/*****************************************************************************
#   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.
#
#*****************************************************************************/
#ifndef OLIGOTAG_INCLUDED
#define OLIGOTAG_INCLUDED


#include    "tag.h"
#include    "primerType.h"

class gotoItem;

class oligoTag : public tag {
public:
   virtual void writeToEditHistoryFileAnythingSpecialForThisTagType();
   virtual void writeToEditHistoryFileAnythingSpecialForThisTagTypeForDeleteTag();

   oligoTag( primerType* pPrimerType, 
             const bool bCloneNotSubcloneTemplate,
             const bool bComplementedWithRespectToWayPhrapCreatedContig,
             const int nPrimerID, // if -1, then make new name
             const RWCString& soComment ); 


   oligoTag(          Contig* pContig,
                      const int nConsPosStart,
                      const int nConsPosEnd,
                      const RWCString& soSource,
                      const RWCString& soDate,
                      const bool bNoTrans,
                      const RWCString& soName,
                      const RWCString& soBases,
                      const int nMeltingTemp,
                      const bool bComplementedWithRespectToWayPhrapCreatedContig,
                      const RWCString& soTemplates,
                      const RWCString& soComment ); 


   virtual ~oligoTag() {}

   virtual bool bTagHasExtraInformation() { return true; }

   virtual void guiDisplayExtraInformation( 
                                           Widget widForm, 
                                           Widget widAbove,
                                           Widget widBelow,
                                           bool& bExtraStuffDisplayed,
                                           Widget& widBottomOfExtraStuff );

   virtual void writeToAceFileAnythingSpecialForThisTagType( 
                                         ofstream& ofsAceFile );

   virtual RWCString soGetExtraInformationForNavigator(const int nMaxLength );

   bool bIsThisThe3PrimeEnd( const int nConsPos );

   virtual void flipOrientation() {
      bComplementedWithRespectToWayPhrapCreatedContig_ =
         !bComplementedWithRespectToWayPhrapCreatedContig_;
   }

   virtual gotoItem* pGetGotoItemForThisTag();


   void searchForOligoBases();


public:
   RWCString soName_;  // unique name for oligo
   RWCString soBases_; // in the case of reverse primer, from right to 
   // left and complemented
   bool bComplementedWithRespectToWayPhrapCreatedContig_;

   int   nMeltingTemperature_;
   unsigned char ucMinQuality_;
   unsigned char ucMinQualityIn3Prime4Bases_;
   int   nScoreOfStickiestFalseMatch_;

   RWCString soContigOfStickiestFalseMatch_;
   int  nUnpaddedOfStickiestFalseMatch_;
   bool bContigOfStickiestFalseMatchIsComplemented_;

   int  nSelfMatchScore_;
   int  nSelfMatchOffsetOfComplementedPrimer_;
   int  nSelfMatchPosOf3PrimeSubOligo_;

   int  nSequenceInFileStickiestScore_;
   int  nSequenceInFileSequenceNumber_;
   int  nSequenceInFileBasePosition_;
   bool bSequenceInFileIsComplemented_;

   // must know which vector file was used.  Perhaps this
   // could be a boolean, or a small flag
   RWCString soVectorFileUsed_;


   RWCString soTemplates_;
};


#endif