trimAlMain.cpp

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/* *****************************************************************************

    trimAl v2.0: a tool for automated alignment trimming in large-scale
                 phylogenetics analyses.

    readAl v2.0: a tool for automated alignment conversion among different
                 formats.

    2009-2019
        Fernandez-Rodriguez V.  (victor.fernandez@bsc.es)
        Capella-Gutierrez S.    (salvador.capella@bsc.es)
        Gabaldon, T.            (tgabaldon@crg.es)

    This file is part of trimAl/readAl.

    trimAl/readAl are 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, the last available version.

    trimAl/readAl are 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 trimAl/readAl. If not, see <http://www.gnu.org/licenses/>.

***************************************************************************** */

#include "InternalBenchmarker.h"
#include "trimalManager.h"
#include "reportsystem.h"

int main(int argc, char *argv[]) {

    // We have to check the output parameter of the timerFactory
    //  before it's called the first time
    #if TimingReport
        timerFactory.checkOutputParameter(argc, argv);
    #endif

    // Debug tag to prevent Debug Messages to be printed on user side
    debug.IsDebug = true;

    // To allow timing the whole program, we must encapsulate
    //  inside it's own scope. Thus, we store the returnValue outside
    //  the scope.
    int returnValue;
    {
        // Create a BenchmarkSnapshot that will report times and/or memory usage
        // upon its destruction
        StartTiming("int main(int argc, char *argv[]) ");

        // Create trimAl Manager
        trimAlManager trimAl;

        returnValue = trimAl.parseArguments(argc, argv);

        if (returnValue == trimAlManager::Final | returnValue == trimAlManager::Errored)
            exit(0);

        // Process them: Incompatibilities and co-dependencies
        trimAl.processArguments(argv);

        // Perform the required actions
        returnValue = trimAl.perform();
    }

    // Return the exit code obtained in the perform method.
    return returnValue;
}