splign_compartment_finder.hpp

ncbi源码

/*
 * ===========================================================================
 * PRODUCTION $Log: splign_compartment_finder.hpp,v $
 * PRODUCTION Revision 1000.0  2004/06/01 18:12:38  gouriano
 * PRODUCTION PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.4
 * PRODUCTION
 * ===========================================================================
 */

#ifndef ALGO_ALIGN_SPLIGN_COMPARTMENT_FINDER__HPP
#define ALGO_ALIGN_SPLIGN_COMPARTMENT_FINDER__HPP

/* $Id: splign_compartment_finder.hpp,v 1000.0 2004/06/01 18:12:38 gouriano Exp $
* ===========================================================================
*
*                            PUBLIC DOMAIN NOTICE                          
*               National Center for Biotechnology Information
*                                                                          
*  This software/database is a "United States Government Work" under the   
*  terms of the United States Copyright Act.  It was written as part of    
*  the author's official duties as a United States Government employee and 
*  thus cannot be copyrighted.  This software/database is freely available 
*  to the public for use. The National Library of Medicine and the U.S.    
*  Government have not placed any restriction on its use or reproduction.  
*                                                                          
*  Although all reasonable efforts have been taken to ensure the accuracy  
*  and reliability of the software and data, the NLM and the U.S.          
*  Government do not and cannot warrant the performance or results that    
*  may be obtained by using this software or data. The NLM and the U.S.    
*  Government disclaim all warranties, express or implied, including       
*  warranties of performance, merchantability or fitness for any particular
*  purpose.                                                                
*                                                                          
*  Please cite the author in any work or product based on this material.   
*
* ===========================================================================
*
* Author:  Yuri Kapustin
*
* File Description:  Compartment Finder
*                   
* ===========================================================================
*/


#include <algo/align/splign/splign_hit.hpp>
#include <corelib/ncbi_limits.hpp>
#include <vector>


BEGIN_NCBI_SCOPE


// Detect all compartments over a hit set
class CCompartmentFinder {

public:

  // hits must be in plus strand
  CCompartmentFinder(vector<CHit>::const_iterator start,
                     vector<CHit>::const_iterator finish);

  // setters and getters
  void SetIntronLimits(size_t intr_min, size_t intr_max) {
    m_intron_min = intr_min;
    m_intron_max = intr_max;
  }

  static size_t GetDefaultIntronMin(void) {
    return 0;
  }

  static size_t GetDefaultIntronMax(void) {
    return 750000;
  }

  void SetPenalty(size_t penalty) {
    m_penalty = penalty;
  }

  void SetMinCoverage(size_t mincov) {
    m_min_coverage = mincov;
  }

  static size_t GetDefaultPenalty(void) {
    return 1000;
  }

  static size_t GetDefaultMinCoverage(void) {
    return 500;
  }


  size_t Run(void); // do the compartment search

  // order compartments by lower subj coordinate
  void OrderCompartments(void);

  // single compartment representation
  class CCompartment {

  public:

    CCompartment(void) {
      m_coverage = 0;
      m_box[0] = m_box[2] = kMax_UInt;
      m_box[1] = m_box[3] = 0;
    }
    
    const vector<const CHit*>& GetMembers(void) {
      return m_members;
    }
    
    void AddMember(const CHit* hit) {
      m_members.push_back(hit);
    }
    
    void UpdateMinMax(void);

    bool GetStrand(void) const;

    const CHit* GetFirst(void) const {
      m_iter = 0;
      return GetNext();
    }

    const CHit* GetNext(void) const {
      if(m_iter < m_members.size()) {
        return m_members[m_iter++];
      }
      return 0;
    }

    const size_t* GetBox(void) const {
      return m_box;
    }

    bool operator < (const CCompartment& rhs) {
      return m_coverage < rhs.m_coverage;
    }

    friend bool PLowerSubj(const CCompartment& c1, const CCompartment& c2) {
      return c1.m_box[2] < c2.m_box[2];
    }

  protected:

    size_t              m_coverage;
    vector<const CHit*> m_members;
    size_t              m_box[4];
    mutable size_t      m_iter;
  };

  // iterate through compartments
  CCompartment* GetFirst(void);
  CCompartment* GetNext(void);


private:

  size_t                m_intron_min, m_intron_max; // intron limits
  size_t                m_penalty;                  // penalty per compartment
  size_t                m_min_coverage;

  vector<const CHit*>   m_hits;         // input hits
  vector<CCompartment>  m_compartments; // final compartments
  int                   m_iter;         // GetFirst/Next index

  // this structure describes the best target reached 
  // at a given query coordinatea  
  struct SQueryMark {
    size_t       m_coord;
    int          m_score;
    int          m_hit;

    SQueryMark(size_t coord, int score, int hit):
      m_coord(coord), m_score(score), m_hit(hit) {}

    bool operator < (const SQueryMark& rhs) const {
      return m_coord < rhs.m_coord;
    }
  };

  struct SHitStatus {

    enum EType {
      eNone, 
      eExtension,
      eOpening
    };

    EType m_type;
    int   m_prev;

    SHitStatus(void): m_type(eNone), m_prev(-1) {}
    SHitStatus(EType type, int prev): m_type(type), m_prev(prev) {}

  };

};


// Facilitate access to compartments over a hit set
class CCompartmentAccessor
{
public:

  // [start,finish) are assumed to share same query and subj
  CCompartmentAccessor(vector<CHit>::iterator start,
                       vector<CHit>::iterator finish,
                       size_t comp_penalty_bps,
                       size_t min_coverage);
  
  bool GetFirst(vector<CHit>& compartment);
  bool GetNext(vector<CHit>& compartment);

  size_t GetCount(void) const {
    return m_pending.size();
  }

  void Get(size_t i, vector<CHit>& compartment) const {
    compartment = m_pending[i];
  }

  const size_t* GetBox(size_t i) const {
    return &m_ranges.front() + i*4;
  }

  bool GetStrand(size_t i) const {
    return m_strands[i];
  }


private:

  vector<vector<CHit> > m_pending;
  vector<size_t>        m_ranges;
  vector<bool>          m_strands;
  size_t                m_iter;


  void x_Copy2Pending(CCompartmentFinder& finder);
};


END_NCBI_SCOPE


/*
 * ===========================================================================
 * $Log: splign_compartment_finder.hpp,v $
 * Revision 1000.0  2004/06/01 18:12:38  gouriano
 * PRODUCTION: IMPORTED [GCC34_MSVC7] Dev-tree R1.4
 *
 * Revision 1.4  2004/05/04 15:23:45  ucko
 * Split splign code out of xalgoalign into new xalgosplign.
 *
 * Revision 1.3  2004/04/23 14:37:44  kapustin
 * *** empty log message ***
 *
 * ==========================================================================
 */

#endif