/*****************************************************************************
#   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 autoFinishExpTag_include
#define autoFinishExpTag_include


#include    "autoFinishPurposes.h"
#include    "tag.h"
#include    "rwtvalorderedvector.h"
#include    "readTypes.h"


class autoFinishExpTag : public tag {
public:

   autoFinishExpTag( Contig* pContig,
                     const int nConsPosStart,
                     const int nConsPosEnd,
                     const RWCString& soSource,
                     const RWCString& soTagDate,
                     const RWCString& soTagData ) :
      // If these stay -1, that will indicate that the ace
      // file did not contain values for them and they are not known.

      nSingleSubcloneBasesFixed_( -1 ),
      dErrorsFixed_( -1 ),
      nExtendingIntoGapThisManyBases_( -1 ),

      tag( NULL,
           pContig,
           "autoFinishExp",
           nConsPosStart,
           nConsPosEnd,
           false, // bWriteToPhdFileNotAceFile
           "", // soComment
           soSource,
           soTagDate,
           false )  // bNoTrans
      { soMiscData_ = soTagData; }


   virtual RWCString soGetExtraInformationForNavigator(const int nMaxLength );


   bool bExperimentWorked();

   void getUnpaddedHighQualityRegion( 
                            int& nUnpaddedHighQualityRegionLeft,
                            int& nUnpaddedHighQualityRegionRight,
                            int& nUnpaddedHighQualityRegionLeftOnConsensus,
                            int& nUnpaddedHighQualityRegionRightOnConsensus,
                            bool& bCompletelyOffConsensus );

   void howWellDidExpClusterExtendContig();

   void howWellDidExpClusterFixErrors();
   
   void howWellDidExpClusterFlankGap();

   void evaluateExperimentCluster();
   void  howWellDidExpClusterCoverSingleSubcloneBases();

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

public:
   RWCString soPrimerBases_;
   int nMeltingTemp_;
   RWTValOrderedVector<RWCString> aTemplates_;
   RWTValOrderedVector<int> aExpID_;


   bool bComplementedFromWayPhrapCreatedContig_;

   // in the case of flank gap experiments, this indicates the strand
   // of the *new* read.  It is precisely the opposite strand from the
   // existing universal primer read.


   int nUnpaddedOffsetToStartOfHighQualityRegion_;
   int nUnpaddedOffsetToEndOfHighQualityRegion_;
   int nUnpaddedOffsetOfBeginningOfReadFromTag_;
   double dErrorsFixed_;
   int nSingleSubcloneBasesFixed_;
   int nReadType_;
   int nPurpose_;
   RWCString soPrimerID_;
   int nExtendingIntoGapThisManyBases_;
   //   int nExtendsIntoWhichGap_; --not useful since phrap may have
   // flipped the contig.  transferConsensusTags.perl would then have
   // to change this field.

   // before these suggested experiments, how many 
   // problems were present.  This will help in determining
   // how well these experiments worked.
   int nOriginalNumberOfSingleSubcloneBases_;
   double dOriginalNumberOfErrors_;
};

#endif