int bandageImage(QStringList arguments)
{
QTextStream out(stdout);
QTextStream err(stderr);
if (checkForHelp(arguments))
{
printImageUsage(&out, false);
return 0;
}
if (checkForHelpAll(arguments))
{
printImageUsage(&out, true);
return 0;
}
if (arguments.size() < 2)
{
printImageUsage(&err, false);
return 1;
}
QString graphFilename = arguments.at(0);
arguments.pop_front();
if (!checkIfFileExists(graphFilename))
{
err << "Bandage error: " << graphFilename << " does not exist" << endl;
return 1;
}
QString imageSaveFilename = arguments.at(0);
arguments.pop_front();
QString imageFileExtension = imageSaveFilename.right(4);
bool pixelImage;
if (imageFileExtension == ".png" || imageFileExtension == ".jpg")
pixelImage = true;
else if (imageFileExtension == ".svg")
pixelImage = false;
else
{
err << "Bandage error: the output filename must end in .png, .jpg or .svg" << endl;
return 1;
}
QString error = checkForInvalidImageOptions(arguments);
if (error.length() > 0)
{
err << "Bandage error: " << error << endl;
return 1;
}
bool loadSuccess = g_assemblyGraph->loadGraphFromFile(graphFilename);
if (!loadSuccess)
{
err << "Bandage error: could not load " << graphFilename << endl;
return 1;
}
int width = 0;
int height = 0;
parseImageOptions(arguments, &width, &height);
//For Bandage image, it is necessary to position node labels at the
//centre of the node, not the visible centre(s). This is because there
//is no viewport.
g_settings->positionTextNodeCentre = true;
//Since frame rate performance doesn't matter for a fixed image, set the
//default node outline to a nonzero value.
g_settings->outlineThickness = 0.3;
bool blastUsed = isOptionPresent("--query", &arguments);
if (blastUsed)
{
if (!createBlastTempDirectory())
{
err << "Error creating temporary directory for BLAST files" << endl;
return 1;
}
QString blastError = g_blastSearch->doAutoBlastSearch();
if (blastError != "")
{
err << blastError << endl;
return 1;
}
}
QString errorTitle;
QString errorMessage;
std::vector<DeBruijnNode *> startingNodes = g_assemblyGraph->getStartingNodes(&errorTitle, &errorMessage,
g_settings->doubleMode,
g_settings->startingNodes,
"all");
if (errorMessage != "")
{
err << errorMessage << endl;
return 1;
}
g_assemblyGraph->buildOgdfGraphFromNodesAndEdges(startingNodes, g_settings->nodeDistance);
g_assemblyGraph->layoutGraph();
MyGraphicsScene scene;
g_assemblyGraph->addGraphicsItemsToScene(&scene);
scene.setSceneRectangle();
double sceneRectAspectRatio = scene.sceneRect().width() / scene.sceneRect().height();
//Determine image size
//If neither height nor width set, use a default of height = 1000.
if (height == 0 && width == 0)
height = 1000;
//If only height or width is set, scale the other to fit.
if (height > 0 && width == 0)
width = height * sceneRectAspectRatio;
else if (height == 0 && width > 0)
height = width / sceneRectAspectRatio;
bool success = true;
QPainter painter;
if (pixelImage)
{
QImage image(width, height, QImage::Format_ARGB32);
image.fill(Qt::white);
painter.begin(&image);
painter.setRenderHint(QPainter::Antialiasing);
painter.setRenderHint(QPainter::TextAntialiasing);
scene.render(&painter);
success = image.save(imageSaveFilename);
painter.end();
}
else //SVG
{
QSvgGenerator generator;
generator.setFileName(imageSaveFilename);
generator.setSize(QSize(width, height));
generator.setViewBox(QRect(0, 0, width, height));
painter.begin(&generator);
painter.fillRect(0, 0, width, height, Qt::white);
painter.setRenderHint(QPainter::Antialiasing);
painter.setRenderHint(QPainter::TextAntialiasing);
scene.render(&painter);
painter.end();
}
int returnCode;
if (!success)
{
out << "There was an error writing the image to file." << endl;
returnCode = 1;
}
else
returnCode = 0;
if (blastUsed)
deleteBlastTempDirectory();
return returnCode;
}
int main(int argc, char *argv[])
{
QApplication a(argc, argv);
QApplication::setApplicationName("Bandage");
QApplication::setApplicationVersion("0.6.2");
QTextStream out(stdout);
QTextStream err(stdout);
//Create the important global objects.
g_settings.reset(new Settings());
g_blastSearch.reset(new BlastSearch());
g_assemblyGraph.reset(new AssemblyGraph());
g_graphicsView = new MyGraphicsView();
QStringList arguments = QCoreApplication::arguments();
arguments.pop_front();
if (checkForVersion(arguments))
{
out << "Version: " << QApplication::applicationVersion() << endl;
return 0;
}
//If the first argument was a recognised command, move to that command's function.
if (arguments.size() > 0)
{
QString first = arguments.at(0);
if (first == "load")
{
arguments.pop_front();
g_settings->commandLineCommand = BANDAGE_LOAD;
return bandageLoad(&a, arguments);
}
else if (first == "image")
{
arguments.pop_front();
g_settings->commandLineCommand = BANDAGE_IMAGE;
return bandageImage(arguments);
}
// else if (first == "contiguous")
// {
// arguments.pop_front();
// return bandageContiguous(arguments);
// }
}
//Since a recognised command was not seen, we now check to see if the user
//was looking for help information.
if (checkForHelp(arguments))
{
out << "" << endl;
out << "Program: Bandage" << endl;
out << "Version: " << QApplication::applicationVersion() << endl;
printUsage(&out, false);
return 0;
}
if (checkForHelpAll(arguments))
{
out << "" << endl;
out << "Program: Bandage" << endl;
out << "Version: " << QApplication::applicationVersion() << endl;
printUsage(&out, true);
return 0;
}
//If the code got here, we assume the user is simply launching Bandage,
//with or without some options to specify settings.
//Check the settings.
QStringList argumentsCopy = arguments;
QString error = checkForInvalidOrExcessSettings(&argumentsCopy);
if (error.length() > 0)
{
err << "Bandage error: " + error << endl;
return 1;
}
//If the code got here, then the settings are good. Parse them now and
//run the program.
parseSettings(arguments);
MainWindow w;
w.show();
return a.exec();
}
