/* This file is part of PhiPack.
 Copyright (c)2005, Trevor Bruen
 Foobar is free software: you can redistribute it and/or modify
 it under the terms of the GNU Lesser General Public License as published by
 the Free Software Foundation, either version 3 of the License, or
 (at your option) any later version.
 
 Foobar 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 Lesser General Public License for more details.
 
 You should have received a copy of the GNU General Public License
 along with PhiPack.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef OPTIONS
#define OPTIONS

typedef struct{

    
  alignmentClass alignKind;
  fileType inFile;

  char seqFile[MAX_SIZE+1];

  cbool doPerm;
  int ntrials;
  cbool otherStats;
  
  double winSize;
  int k;

  cbool verbose;
  
  cbool printMatrix;
  int graphType;
  cbool embellish;
  
  cbool printBreakpoints;
  int breakWindow;
  
 

} options;


#endif
