x2drag = false;
y1drag = false;
y2drag = false;
image = QImage();
pixmap = scene.addPixmap(QPixmap());
pixmap->setZValue(0);
QPen pen;
pen.setColor(QColor(255,255,0));
pen.setStyle(Qt::DashLine);
// limit lines
x1line = scene.addLine(QLineF(), pen);
x1line->setZValue(1);
x2line = scene.addLine(QLineF(), pen);
x2line->setZValue(1);
y1line = scene.addLine(QLineF(), pen);
y1line->setZValue(1);
y2line = scene.addLine(QLineF(), pen);
y2line->setZValue(1);
pen.setColor(QColor(255,0,0));
pen.setStyle(Qt::SolidLine);
// projections, beam profile, centroid
xprojection = scene.addPath(QPainterPath(), pen);
xprojection->setZValue(2);
yprojection = scene.addPath(QPainterPath(), pen);
yprojection->setZValue(2);
ellipse = scene.addEllipse(0,0,0,0, pen);
ellipse->setZValue(2);
centerAline = scene.addLine(QLineF(), pen);
centerAline->setZValue(2);
centerBline = scene.addLine(QLineF(), pen);
centerBline->setZValue(2);
QObject::connect(&scene, SIGNAL(mouseMoved()), this, SLOT(mouseMovedOnScene()));
QObject::connect(&scene, SIGNAL(mousePressed()), this, SLOT(mousePressedOnScene()));
QObject::connect(&scene, SIGNAL(mouseReleased()), this, SLOT(mouseReleasedOnScene()));
QObject::connect(&scene, SIGNAL(mouseLeft()), this, SLOT(mouseLeftScene()));
graphicsView->setScene(&scene);
graphicsView->setContextMenuPolicy(Qt::CustomContextMenu);
X1SpinBox->setRange(0, MAX_HEIGHT-1);
X2SpinBox->setRange(0, MAX_HEIGHT-1);
Y1SpinBox->setRange(0, MAX_WIDTH-1);
Y2SpinBox->setRange(0, MAX_WIDTH-1);
scaleLabel->setScaledContents(true);
AllocateMemory();
dataloaded = false;
refloaded = false;
RestoreSession();
LoadRef(reffile);
LoadData(datafile);
// Scale image
scale = QImage(20, 256, QImage::Format_Indexed8);
SetColorTable();
for(int i=0; i<20; i++)
for(int j=0; j<=255; j++)
scale.setPixel(i, j, 255-j);
scaleLabel->setPixmap(QPixmap::fromImage(scale));
graphicsView->scale(pow(2,zoom/2), pow(2,zoom/2));
InitializeShortcuts();
UpdateVisibility();
}
