/*****************************************************************************
#   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 CONSENSUSTAG_INCLUDED
#define CONSENSUSTAG_INCLUDED


#include    "rwcstring.h"
#include    <iostream>
using namespace std;
#include    <fstream>
#include    "bool.h"
#include    "soEmptyString.h"
#include    <X11/Intrinsic.h>  // for Widget
#include    "rwtptrorderedvector.h"


class Contig;
class LocatedFragment;
class guiPopupTagInfo;
class userDefinedTagField;
class userDefinedTagType;
class gotoItem;

static const RWCString soConsed = "consed";

const int nUndefinedTagID = -666;

class tag {
public: 


   // for adding consed edit tags in locatedFragment.cpp by cons pos
   // Also, commentTag ctor uses this
   // editAddTagWithoutComment uses this

   tag(
        LocatedFragment* pLocFrag,
        Contig* pContig,
        const RWCString& soType,
        const int nConsPosStart,
        const int nConsPosEnd,
        const bool bWriteToPhdFileNotAceFile,
        const RWCString& soComment, //= soEmptyString,
        const RWCString& soSource, //  = soConsed,
        const RWCString& soDate, //  = soEmptyString,
        const bool bNoTrans ); //  = false );


   // this is so that when a tag pointer points to an oligoTag or commentTag,
   // the extra memory for the oligoTag/commentTag is also released
   virtual ~tag() {}


   // If there are two comment tags on the same location, overload this
   // operator by saying that the comments must be identical also

//    virtual RWBoolean operator==( const tag& ctag) const  {
//       return( ( nPaddedConsPosStart_ == ctag.nPaddedConsPosStart_ ) &&
//               ( nPaddedConsPosEnd_   == ctag.nPaddedConsPosEnd_ ) &&
//               ( soType_           == ctag.soType_ ) &&
//               ( soSource_         == ctag.soSource_ ) &&
//               ( soDate_           == ctag.soDate_ ) ); }

   bool operator==( const tag& ctag ) const {
      return( this == &ctag );
   }


   virtual bool operator<( const tag& tagg) const {
      if (nPaddedConsPosStart_ == tagg.nPaddedConsPosStart_ ) {
         if ( nPaddedConsPosEnd_ == tagg.nPaddedConsPosEnd_ ) {
            if ( soDate_ == tagg.soDate_ ) {

               if (soType_ == tagg.soType_ )
                 return( soSource_ < tagg.soSource_ );
               else
                 return( soType_ < tagg.soType_ );
            }
            else 
              return( soDate_ < tagg.soDate_ );
         }
         else
            return( nPaddedConsPosEnd_ < tagg.nPaddedConsPosEnd_ );
      }
      else
         return( nPaddedConsPosStart_ < tagg.nPaddedConsPosStart_ );
   }

   // only used in the case of oligoTag and autoFinishExp
   virtual void flipOrientation() {}


   // write the basics here
   void writeTagToEditHistoryFile();

   // only overridden in case of commentTag and oligoTag
   virtual void writeToEditHistoryFileAnythingSpecialForThisTagType() {}

   void writeDeleteTagToEditHistoryFile();


   virtual void writeToEditHistoryFileAnythingSpecialForThisTagTypeForDeleteTag() {}


   bool bTagIsOnScreen( 
                            const int nScreenConsPosMin, 
                            const int nScreenConsPosMax,
                            int& nVisibleConsPosMin,
                            int& nVisibleConsPosMax );

   bool bTouchesThisConsPos( const int nConsPos ) {
      return( ( nPaddedConsPosStart_ <= nConsPos ) &&
              ( nConsPos <= nPaddedConsPosEnd_ ) );
   }

   void popupTagInfoForOneTag( 
                              const int nNumberOfTagsAlreadyPoppedUp,
                              void* pGuiContigWinOrGuiTeditor, 
                              const bool bIsGuiContigWin );

   virtual bool bTagHasExtraInformation();

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

   void displayUserDefinedTagFields( Widget widForm, 
                                     Widget widAbove2, 
                                     Widget widBelow, 
                                     Widget& widBottomOfExtraStuff );

   virtual void askUserForExtraTagInformation( bool& bUserPushedCancel );

   virtual RWCString soGetExtraInformationForNavigator(const int nMaxLength ); 

   RWCString soGetBasicInformation();

   bool bCheckTag(  const int nPerhapsStartTagUnpaddedConsPos,
                               const int nPerhapsEndTagUnpaddedConsPos );


   void changeTag(  const int nPerhapsStartTagUnpaddedConsPos,
                               const int nPerhapsEndTagUnpaddedConsPos );

   void changeTagComment( const RWCString& soComment );

   virtual bool bCheckTagExtraInformation() { return true; }

   virtual void changeTagExtraInformation() {}
   
   void writeTagToPHDFile( ofstream& ofsPHD );

   virtual void writeToPHDFileAnythingSpecialForThisTagType( 
                                                  ofstream& ofsPHD );

   void adjustTagPosition(const int nAdjustToRightOfThisConsPos,
                              const int nAmountToAdjust );

   void complementSelf( );

   // for use by pGetGuiColorTextForTag 
   RWCString soGetTagType() { return( soType_ ); }

   void writeTagToAceFile( ofstream& ofsAceFile );

   virtual void writeToAceFileAnythingSpecialForThisTagType( 
                                         ofstream& ofsAceFile );

   friend void cbMatchElsewhereTagSearchForString( Widget wid,
                                         XtPointer pClientData,
                                         XtPointer pCallData );

   void matchElsewhereTagSearchForString();

   // works even if the tag is a read tag
   Contig* pGetContig();


   int nGetUnpaddedStart();
   int nGetUnpaddedEnd();

   void clearUserDefinedFields();

   void writeUserDefinedTagTypeFields( ofstream& ofsAceFile );
   
   void dealWithPointerFields( RWCString& soErrorMessage );

   virtual gotoItem* pGetGotoItemForThisTag();


public:
   bool bReadTagNotConsensusTag_;
   LocatedFragment* pLocFrag_;
   Contig* pContig_;
   RWCString soType_;
   RWCString soSource_;
   bool bCoordinatesAreUnpaddedRead_; /* used for adding reads when 
                                      can't convert unpadded to padded
                                      yet.  These are not
                                      complemented--in direction of
                                      sequencing */
                                      
   int nPaddedConsPosStart_;
   int nPaddedConsPosEnd_;
   RWCString soDate_; 
   bool bWriteToPhdFileNotAceFile_;

   // this serves as a flag of whether the tag is already
   // popped up
   guiPopupTagInfo* pGuiPopupTagInfo_;
   bool bNoTrans_;  // flag on consensus tags for
   // transferConsensusTags.perl to not transfer them

   RWCString soMiscData_;
   RWCString soComment_;
   long lID_;
   RWTPtrOrderedVector<userDefinedTagField>* pArrayOfUserDefinedTagFields_;
   userDefinedTagType* pUserDefinedTagType_; // only used for userDefinedTagType's
};

void cbMatchElsewhereTagSearchForString( Widget wid,
                                         XtPointer pClientData,
                                         XtPointer pCallData );




#endif