/**
 * 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 "BlastTaskSettings.h"

namespace U2 {

BlastTaskSettings::BlastTaskSettings() {
    offsInGlobalSeq=0;
    aobj=NULL;
    alphabet=NULL;
    isNucleotideSeq=false;
    numberOfHits=0;
    isDefaultMatrix=true;
    isDefautScores=true;
    isDefaultCosts=true;
    isGappedAlignment=true;
    isDefaultThreshold=true;
    isSequenceCircular=false;
    reset();
}

void BlastTaskSettings::reset() {
    programName="";
    databaseNameAndPath="";
    expectValue=10.0;
    megablast=false;
    wordSize=11;
    gapOpenCost=0;
    gapExtendCost=0;
    mismatchPenalty=0;
    matchReward=0;
    matrix="";
    queryFile="";
    outputType=0;
    outputResFile="";
    numberOfProcessors=1;
    needCreateAnnotations=true;
    filter="";
    isGappedAlignment=true;
    xDropoffGA=0;
    xDropoffUnGA=0;
    xDropoffFGA=0;
    windowSize=0;
    threshold=0;
    isDefaultThreshold=true;
    isSequenceCircular=false;
    directStrand = TriState_Unknown;
    querySequenceObject = NULL;
}

}//namespace
