/*****************************************************************************
#   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 CONSEDPARAMETERS_INCLUDED
#define CONSEDPARAMETERS_INCLUDED

#include    "rwcstring.h"
#include    "rwtvalorderedvector.h"
#include    "sysdepend.h"
#include    "filename.h"
#include    "consedResources.h"
#include    <stdio.h>
#include    "mbtPtrOrderedVector.h"
#include    "restrictionEnzyme.h"
#include    "assemblyViewTagTypeAndLine.h"
#include    "mbtValOrderedVectorOfRWCString.h"
#include    <time.h>
#include    "whatIsRunning.h"

class pickPCRPrimers;
class library;
class listOfLibraries;


static const int nDontShowProteinTranslation = 0;
static const int nShowProteinTranslationTopStrand = 1;
static const int nShowProteinTranslationBottomStrand = -1;

// static const int nAutofinishIsRunning = 1;
// static const int nConsedIsRunning = 2;
// static const int nAddReadsToAceFileIsRunning = 3;    
// static const int nAutoPCRAmplifyIsRunning = 4;
// static const int nAutoEditIsRunning = 5;
// static const int nAutoReportIsRunning = 6;
// static const int nPrintSingleSignalIsRunning = 7;
// static const int nAddReadsWithExistingAlignmentsIsRunning = 8;


#define pCP consedParameters::pGetConsedParameters() 


class consedParameters {
 public:
   consedParameters( consedResources* pRes );
   // this member function provides read access to the
   // sole instance

    // this is used just to get a bunch of space to save and
    // retrieve saved parameters
   consedParameters();
   static consedParameters* pGetConsedParameters() { return pGlobalConsedParameters_; }

   void processDoNotFinishTagTypes();
   void processDoNotExtendTagTypes();
   void postProcessing();
   void postProcessingAfterTagTypes();

   RWCString soGetDocumentation();
   void setDocumentation();

   void setParametersForSequencingPrimersNotPCRPrimers( 
                        const bool bSequencingNotPCR );

   void copyPrimerPickingParametersToSelf( consedParameters* pCPSource );

   void makeListOfRestrictionEnzymes();

   void readFileToOrderReadsInAlignedReadsWindow();

   // data members that are not resources or not standard resources
 public:
   RWCString soCommandLine_;
   bool     bWarnUserAboutOverstrikingWithUppercase_;
   bool     bErrorMessageDisplayedAtStartup_;
   int      nAutoFinishLastUsedPrimerNumber_;
   bool     bOKToUseGui_;
   int      nWhatIsRunning_;
   bool     bReadOnly_;
   bool     bCreateSocketToControlConsed_;
   int      nCreateSocketToControlConsedOnThisLocalPort_;
   int      nSocketToControlConsed_;
   int      nSocketSuccessfullyCreatedOnThisLocalPort_;
   int      nShowProteinTranslation_;  // top strand, bottom strand, or not at all
   int      nAutoFinishNumberOfCloningSitesFound_;
   RWCString soSavedReadListOptions_;
   bool     bWillDoExperiments_;
   int      nLastUsedExpID_;
   int      nAutoFinishForwardReverseCalculatedAverageInsertSize_;
   int      nAutoFinishAverageInsertSizeToUse_;
   int      nPrimersALittleLessThanAverageInsertSizeOfASubcloneToUse_;
   RWTValOrderedVector<RWCString> aAutoFinishTagsToNotFinish_;
   RWTValOrderedVector<RWCString> aAutoFinishTagsToNotExtend_;
   FileName filAutoFinishFilenamesFile_;
   FileName filAutoFinishReversesSummary_;
   FileName filAutoFinishForwardsSummary_;
   FileName filAutoFinishCustomPrimersSummary_;
   FileName filAutoFinishSortedSummary_;
   FileName filAutoFinishFullOutput_;
   FileName filAutoFinishCustomNavigation_;
   FileName filAutoFinishMinilibrariesSummary_;
   FILE*    pAutoFinishFilenamesFile_;
   FILE*    pAutoFinishReversesSummary_;
   FILE*    pAutoFinishForwardsSummary_;
   FILE*    pAutoFinishCustomPrimersSummary_;
   FILE*    pAutoFinishSortedSummary_;

   // why do I have both of the below?  One is pAO and the other pFILE
   // pFILE is set to stdout for consed and thus the same code can be
   // used for both consed and autoEdit, autofinish, etc.  I still don't
   // understand, however, why both are needed.  (DG, 11/2002)
   FILE*    pAutoFinishFullOutput_;
   FILE*    pOutputForConsedOrAutoFinish_;
   FILE*    pAutoFinishCustomNavigation_;
   FILE*    pAutoFinishMinilibrariesSummary_;
   RWCString soDocumentation_;
   double   dAutoFinishMinNumberOfErrorsFixedByAnExpToUse_;
   FileName filFileOfPhdFiles_; // this is for -fileOfPhdFiles command line argument
   FileName filNewFileOfPhdFilesFullPath_;
   FileName filFileOfPhdFilesCurrentlyBeingRead_;
   bool     bTerminateAfterStartup_;
   RWTValOrderedVector<int> aUserDefinedKeys_;
   RWTValOrderedVector<RWCString> aProgramsForUserDefinedKeys_;
   RWTValOrderedVector<RWCString> aArgumentsToPassToUserDefinedPrograms_;
   RWTValOrderedVector<RWCString> aTagsToApplyWithUserDefinedKeys_;
   pickPCRPrimers* pPickPCRPrimers_;
   bool bReadyToPickSecondPCRPrimer_;
   int  nPrimersMinimumLengthOfAPrimerToUse_;
   int  nPrimersMaximumLengthOfAPrimerToUse_;
   int  nPrimersMinMeltingTempToUse_; 
   int  nPrimersMaxMeltingTempToUse_; 
   int  nPrimersWindowSizeInLookingToUse_;
   int  nPrimersMaxMatchElsewhereScoreToUse_;
   library* pDefaultLibrary_;
   listOfLibraries* pListOfLibraries_;
   int  nPhdFilesRead_;
   mbtPtrOrderedVector<restrictionEnzyme> aRestrictionEnzymes_;
   RWTValOrderedVector<RWCString> aCommonRestrictionEnzymes_;
   bool     bNeedToSetContigTemplateArrays_;
   char cFindRestrictionEnzymeSitesLastUsedWholeCloneOrPartOfCloneOrWholeContig_;
   RWCString soFindRestrictionEnzymeSitesLastUsedUserEnteredContigMap_;
   int nFindRestrictionEnzymeSitesLastUsedStartUnpaddedConsPos_;
   int nFindRestrictionEnzymeSitesLastUsedEndUnpaddedConsPos_;
   RWCString soFindRestrictionEnzymeSitesLastUsedContigAbbreviatedName_;
   enum { cDELETE_READS = 'd', cPUT_EACH_READ_IN_ITS_OWN_CONTIG = 'p' };
   char cRemoveReadsLastUsedDeleteOrJustPutInOwnContig_;
   RWTValOrderedVector<RWCString> aListOfContigNamesForMiniassembly_; 
   bool bWarnUserAboutAmbiguityCodes_;
   FILE*    pDebugFile_;    

   mbtPtrOrderedVector<assemblyViewTagTypeAndLine> aAssemblyViewDisplayTheseTagTypes_;
   RWCString soAssemblyViewContigsToShow_;

   RWTPtrOrderedVector<RWCRegexp> aShowReadsInAlignedReadsWindowOrderGivenByFile_;

   mbtValOrderedVectorOfRWCString aAutoReportPatternsOfReadsToIgnore_;
   bool bAllowTimestampMismatch_;
   time_t myTime_;
   int nNumberOfStartupErrors_;
   bool bLimitNumberOfErrorsReported_;
   bool bPrintInFigureOutContigOrderAndOrientation_;
   RWCString soDateTimeDotInMiddle_;


   // data members that are also resources:
public: