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//Copyright 2017 Ryan Wick
//This file is part of Bandage
//Bandage is free software: you can redistribute it and/or modify
//it under the terms of the GNU General Public License as published by
//the Free Software Foundation, either version 3 of the License, or
//(at your option) any later version.
//Bandage is distributed in the hope that it will be useful,
//but WITHOUT ANY WARRANTY; without even the implied warranty of
//MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
//GNU General Public License for more details.
//You should have received a copy of the GNU General Public License
//along with Bandage. If not, see <http://www.gnu.org/licenses/>.
#include "../ui/mainwindow.h"
#include <QApplication>
#include <QStringList>
#include <QString>
#include <QCommandLineParser>
#include <QTextStream>
#include "../command_line/load.h"
#include "../command_line/info.h"
#include "../command_line/image.h"
#include "../command_line/querypaths.h"
#include "../command_line/reduce.h"
#include "../command_line/commoncommandlinefunctions.h"
#include "../program/settings.h"
#include "../program/memory.h"
#include "../program/globals.h"
#include "../blast/blastsearch.h"
#include "../graph/assemblygraph.h"
#include "../ui/mygraphicsview.h"
#ifndef Q_OS_WIN32
#include <sys/ioctl.h>
#endif //Q_OS_WIN32
void printUsage(QTextStream * out, bool all)
{
QStringList text;
text << "";
text << "Usage: Bandage <command> [options]";
text << "";
text << "Commands: <blank> Launch the Bandage GUI";
text << "load Launch the Bandage GUI and load a graph file";
text << "info Display information about a graph";
text << "image Generate an image file of a graph";
text << "querypaths Output graph paths for BLAST queries";
text << "reduce Save a subgraph of a larger graph";
text << "";
text << "Options: --help View this help message";
text << "--helpall View all command line settings";
text << "--version View Bandage version number";
text << "";
if (all)
getSettingsUsage(&text);
getOnlineHelpMessage(&text);
outputText(text, out);
}
int main(int argc, char *argv[])
{
QStringList arguments = getArgumentList(argc, argv);
QString first;
if (arguments.size() > 0)
first = arguments[0];
//When launched from the app bundle, OS X can pass a process serial number
//as the first argument. If so, we throw it out.
if (first.contains("-psn_"))
{
arguments.pop_front();
first = "";
if (arguments.size() > 0)
first = arguments[0];
}
// Create the application. Some ways of running Bandage require the normal platform while other command line only
// ways use the minimal platform. Frustratingly, Bandage image cannot render text properly with the minimal
// platform, so we need to use the full platform if Bandage image is run with text labels.
bool imageWithText = (first.toLower() == "image") &&
(arguments.contains("--names") || arguments.contains("--lengths") ||
arguments.contains("--depth") || arguments.contains("--blasthits"));
bool guiNeeded = (first == "") || first.startsWith("-") || (first.toLower() == "load") || imageWithText;
if (checkForHelp(arguments) || checkForHelpAll(arguments))
guiNeeded = false;
if (!guiNeeded)
qputenv("QT_QPA_PLATFORM", QByteArrayLiteral("minimal"));
new QApplication(argc, argv);
//Create the important global objects.
g_settings.reset(new Settings());
g_memory.reset(new Memory());
g_blastSearch.reset(new BlastSearch());
g_assemblyGraph.reset(new AssemblyGraph());
g_graphicsView = new MyGraphicsView();
//Save the terminal width (useful for displaying help text neatly).
#ifndef Q_OS_WIN32
struct winsize ws;
ioctl(0, TIOCGWINSZ, &ws);
g_memory->terminalWidth = ws.ws_col;
if (g_memory->terminalWidth < 50) g_memory->terminalWidth = 50;
if (g_memory->terminalWidth > 300) g_memory->terminalWidth = 300;
#endif //Q_OS_WIN32
QApplication::setApplicationName("Bandage");
QApplication::setApplicationVersion(APP_VERSION);
QTextStream out(stdout);
QTextStream err(stderr);
//If the first argument was a recognised command, move to that command's function.
if (arguments.size() > 0)
{
if (checkForVersion(arguments))
{
out << "Version: " << QApplication::applicationVersion() << Qt::endl;
return 0;
}
if (first.toLower() == "load")
{
arguments.pop_front();
g_memory->commandLineCommand = BANDAGE_LOAD;
return bandageLoad(arguments);
}
else if (first.toLower() == "info")
{
arguments.pop_front();
g_memory->commandLineCommand = BANDAGE_INFO;
return bandageInfo(arguments);
}
else if (first.toLower() == "image")
{
arguments.pop_front();
g_memory->commandLineCommand = BANDAGE_IMAGE;
return bandageImage(arguments);
}
else if (first.toLower() == "querypaths")
{
arguments.pop_front();
g_memory->commandLineCommand = BANDAGE_QUERY_PATHS;
return bandageQueryPaths(arguments);
}
else if (first.toLower() == "reduce")
{
arguments.pop_front();
g_memory->commandLineCommand = BANDAGE_REDUCE;
return bandageReduce(arguments);
}
//Since a recognised command was not seen, we now check to see if the user
//was looking for help information.
else if (checkForHelp(arguments))
{
out << Qt::endl;
out << getBandageTitleAsciiArt() << Qt::endl;
out << "Version: " << QApplication::applicationVersion();
printUsage(&out, false);
return 0;
}
else if (checkForHelpAll(arguments))
{
out << Qt::endl;
out << getBandageTitleAsciiArt() << Qt::endl;
out << "Version: " << QApplication::applicationVersion();
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)
{
outputText("Bandage error: " + error, &err);
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 QApplication::exec();
}
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