TraceBackerBasic Class Reference

#include <MatchAligner.h>

Collaboration diagram for TraceBackerBasic:

[legend]List of all members.

Public Member Functions
	TraceBackerBasic (AlignBreakType p1Gap, AlignBreakType p2Gap, Alignment &alignment)
bool	operator() (PathMatrix< PathType >::CellIterator &current)
Private Attributes
AlignBreakType	p1Gap_
AlignBreakType	p2Gap_
Alignment &	alignment_

---

Detailed Description

Definition at line 669 of file MatchAligner.h.

---

Constructor & Destructor Documentation

TraceBackerBasic::TraceBackerBasic	(	AlignBreakType	p1Gap,
		AlignBreakType	p2Gap,
		Alignment &	alignment
	)			[inline]

Definition at line 672 of file MatchAligner.h.

                                           :
    p1Gap_(p1Gap), p2Gap_(p2Gap),
    alignment_(alignment) {}

---

Member Function Documentation

bool TraceBackerBasic::operator()

(

PathMatrix< PathType >::CellIterator &

current

)

Definition at line 1139 of file MatchAligner.cpp.

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

{
  //  cout << (int)(current.second-current.first->begin());

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

  if (*current.second&fromFinished)
  {
    //    cout << "finished traceback" << endl;
    return false;
  } // ~if
  else if (*current.second&fromW)
  {
    //    cout << "going W" << endl;
    current.second 
      = (current.first-1)->begin() 
      + (current.second-current.first->begin());
    --current.first;
    alignment_.front().numMatches++; // doesn't check for mismatch
  } // ~else if
  else if (*current.second&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&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 assert (1==0);

  return true;
} // ~bool TraceBackerBasic::operator()

---

Member Data Documentation

AlignBreakType TraceBackerBasic::p1Gap_ [private]

Definition at line 679 of file MatchAligner.h.

AlignBreakType TraceBackerBasic::p2Gap_ [private]

Definition at line 680 of file MatchAligner.h.

Alignment& TraceBackerBasic::alignment_ [private]

Definition at line 681 of file MatchAligner.h.

---

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

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

---