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/**
* @author Mark Larkin, Conway Institute, UCD. mark.larkin@ucd.ie
*
* Changes:
*
* 03-02-07,Nigel Brown(EMBL): removed 'globalLastDir.h' dependency
* and 'lastDir' global initialization.
*
* 24-05-07,Nigel Brown(EMBL): changed saving of executablePath to use
* Resources class instead of MainWindow.
*
* 2007-12-03, Andreas Wilm (UCD): added support for infile flag
* (commandline)
*
* 2007-12-06, Andreas Wilm (UCD): added full clustalw command line support
*
****************************************************************************/
#include <QApplication>
//#include <QTranslator>
#include "clustalW/substitutionMatrix/SubMatrix.h"
#include "QTUtility.h"
#include "clustalW/general/UserParameters.h"
#include "mainwindow.h"
#include <QString>
#include <QDir>
#include "version.h"
// - nige: Resources.h
#include "Resources.h"
#include "clustalW/interface/CommandLineParser.h"
namespace clustalw
{
UserParameters* userParameters;
Utility* utilityObject;
SubMatrix *subMatrix;
Stats* statsObject;
}
/**
* The main function. It creates a new MainWindow widget and displays it.
*/
using namespace clustalw;
int main(int argc, char *argv[])
{
//QTranslator translator;
//translator.load("clustalx_la");
// Note the path to the executable is usually passed in as argv[0]
// This will be used if we cannot find the help or the xml files in current dir.
Resources *resources = Resources::Instance();
resources->setPathToExecutable(QString(argv[0]));
//resources->dump(); //debug: nige
userParameters = new UserParameters(false);
subMatrix = new SubMatrix(); // Mark April 11th 2007
userParameters->setInteractive(true);
userParameters->setGui(true); // gui is not the same as interactive - text menus are interactive but not gui
statsObject = new Stats();// actually only needed in clustalw
QApplication app(argc, argv);
//app.installTranslator(&translator);
psPrintParams params;
MainWindow window;
utilityObject = new QTUtility(&window);
window.show();
// parse command line if we got some non-Qt args
// must be done after we've setup utilityObject
if (argc > 1)
{
vector<string> args;
for (int i = 1; i < argc; ++i)
{
args.push_back(argv[i]);
}
userParameters->setMenuFlag(false);
CommandLineParser cmdLineParser(&args, true);
}
// if profiles were given on the command line, we need to switch to two window mode
if(clustalw::userParameters->getProfileNum() > 0) // profile mode
{
window.setProfileModeCmd();
window.loadProfile1(clustalw::userParameters->getProfile1Name());
window.loadProfile2(clustalw::userParameters->getProfile2Name());
}
else // multiple alignment mode
{
// infile parsed? then load
string seqname = userParameters->getSeqName();
if (seqname.length())
window.loadSequences(QString(seqname.c_str()));
}
// Andreas Wilm (UCD):
// if help flag is given, show graphical clustax help on cmd line
// flags, instead of trying to load clustalw help (as 1.83 did!)
//
if (userParameters->getHelpFlag() ||userParameters->getFullHelpFlag() )
window.commandLineHelp();
return app.exec();
delete userParameters;
delete utilityObject;
delete subMatrix;
}
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