/*****************************************************************************
#   Copyright (C) 1994-2008 by David Gordon.
#   All rights reserved.                           
#                                                                           
#   This software is part of a beta-test version of the Consed/Autofinish
#   package.  It should not be redistributed or
#   used for any commercial purpose, including commercially funded
#   sequencing, without written permission from the author and the
#   University of Washington.
#   
#   This software is provided ``AS IS'' and any express or implied
#   warranties, including, but not limited to, the implied warranties of
#   merchantability and fitness for a particular purpose, are disclaimed.
#   In no event shall the authors or the University of Washington be
#   liable for any direct, indirect, incidental, special, exemplary, or
#   consequential damages (including, but not limited to, procurement of
#   substitute goods or services; loss of use, data, or profits; or
#   business interruption) however caused and on any theory of liability,
#   whether in contract, strict liability, or tort (including negligence
#   or otherwise) arising in any way out of the use of this software, even
#   if advised of the possibility of such damage.
#
#   Building Consed from source is error prone and not simple which is
#   why I provide executables.  Due to time limitations I cannot
#   provide any assistance in building Consed.  Even if you do not
#   modify the source, you may introduce errors due to using a
#   different version of the compiler, a different version of motif,
#   different versions of other libraries than I used, etc.  For this
#   reason, if you discover Consed bugs, I can only offer help with
#   those bugs if you first reproduce those bugs with an executable
#   provided by me--not an executable you have built.
# 
#   Modifying Consed is also difficult.  Although Consed is modular,
#   some modules are used by many other modules.  Thus making a change
#   in one place can have unforeseen effects on many other features.
#   It may takes months for you to notice these other side-effects
#   which may not seen connected at all.  It is not feasable for me to
#   provide help with modifying Consed sources because of the
#   potentially huge amount of time involved.
#
#*****************************************************************************/
//
// Quality.h
//
// header file for Quality class
//
// all this is to hide the true nature of a Quality object,
// which right now is just an unsigned char but in the
// future will probably become more complicated.  use
// predefined values ('ucQualityLow', 'ucQualityHigh', etc.) and
// comparison operators rather than try and extract the private
// data (which will break as soon as the object becomes more
// complex).
//
//

#ifndef QUALITY_INCLUDED
#define QUALITY_INCLUDED





// for internal use.  instead of using these in client
// code, use the actual const Quality objects declared below.
static const unsigned char ucQualityMin = 0;
static const unsigned char ucQualityLow = 0;
static const unsigned char ucQualityWithoutPhdFiles = 15;
static const unsigned char ucDefQualValue = 20;
static const unsigned char ucQualityHigh = 50;
static const unsigned char ucQualityLowEdited = 98;
static const unsigned char ucQualityHighEdited = 99;
static const unsigned char ucDefaultQualityEdited = ucQualityLowEdited;
static const unsigned char ucQualityMax = 100;


inline void convertFrom9899QualityToNormalQuality( unsigned char& ucQuality ) {
   if (ucQuality == ucQualityLowEdited )
      ucQuality = ucQualityMin;

   if (ucQuality == ucQualityHighEdited )
//      ucQuality = ucQualityHigh;
     ucQuality = 60;  // Phil wanted it this way Dec 1997
                      // for data quality exercise to increase the
                      // the quality of pads between base 99's

}


typedef unsigned char Quality;
#endif  // QUALITY_INC