/*****************************************************************************
#   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 autoReport_included
#define autoReport_included


class Contig;
class LocatedFragment;

#include    "rwtvalvector.h"
#include    "mbtValOrderedVectorOfRWCString.h"
#include    "rwtptrorderedvector.h"
#include    "filename.h"
#include    "mbtValVectorOfBool.h"
#include    "rwtptrvector.h"


typedef RWTValVector<char> RWTValVectorOfBases;
typedef RWTValVector<signed char> RWTValVectorOfQualities;
typedef RWTValVector<bool> RWTValVectorOfHighQualitySegmentFlags;
typedef RWTPtrVector<LocatedFragment> RWTPtrVectorOfLocatedFragment;
typedef RWTValVector<int> RWTValVectorOfUnpaddedReadPositionsInDirectionOfSequencing;

class autoReport {
 public:
   void doIt();
   autoReport( const FileName& filAceFileToOpen );

   void parseSpecies();
   void printThisContig( Contig* pContig );
   void dumpSpeciesAlignmentForOneContig( Contig* pContig );
   void dumpSpeciesAlignment();
   void readReadFile();
   void printReadAlignment();
   void printReadAlignmentForOneContig( Contig* pContig );
   void findListOfReadsInThisContig( 
         Contig* pContig,
         RWTPtrOrderedVector<LocatedFragment>* pArrayOfReads );
   void printDiscrepantRegions();
   void printBasesInDiscrepantRegions();

   void printMinimumQualityHistogram();

   void printNumberOfIsolatedPads();

   void printNumberOfIsolatedPadsForEachSpecies();

   void printAgreeDisagreeBetweenPairsOfSpecies();
   void printAgreeDisagreeBetweenPairsOfSpecies2();

   void printScaffolds();

   void calculateErrorProbabilitiesByComparingPTroPPan();

   void  printIfReadsAreCorrectlyAligned();

   void printLengthsOfUnalignedHighQualitySegments();

   void printLengthsOfAlignedSegments();

   void printHighlyDiscrepantRegions();

   void compareTopAndBottomStrands();
   void compareTopAndBottomStrands2();
   void compareTopAndBottomStrands3();
   void compareTopAndBottomStrands4();
   void compareTopAndBottomStrandsWithHuman();
   void compareTopAndBottomStrandsNoHuman();

   void singleSignalInfo();
   void singleSignalInfo2();

   void countColumnsForGroupsOfSpecies();

   void compareHQSWithLQS();

   void lowQualityBasesInHQS();

   void singleSignalOrQuality();

   void discrepancyRateInFlankedRegions();
   void discrepancyRateInFlankedRegions2();
   void discrepancyRateInFlankedRegions4();
   void discrepancyRateInFlankedRegions5();

   void countReadsDueToBugInGoodReads();

   void highQualitySegmentData();

   void printFlankedColumns();

   void printFlankedColumns2();
   void printFlankedColumns3();
   void printFlankedColumns4();

   void countAcceptableColumnsWithNoneOnLeft();

   void countAllMutations();
   void countAllMutationsML();

   void printHighQualityDiscrepancies();
   void printLowConsensusQualityRegions();
   void printSingleSubcloneRegions();
   void printLinkingForwardReversePairs();
   void printFilteredInconsistentForwardReversePairs();

   void printMutationsWithContext();

   void printCrudeChimpHumanMutations();

   void printToCompareToReich();

   void printAssemblySummary();

 public:
   FileName filAceFileToOpen_;

   mbtValOrderedVectorOfRWCString aArrayOfSpecies_;
   mbtValOrderedVectorOfRWCString aArrayOfReads_;

   // in each of these arrays, there is a pointer (to an array)
   // for each species
   RWTPtrOrderedVector<RWTValVectorOfBases> aArrayOfPtrsToArraysOfBases_;
   RWTPtrOrderedVector<RWTValVectorOfQualities> aArrayOfPtrsToArraysOfQualities_;
   RWTPtrOrderedVector<RWTValVectorOfHighQualitySegmentFlags> aArrayOfPtrsToArraysOfHighQualitySegmentFlags_;
   RWTPtrOrderedVector<RWTPtrVectorOfLocatedFragment> aArrayOfPtrsToArraysOfLocatedFragments_;
   RWTPtrOrderedVector<RWTValVectorOfUnpaddedReadPositionsInDirectionOfSequencing> aArrayOfPtrsToArraysOfReadPositionsInDirectionOfSequencing_;





};


#endif