/*****************************************************************************
#   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 TAGTYPES_INCLUDED
#define TAGTYPES_INCLUDED

#include    "rwtptrsortedvector.h"
#include    "guicolortext.h"


class tag;
class LocatedFragment;
class Contig;
class userDefinedTagFieldType;
class userDefinedTagField;


class tagType {
public:
   enum readOrConsensusType { read = 0x1, consensus = 0x2, both = 0x3,
                              undefined = 0x0 };

   tagType( const RWCString& soTagType, 
            const RWCString& soColor,
            GuiColorText* pGuiColorText,
            const readOrConsensusType readOrConsensus,
            const bool bCanBeCreatedBySwiping ) :
      soTagType_( soTagType), 
      soColor_( soColor ),
      pGuiColorText_( pGuiColorText ),
      readOrConsensus_( readOrConsensus ),
      bCanBeCreatedBySwiping_( bCanBeCreatedBySwiping) {}

   bool operator==( const tagType& tt ) const {
      return( soTagType_ == tt.soTagType_ ); }
   bool operator<( const tagType& tt ) const {
      return( soTagType_ < tt.soTagType_ ); }

   virtual bool bIsAUserDefinedTagType() { return false; }

public:
   RWCString    soTagType_;
   RWCString    soColor_;
   GuiColorText* pGuiColorText_;
   readOrConsensusType   readOrConsensus_;
   bool         bCanBeCreatedBySwiping_;
};


class userDefinedTagType : public tagType {
public:

   userDefinedTagType( const RWCString& soTagType,
                       const RWCString& soColor,
                       GuiColorText* pGuiColorText,
                       const readOrConsensusType readOrConsensus,
                       const bool bCanBeCreatedBySwiping ) :
      tagType( soTagType, soColor, pGuiColorText, readOrConsensus,
               bCanBeCreatedBySwiping ) {}

   virtual bool bIsAUserDefinedTagType() { return true;}


   bool bCorrectNumberOfEachField( 
            RWTPtrOrderedVector<userDefinedTagField>* 
            pArrayOfUserDefinedTagFields,
            RWCString& soErrorMessage );


public:
   RWTPtrOrderedVector<userDefinedTagFieldType> aUserDefinedTagFieldType_;
   // I do not believe this is used (DG, July 2009)
   RWTPtrOrderedVector<GuiColorText> aGuiColorText_;
};


class tagTypes {
public:
   tagTypes();

   static tagTypes* pGetTagTypes() {
      return( pGlobalTagTypes_ ); }

   bool bIsAValidTagType( const RWCString& soTagType );

   tagType* pGetTagType( const RWCString& soTagType );


   GuiColorText* pGetGuiColorTextForTag( tag* pTag );

   GuiColorText* pGetGuiColorTextForTagType( 
                                 const RWCString& soTagType );

   GuiColorText* pGetGuiColorTextForTagsOverlap();
   
   void assignValidTagType( const RWCString& soTagType, 
                            const RWCString& soColor,
                            const tagType::readOrConsensusType readOrConsensus ,
                            const bool bCanBeCreatedBySwiping );

   RWCString soGetTagType( const int nIndex ) {
      return( aTagTypes_[ nIndex ]->soTagType_ );
   }

   tagType::readOrConsensusType rcGetTagReadOrConsensusType( const int nIndex ) {
      return( aTagTypes_[ nIndex ]->readOrConsensus_ );
   }

   int nGetNumberOfTagTypes() { return( aTagTypes_.length() ); }

   tag* pCreateReadTag( const RWCString& soTagType, 
                        const RWCString& soComment,
                     const int nConsPosStart,
                     const int nConsPosEnd,
                     LocatedFragment* pLocFrag,
                     const bool bWriteToPhdFileNotAceFile,
                     bool& bUserPushedCancel );

   tag* pCreateConsensusTag( 
                                     const RWCString& soTagType,
                                     const RWCString& soComment,
                                     const int nConsPosStart,
                                     const int nConsPosEnd,
                                     Contig* pContig,
                                     const bool bNoTrans,
                                     bool& bUserPushedCancel,
                                     const RWCString& soContigName );

   tag* pDuplicateTag( tag* pTag );

   bool bTagTypeCanBeCreatedBySwiping( const int nTagType ) {
      return aTagTypes_[ nTagType ]->bCanBeCreatedBySwiping_;
   }


   void getColumnHeadingsForNavigatorBox( 
                                       const RWCString& soTagType,
                                       RWCString& soColumnHeading1,
                                       RWCString& soColumnHeading2 );
   
   void setTagTypesToHide( char* szTagTypesToHide );
   bool bAreTagsOfThisTypeHidden( const RWCString& soTagType );

   void checkingAfterStoringAllTagTypes();
 
public:
   static     tagTypes*   pGlobalTagTypes_;

   // fail if anyone tries to create a second object.
   static bool bTagTypesCreated_;
   RWTPtrSortedVector<tagType> aTagTypes_;

   // comma separated and comma before and after the list
   RWCString soTagTypesToHide_;

   bool bCurrentlyShowAllTagTypes_;

};




#endif