/*****************************************************************************
#   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.
#
#*****************************************************************************/
#include    "createTearTags.h"
#include    "tag.h"
#include    "assembly.h"
#include    "tagTypes.h"
#include    "contig.h"
#include    "consed.h"
#include    "userDefinedTagFieldType.h"
#include    "userDefinedTagField.h"


void createTearTags( Contig* pLeftContig,
                     const int nLeftConsPos,
                     const RWCString& soLeftTagComment,
                     Contig* pRightContig,
                     const int nRightConsPos,
                     const RWCString& soRightTagComment ) {


   RWCString soTear = "tear";

   tag* pLeftTearTag = 
      new tag( NULL,
               pLeftContig,
               soTear,
               nLeftConsPos,
               nLeftConsPos,
               false, // bWriteToPhdFileNotAceFile,
               soLeftTagComment, // soComment
               soConsed, // consed
               soEmptyString, // date will be current date
               false ); // bNoTrans

   tag* pRightTearTag =
      new tag( NULL,
               pRightContig,
               soTear,
               nRightConsPos,
               nRightConsPos,
               false, // bWriteToPhdFileNotAceFile
               soRightTagComment, // soComment
               soConsed, //consed
               soEmptyString, // date will be current date
               false ); // bNoTrans


   Assembly* pAssembly = ConsEd::pGetAssembly();


   ++pAssembly->lLastUsedTagID_;
   pLeftTearTag->lID_ = pAssembly->lLastUsedTagID_;

   ++pAssembly->lLastUsedTagID_;
   pRightTearTag->lID_ = pAssembly->lLastUsedTagID_;

   

   userDefinedTagType* pTearTagType = (userDefinedTagType*) tagTypes::pGetTagTypes()->pGetTagType( soTear );
   assert( pTearTagType );
   assert( pTearTagType->bIsAUserDefinedTagType() );

   // When I wrote this, the tear tag type had only one user-defined
   // field, called "other_tear_tag" of field type "pointer".  If that
   // ever changes, this code will need to be changed.

   assert( pTearTagType->aUserDefinedTagFieldType_.length() == 1 );
   assert( (pTearTagType->aUserDefinedTagFieldType_[0])->soFieldName_ ==
           "other_tear_tag" );
   assert( pTearTagType->aUserDefinedTagFieldType_[0]->eFieldType_ ==
           userDefinedTagFieldType::ePointer );
   assert( pTearTagType->aUserDefinedTagFieldType_[0]->soPointerToWhichTagType_
           == "tear" );


   pLeftTearTag->pUserDefinedTagType_ =  pTearTagType;
   pRightTearTag->pUserDefinedTagType_ = pTearTagType;

   pLeftTearTag->pArrayOfUserDefinedTagFields_ = 
      new RWTPtrOrderedVector<userDefinedTagField>;
   pRightTearTag->pArrayOfUserDefinedTagFields_ = 
      new RWTPtrOrderedVector<userDefinedTagField>;

   pLeftTearTag->pArrayOfUserDefinedTagFields_->soName_ =
      "tag::pArrayOfUserDefinedTagFields";
   pRightTearTag->pArrayOfUserDefinedTagFields_->soName_ =
      "tag::pArrayOfUserDefinedTagFields";

   userDefinedPointerTagField* pLeftUserDefinedPointerTagField = 
      new userDefinedPointerTagField();

   userDefinedPointerTagField* pRightUserDefinedPointerTagField = 
      new userDefinedPointerTagField();



   pLeftUserDefinedPointerTagField->pUserDefinedTagFieldType_ = 
      pTearTagType->aUserDefinedTagFieldType_[0];

   pRightUserDefinedPointerTagField->pUserDefinedTagFieldType_ = 
      pTearTagType->aUserDefinedTagFieldType_[0];

   pLeftUserDefinedPointerTagField->lID_ = pRightTearTag->lID_;
   pRightUserDefinedPointerTagField->lID_ = pLeftTearTag->lID_;

   pLeftUserDefinedPointerTagField->pTag_ = pRightTearTag;
   pRightUserDefinedPointerTagField->pTag_ = pLeftTearTag;


   

   pLeftTearTag->pArrayOfUserDefinedTagFields_->insert( 
       (userDefinedTagField*) pLeftUserDefinedPointerTagField );
   pRightTearTag->pArrayOfUserDefinedTagFields_->insert(
       (userDefinedTagField*) pRightUserDefinedPointerTagField );


   pLeftContig->addConsensusTag( pLeftTearTag );
   pRightContig->addConsensusTag( pRightTearTag );
}