/**
 * UGENE - Integrated Bioinformatics Tools.
 * Copyright (C) 2008-2017 UniPro <ugene@unipro.ru>
 * http://ugene.net
 *
 * This program 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 2
 * of the License, or (at your option) any later version.
 *
 * This program 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 this program; if not, write to the Free Software
 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston,
 * MA 02110-1301, USA.
 */

#include <U2Core/AppContext.h>

#include "BowtieSupport.h"

namespace U2 {

// BowtieSupport

BowtieSupport::BowtieSupport(const QString &name, const QString &path):
    ExternalTool(name, path)
{
    if (AppContext::getMainWindow()) {
        icon = QIcon(":external_tool_support/images/cmdline.png");
        grayIcon = QIcon(":external_tool_support/images/cmdline_gray.png");
        warnIcon = QIcon(":external_tool_support/images/cmdline_warn.png");
    }
    if(ET_BOWTIE == name) {
#ifdef Q_OS_WIN
        executableFileName="bowtie.exe";
#else
    #if defined(Q_OS_UNIX)
        executableFileName="bowtie";
    #endif
#endif
    } else {
#ifdef Q_OS_WIN
        executableFileName="bowtie-build.exe";
#else
    #if defined(Q_OS_UNIX)
        executableFileName="bowtie-build";
    #endif
#endif
    }
    validationArguments.append("--version");
    validMessage="version";
    description=tr("<i>Bowtie</i> is an ultrafast, memory-efficient short read aligner. "
                   "It aligns short DNA sequences (reads) to the human genome at "
                   "a rate of over 25 million 35-bp reads per hour. "
                   "Bowtie indexes the genome with a Burrows-Wheeler index to keep "
                   "its memory footprint small: typically about 2.2 GB for the human "
                   "genome (2.9 GB for paired-end).");
    versionRegExp=QRegExp("version (\\d+\\.\\d+\\.\\d+)");
    toolKitName="Bowtie";
}

} // namespace U2
