TraceBacker3D Class Reference

#include <MatchAligner.h>

Collaboration diagram for TraceBacker3D:

[legend]List of all members.

Public Member Functions
	TraceBacker3D (int queryFinalFrame, int subjectFinalFrame, bool p1IsQuery, Alignment &alignment)
bool	operator() (PathMatrix< PathType3D >::CellIterator &current)
Private Attributes
AlignBreakType	p1Gap_
AlignBreakType	p2Gap_
AlignBreakType	p1FrameShift_
AlignBreakType	p2FrameShift_
int	k_
int	l_
Alignment &	alignment_

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Detailed Description

Definition at line 927 of file MatchAligner.h.

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Constructor & Destructor Documentation

TraceBacker3D::TraceBacker3D	(	int	queryFinalFrame,
		int	subjectFinalFrame,
		bool	p1IsQuery,
		Alignment &	alignment
	)			[inline]

Definition at line 937 of file MatchAligner.h.

00939                                         :
00940     p1Gap_( (p1IsQuery) ? 
00941             alignBreakGapQuery : alignBreakGapSubject ),
00942     p2Gap_( (p1IsQuery) ? 
00943             alignBreakGapSubject : alignBreakGapQuery ),
00944     p1FrameShift_( (p1IsQuery) ? 
00945                    alignBreakFrameShiftQuery : alignBreakFrameShiftSubject ),
00946     p2FrameShift_( (p1IsQuery) ? 
00947                    alignBreakFrameShiftSubject : alignBreakFrameShiftQuery ),
00948     k_( (p1IsQuery) ? 
00949         queryFinalFrame : subjectFinalFrame ), 
00950     l_( (p1IsQuery) ? 
00951         subjectFinalFrame : queryFinalFrame ), 
00952     alignment_(alignment) 
00953     {}
  bool operator()( PathMatrix<PathType3D>::CellIterator& current );

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Member Function Documentation

bool TraceBacker3D::operator()

(

PathMatrix< PathType3D >::CellIterator &

current

)

Definition at line 1410 of file MatchAligner.cpp.

References alignBreakNull, fromFinished, fromN, fromPrevFrame1, fromPrevFrame2, fromSW, and fromW.

{

  //    cout << (int)(current.second-current.first->begin())
  // << " frame1: " << k_ << " frame2: " << l_ 
  // << endl;

  alignment_.push_front( AlignInfo() );
  alignment_.front().breakType=alignBreakNull;

  if (((*current.second)[k_][l_])&fromFinished)
  {
    return false;
  }
  else if (((*current.second)[k_][l_])&fromW)
  {
    //  cout << "going W" << endl;
    current.second 
      = (current.first-1)->begin() 
      + (current.second-current.first->begin());
    --current.first;
    alignment_.front().numMatches++;
  } // ~else if
  else if (((*current.second)[k_][l_])&fromN)
  {
    //    cout << "going N" << endl;
    assert(current.second!=current.first->begin());
    --current.second;
    alignment_.push_front( AlignInfo() );
    alignment_.front().breakType=p1Gap_;
  } // ~else if
  else if (((*current.second)[k_][l_])&fromSW)
  {
    //    cout << "going SW" << endl;
    current.second 
      = (current.first-1)->begin() 
      + (current.second-current.first->begin());
    ++current.second;
    --current.first;
    alignment_.push_front( AlignInfo() );
    alignment_.front().breakType=p2Gap_;
  } // ~else if
  else if (((*current.second)[k_][l_])&fromPrevFrame1)
  {
    //    cout << "shifting frame p1" << endl;
    if (k_==0)
    { // then need to do a SW shift
      // (equivalent to a W shift in the full d.p. matrix)
      current.second 
        = (current.first-1)->begin() 
        + (current.second-current.first->begin());
      ++current.second;
      --current.first;
      k_=2;
    } // ~if
    else k_--;
    alignment_.push_front( AlignInfo() );
    alignment_.front().breakType=p1FrameShift_;
  } // ~else if
  else if (((*current.second)[k_][l_])&fromPrevFrame2)
  {
    //    cout << "shifting frame p2" << endl;
    if (l_==0)
    { // then need to do a N shift
      // (equivalent to a N shift in the full d.p. matrix)
      assert(current.second!=current.first->begin());
      --current.second;
      l_=2;
    } // ~if
    else l_--;
    alignment_.push_front( AlignInfo() );
    alignment_.front().breakType=p2FrameShift_;
  } // ~else if
  else assert (1==0);

  return true;

} // ~bool TraceBacker3D::operator()

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Member Data Documentation

AlignBreakType TraceBacker3D::p1Gap_ [private]

Definition at line 957 of file MatchAligner.h.

AlignBreakType TraceBacker3D::p2Gap_ [private]

Definition at line 958 of file MatchAligner.h.

AlignBreakType TraceBacker3D::p1FrameShift_ [private]

Definition at line 959 of file MatchAligner.h.

AlignBreakType TraceBacker3D::p2FrameShift_ [private]

Definition at line 960 of file MatchAligner.h.

int TraceBacker3D::k_ [private]

Definition at line 962 of file MatchAligner.h.

int TraceBacker3D::l_ [private]

Definition at line 963 of file MatchAligner.h.

Alignment& TraceBacker3D::alignment_ [private]

Definition at line 964 of file MatchAligner.h.

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The documentation for this class was generated from the following files:

• QueryManager/MatchAligner.h
• QueryManager/MatchAligner.cpp

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