/*****************************************************************************
#   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.
#
#*****************************************************************************/
//
// Ntide.h
//
// header file for Ntide class
//
//

#ifndef NTIDE_INCLUDED 
#define NTIDE_INCLUDED


#ifdef SCCS_ID
static const char* ntideSccsId = "@(#)ntide.h	1.18 05/21/96 09:49:52";
#endif


#include <ctype.h>
#include <iostream>
using namespace std;

#include    "sysdepend.h"
#include    "quality.h"
#include    "cComplementBase.h"
#include    "assert.h"

// char used to represent pad application-wide is defined here
static const char ntidePadChar = '*';
static const int nGetBaseUpperOrLowerLookupFirstSubscript = 256;
static const int nGetBaseUpperOrLowerLookupSecondSubscript = 100;

class Ntide {

 public:
   // simple character representation
   char cBase_;

   // quality object is currently an int score stored in 1 byte
   Quality ucQual_;

   static unsigned char ucGetBaseUpperOrLowerSetQualityThreshold_;
   static char cGetBaseUpperOrLowerLookup_[ nGetBaseUpperOrLowerLookupFirstSubscript ][ nGetBaseUpperOrLowerLookupSecondSubscript ];
   

 public:
   Ntide() 
     : 
       cBase_( '\0' ),
       ucQual_ ( ucDefQualValue ) {};

   ~Ntide() {};   // for our subclasses

   // quality values are still indicated by upper/lower case
   // in the phrap output. 
   Ntide(char c) 
     :
     cBase_(c)
   {
      initQualFromChar(c);
   } 

   // ctor taking all members for args
   Ntide(char c,
         const Quality q )
     : 
       cBase_( c ),
       ucQual_ ( q ) {
          assert( ucQualityMin <= q );
          assert( q <= ucQualityMax );
   }
 
   // cast to char
   operator char() const { return cBase_; }

   // ok--now I've tried the (char) cast, but I still like explicit
   // methods better:
   char cGetBase() const { return cBase_; }

   // returns upper or lower case base according to quality threshold
   char cGetBaseUpperOrLower() const;
   char cGetBaseUpperOrLowerUnsafe() const;


   static void setGetBaseUpperOrLowerLookupTableIfNecessary();


   // simple assignment operator
   // Without this, the sgi compiler would handle, for example:
   // daReadNtidesBeforeEdit_.append( 
   // pLocatedFragment_->ntGetFragFromConsPos( nCons )
   //                                );
   // by using the "operator char()" above to get a char from 
   // pLocatedFragment_->ntGetFragFromConsPos( nCons )
   // and then use the 
   // "operator=( const char c )" (below) to do the append which
   // does an assignment.  "operator=(const char c)" sets the
   // quality to 0.  This caused quality to become zero when
   // making and undoing making bases n's or overstriking.

   Ntide& operator= (const Ntide& nt);

   // comparison does not take into account point position
   bool operator == (const Ntide& nt) const {
      return (cBase_ == nt.cBase_) && (ucQual_ == nt.ucQual_);
   }  

   // assignment from char 
   Ntide& operator=(const char c) {
      cBase_ = c;
      initQualFromChar(c);   // same conversion from char as above
      return *this;
   }


   // sets the base (while leaving the point position and quality)
   // (This is used in changing bases to N )
   void setBase(const char cBase) { cBase_ = cBase; }



   // returns quality object
   const Quality& qualGetQuality() const { return ucQual_; }

   const Quality qualGetQualityWithout98or99() const {
      Quality uc = ucQual_;
      convertFrom9899QualityToNormalQuality( uc );
      return( uc );
   }


   const Quality qualGetQualityWithout98or99X0() const {
      if ( cBase_ == 'x' ) {
         return 0;
      }
      else {
         return qualGetQualityWithout98or99();
      }
   }


   // sets the quality object
   void setQuality(const Quality& q) { 
      assert( ucQualityMin <= q );
      assert( q <= ucQualityMax );
      ucQual_ = q; }

   // returns bool indicating if base == pad char.
   // avoids proliferating ascii constant pad char
   // ie. "if (ntide.bIsPad())" instead of if "(ntide == '*')"
   bool bIsPad() const { return cBase_ == ntidePadChar; }

   //   friend ostream& operator << (ostream& os, const Ntide& nt);

   void complementBase() {
      cBase_ = cComplementBase( cBase_ );
   }

//    // complements the ntide object and returns a reference to itself
//    Ntide& ntComplementNtide() {
//       cBase_ = cComplementBase( cBase_ );
//       return( *this );
//    }

//    // this variant complements the point position as well
//    Ntide& ntComplementNtide(const short int nMaxPos) {
//       // trying to complement the point position of
//       // an Ntide which has never been set throws exception
// //      assert (nPointPos_ != nUninitializedPointPos);
//       // I think point positions start at 1, so add 1 (DG)
//       // No--point positions start at 0
//       nPointPos_ = nMaxPos - nPointPos_;
//       return ntComplementNtide();  // then call above version
//    }

 private:
   void initQualFromChar(const char c) {
      if (c == ntidePadChar) {
         ucQual_ = ucQualityMin;
      }  
      else if (isalpha(c)) {
         if ((c == 'n') || (c == 'N')) {
            ucQual_ = ucQualityMin;
         }
         else if (isupper(c)) {
            ucQual_ = ucQualityHigh;
         }
         else {
            ucQual_ = ucQualityLow;
         }
      }
      else {
         assert (false);  // bomb 
      }
   }  // initQualFromChar

};   // class Ntide

// Ntide objects can be intermixed with predefined insertion
// operators for ostreams (e.g. "cout << ntideMine << endl;")
ostream& operator << (ostream& os, const Ntide& nt);


#endif  // NTIDE_INCLUDED