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src/cpsp/SideChain/chain_threading.h

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/*
 *  Main authors:
 *     Mohamad Rabbath <rabbath@informatik.uni-freiburg.de>
 *
 *  Contributing authors:
 *     Martin Mann <mmann@informatik.uni-freiburg.de>
 *     Sebastian Will <will@informatik.uni-freiburg.de>
 *
 *  This file is part of the CPSP-tools package:
 *     http://www.bioinf.uni-freiburg.de/sw/cpsp/
 *
 *  See the file "LICENSE" for information on usage and
 *  redistribution of this file, and for a
 *     DISCLAIMER OF ALL WARRANTIES.
 *
 */

#ifndef THREADING_H_
#define THREADING_H_
#include <gecode/kernel.hh>
#include <gecode/int.hh>
#include <gecode/search.hh>
#include <gecode/minimodel.hh>

#include <gecode/int/branch.hh>

#include <string>
#include <vector>
#include <cpsp/HCore.hh>

#include <cpsp/gecode/GC_LatticeNeighbored2.hh>
#include <cpsp/gecode/GC_ValNearCenter.hh>

#include <cpsp/gecode/gecodeExtensions.hh>

#include <biu/LatticeFrame.hh>


using namespace Gecode;
namespace cpsp{
//side chain threading
namespace scth{
class SideChainThreading : public Gecode::Space {
private:
    IntSet HDomain;

    IntSet BHDomain;

    IntSet OutCoreDomain;

    //Here are the constraints
    void BsNeighbours(const std::string *sequence,const biu::IndexVec* neighVecs);

    void B_PsNeighbours(const biu::IndexVec* neighVecs);

    void B_HsNeighbours(const biu::IndexVec* neighVecs);

    void inCore(cpsp::HCore* );

    void attachedToCore(cpsp::HCore* );

    void outCore(const std::string *sequence,cpsp::HCore* );

    void selfAvoid();

    //Here are helping functions
    void setHDomain(const biu::LatticeFrame* latFrame,cpsp::HCore* hCore);

    void setOutCoreDomain(const std::string *sequence,const biu::LatticeFrame* latFrame,cpsp::HCore* hCore);

    void setBHDomain(const biu::LatticeFrame* latFrame,cpsp::HCore* hCore);

    int getMaxHull(const std::string *sequence);

    void printSol(const std::string* seq,const biu::LatticeFrame* latFrame);

    std::string printAsMoves(const std::string* seq,const biu::LatticeFrame* latFrame);

    void printAsDrowMoves(const std::string* seq,const biu::LatticeFrame* latFrame);
public:
    SideChainThreading(const std::string *sequence,
            const biu::LatticeFrame* latFrame,const biu::IndexVec* neighVecs,
            cpsp::HCore* hCore,const biu::IPointVec* shiftVec=NULL, bool withBreakingSymmetry=true);

    SideChainThreading(bool , SideChainThreading& );

    virtual Gecode::Space* copy(bool share);

    virtual std::string print(const std::string* sequence,const biu::LatticeFrame* latFrame,int option=0);


    virtual ~SideChainThreading();

    IntVarArray Hs;

    IntVarArray Ps;

    IntVarArray BHs;

    IntVarArray BPs;

};
}
}
#endif