PathMatrix< PATH_TYPE > Class Template Reference

#include <MatchAligner.h>

List of all members.

Public Types
typedef pair< vector< vector< PATH_TYPE > >::iterator, vector< PATH_TYPE >::iterator >	CellIterator
Public Member Functions
template<class MATRIX_FILLER>
ScoreType	fillIn (MATRIX_FILLER &doMatrix)
template<class TRACE_BACKER>
void	traceBack (TRACE_BACKER &doCell)
Public Attributes
CellIterator	lastCell_

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Detailed Description

template<class PATH_TYPE>
class PathMatrix< PATH_TYPE >

Definition at line 518 of file MatchAligner.h.

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Member Typedef Documentation

template<class PATH_TYPE>

typedef pair<vector<vector<PATH_TYPE> >::iterator, vector<PATH_TYPE>::iterator> PathMatrix< PATH_TYPE >::CellIterator

Definition at line 523 of file MatchAligner.h.

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Member Function Documentation

template<class PATH_TYPE>

template<class MATRIX_FILLER>

ScoreType PathMatrix< PATH_TYPE >::fillIn

(

MATRIX_FILLER &

doMatrix

)

[inline]

Definition at line 525 of file MatchAligner.h.

Referenced by MatchAlignerTranslated::createAlignment(), and MatchAligner::createAlignment().

  {
    return doMatrix(*this);
  } // ~fillIn

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template<class PATH_TYPE>

template<class TRACE_BACKER>

void PathMatrix< PATH_TYPE >::traceBack

(

TRACE_BACKER &

doCell

)

[inline]

Definition at line 531 of file MatchAligner.h.

References PathMatrix< PATH_TYPE >::lastCell_.

Referenced by MatchAlignerTranslated::createAlignment(), and MatchAligner::createAlignment().

  {
    // NB we are tracing back from finish to start
    //    CellIterator start; 
    //    start.first = &front();
    //  start.second = front().begin()+startPos;
    //    finish.first =  &back();  
    //    finish.second = back().begin()+finishPos;
 
    CellIterator current = lastCell_;
    //    current.first =  &back();  
    //  current.second = back().begin()+finishPos;
    //    cout << "Cell iterator - column: " << current.first-begin()
    //  << " row: " << current.second-current.first->begin() << endl;
    while( doCell(current) );
    // {
    //   cout << "Cell iterator - column: " << current.first-begin()
    //   << " row: " << current.second-current.first->begin() << endl;
    // }

  } // ~traceBack

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Member Data Documentation

template<class PATH_TYPE>

CellIterator PathMatrix< PATH_TYPE >::lastCell_

Definition at line 553 of file MatchAligner.h.

Referenced by ColumnFillerBasic::operator()(), and PathMatrix< PATH_TYPE >::traceBack().

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

• QueryManager/MatchAligner.h

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