text: /**
   * UGENE - Integrated Bioinformatics Tools.
   * Copyright (C) 2008-2020 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;
      strandSource = QueryFrame;
      filter = "";
      isGappedAlignment = true;
      xDropoffGA = 0;
      xDropoffUnGA = 0;
      xDropoffFGA = 0;
      windowSize = 0;
      threshold = 0;
      isDefaultThreshold = true;
      isSequenceCircular = false;
      directStrand = TriState_Unknown;
      querySequenceObject = NULL;
  }
  
  }    // namespace U2
  