MatchAlignerTranslatedDNA Class Reference

#include <MatchAligner.h>

Inheritance diagram for MatchAlignerTranslatedDNA:

[legend]Collaboration diagram for MatchAlignerTranslatedDNA:

[legend]List of all members.

Public Member Functions
	MatchAlignerTranslatedDNA (int numCols=80, int bandExtension=0, ostream &outputStream=cout)
virtual void	formatAlignment (Alignment &alignment, const char *pQuery, int queryStart, int queryEnd, const char *pSubject, int subjectStart, int subjectEnd)

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Detailed Description

Definition at line 357 of file MatchAligner.h.

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Constructor & Destructor Documentation

MatchAlignerTranslatedDNA::MatchAlignerTranslatedDNA	(	int	numCols = 80,
		int	bandExtension = 0,
		ostream &	outputStream = cout
	)			[inline]

Definition at line 360 of file MatchAligner.h.

                                                          :
    MatchAlignerTranslated( numCols, 
                            bandExtension,
                            false, 
                            false, 
                            outputStream )
    {} // ~MatchAlignerTranslatedDNA::MatchAlignerTranslatedDNA

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Member Function Documentation

void MatchAlignerTranslatedDNA::formatAlignment	(	Alignment &	alignment,
		const char *	pQuery,
		int	queryStart,
		int	queryEnd,
		const char *	pSubject,
		int	subjectStart,
		int	subjectEnd
	)			[virtual]

Reimplemented from MatchAligner.

Definition at line 874 of file MatchAligner.cpp.

References alignBreakFrameShiftQuery, alignBreakFrameShiftSubject, alignBreakMismatch, MatchAligner::matchChar(), MatchAligner::numCols_, MatchAligner::outputAlignmentColumn(), MatchAligner::outputAlignmentLine(), MatchAligner::outputStream_, MatchAligner::pBufSeq1_, MatchAligner::pCursorAlign_, MatchAligner::pCursorSeq1_, MatchAligner::pCursorSeq2_, and Alignment::totalScore_.

{

  outputStream_ << "Alignment score: " << alignment.totalScore_ << endl;

  int queryNext(queryStart);
  int subjectNext(subjectStart);
  char codonChar;

  pCursorSeq1_ = &pBufSeq1_[numCols_]; // triggers reset to start of line

  *pBufSeq1_='\0'; // ensures 3 null strings are printed at first line break 
  //  *pBufSeq2_='\0'; // - this line not necessary??
  //  *pBufAlign_='\0'; // - this line not necessary??

  Alignment::iterator i(alignment.begin());

  while( i!=alignment.end() ) 
  {
    //    cout << queryNext << " " << subjectNext << endl;
    
    if (i->numMatches>0)
    { // TBD do these en masse?
      codonChar = getCodon( pQuery );
      if ((codonChar!='X')&&(codonChar == getCodon(pSubject)))
      {
        outputAlignmentColumn
        (
         *(pQuery++),
         codonChar,
         *(pSubject++), 
         queryNext++, 
         subjectNext++ 
        ); 
        outputAlignmentColumn
          (*(pQuery++), '.', *(pSubject++), queryNext++, subjectNext++ ); 
        outputAlignmentColumn
        (*(pQuery++), '.', *(pSubject++), queryNext++, subjectNext++ ); 
      } // ~if
      else
      {
        outputAlignmentColumn
          ( *pQuery, matchChar(*pQuery,*pSubject) ? '|' : 'x', *pSubject, queryNext++, subjectNext++ );
        pQuery++; pSubject++;
        outputAlignmentColumn
          ( *pQuery, matchChar(*pQuery,*pSubject) ? '|' : 'x', *pSubject, queryNext++, subjectNext++ );
        pQuery++; pSubject++;
        outputAlignmentColumn
          ( *pQuery, matchChar(*pQuery,*pSubject) ? '|' : 'x', *pSubject, queryNext++, subjectNext++ );
        pQuery++; pSubject++;
      } // ~else

    i->numMatches--;
    }
    else
    {
#ifdef XXX
      if (i->breakType==alignBreakMismatch)
      {
        outputAlignmentColumn
          (*(pQuery++), 'x', *(pSubject++), queryNext++, subjectNext++ ); 
        outputAlignmentColumn
          (*(pQuery++), 'x', *(pSubject++), queryNext++, subjectNext++ ); 
        outputAlignmentColumn
          (*(pQuery++), 'x', *(pSubject++), queryNext++, subjectNext++ ); 
      } // ~if
      else 
#endif
      if (i->breakType==alignBreakFrameShiftQuery)
      {
        outputAlignmentColumn
          (*(pQuery++), ' ', '-', queryNext++, subjectNext ); 

      } // ~else if
      else if (i->breakType==alignBreakFrameShiftSubject)
      {
        outputAlignmentColumn
          ( '-', ' ', *(pSubject++), queryNext, subjectNext++ ); 
      } // ~else if
      i++;
    } // ~else

  } // ~while

  *pCursorSeq1_='\0';
  *pCursorSeq2_='\0';
  *pCursorAlign_='\0';

  outputAlignmentLine();



} // ~MatchAlignerTranslatedDNA::formatAlignment

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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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