/*****************************************************************************
#   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 guiFindRestrictionEnzymeSites_included
#define guiFindRestrictionEnzymeSites_included

#include    <Xm/Xm.h>
#include    "bool.h"
#include    "rwtvalorderedvector.h"
#include    "rwtptrorderedvector.h"

class Contig;
class restrictionFragment;
class digestForOneEnzyme;
class guiDisplayDigest;

class guiFindRestrictionEnzymeSites {
public:
   guiFindRestrictionEnzymeSites();
   void getUsersAnswers();
   ~guiFindRestrictionEnzymeSites();
   void userPushedOK();

   bool bGetUsersChoices();

   void fillInContigBox();

   void doSearch();

   void readVectorSequence();
   void getVectorFragments( 
        RWTPtrOrderedVector<unsigned char>& aIndexedByEnzymeBases,
        RWTPtrOrderedVector<restrictionFragment>& aRestrictionFragments,
        RWTPtrOrderedVector<restrictionFragment>& 
            aRestrictionFragmentsEndingAtAVectorInsertJunction );


   void createListOfDigestForOneEnzyme();
   void readActualGelSizesFile();

   void radioButtonChanged( Widget wid, XtPointer pCallData );


public:
   Widget widPopupShell_;
   Widget widOKButton_;
   Widget widCommonEnzymesList_;
   Widget widHugeEnzymesList_;
   Widget widContigsList_;
   Widget widPathnameOfVectorSequence_;
   Widget widPathnameOfSizesFile_;
   Widget widContigOrderAndOrientation_;

   Widget widDigestEntireClone_;
   Widget widDigestJustPartOfClone_;
   Widget widDigestSingleContig_;

   Widget widWhatToDigest_;
   Widget widWhatToDigestLabel2_;

   Widget widLeftContigStartPosLabel_;
   Widget widLeftContigStartPos_;
   Widget widRightContigEndPosLabel_;
   Widget widRightContigEndPos_;

   Widget widSingleEntireContigLabel_;
   Widget widSingleEntireContig_;

   // used to tell which contig is represented by a push button in the option
   // menu for digesting an entire single contig
   RWTValOrderedVector<Widget> aContigNameWidgets_;
   
   RWTValOrderedVector<RWCString> aSelectedEnzymeNames_;
   RWTValOrderedVector<RWCString> aSelectedEnzymeBases_;

   enum { cWHOLE_CLONE = 'w', cPART_OF_CLONE = 'p', cWHOLE_CONTIG = 't' };
   char cWholeCloneOrPartOfCloneOrWholeContig_;
   RWCString soUserEnteredContigMap_;
   int nStartUnpaddedConsPos_;
   int nEndUnpaddedConsPos_;


   guiDisplayDigest* pGuiDisplayDigest_;
};


#endif