MatchAlgorithmUngapped Class Reference

#include <MatchStoreUngapped.h>

Inheritance diagram for MatchAlgorithmUngapped:

[legend]Collaboration diagram for MatchAlgorithmUngapped:

[legend]List of all members.

Public Member Functions
	MatchAlgorithmUngapped (int minToProcess, int numRepeats)
virtual void	generateMatches (HitListVector &hitList, MatchAdder &addMatch)
Private Attributes
int	minToProcess_

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Detailed Description

Definition at line 58 of file MatchStoreUngapped.h.

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Constructor & Destructor Documentation

MatchAlgorithmUngapped::MatchAlgorithmUngapped	(	int	minToProcess,
		int	numRepeats
	)			[inline]

Definition at line 62 of file MatchStoreUngapped.h.

                                        :
    minToProcess_( minToProcess ),
    MatchAlgorithm( numRepeats )
    {}

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Member Function Documentation

void MatchAlgorithmUngapped::generateMatches	(	HitListVector &	hitList,
		MatchAdder &	addMatch
	)			[virtual]

Implements MatchAlgorithm.

Definition at line 65 of file MatchStoreUngapped.cpp.

References DEBUG_L2, and gNumReadingFrames.

  {

    //    HitListVector hitList;
    //    subjectTable.matchSequence( querySeq, hitList, numRepeats_ );
    //   subjectTable.setNumRepeats(numRepeats_);
    //  subjectTable.matchSequence( querySeq, hitList );

    if (dynamic_cast<MatchAdderCodonCodon*>(&addMatch)
        ||dynamic_cast<MatchAdderCodonProtein*>(&addMatch))
    {
      wordLength_ *= gNumReadingFrames; // %%%%%%%%%%%%%% these need to be
      stepLength_ *= gNumReadingFrames; // reset to do proteins again %%%
    }

    sort( hitList.begin(), hitList.end() );

    // for (HitListVector::iterator i(hitList.begin()); i != hitList.end();++i)
    //  DEBUG_L2( "hit "<<i->subjectNum<<" "<< i->diff << " " << i->queryPos );

    if ( hitList.size() == 0 ) return;

    HitListVector::const_iterator i ( hitList.begin() );

    int adjacentBases = wordLength_;
    SequenceNumber adjacentStart = i->queryPos;
    int basesToAdd;

    HitListVector::const_iterator lastHit( i );
    ++i;

    for (  ; i != hitList.end() ; ++i )
    {

      if (    ( i->subjectNum == lastHit->subjectNum )
           && ( i->diff == lastHit->diff ) )
      {
        /*
        if ( i->queryPos - lastHit->queryPos == stepLength_ )
          {
            adjacentBases += stepLength_;
          } // ~if
        */
        basesToAdd = i->queryPos - lastHit->queryPos;
        if (basesToAdd <= stepLength_) 
          // %%%% chg to stepLength + x to handle gaps in query
          {
            adjacentBases += basesToAdd;
          } // ~if
        
        else
        {
          if ( adjacentBases>=minToProcess_)
          {
            DEBUG_L2(lastHit->subjectNum << " " << 
                          adjacentBases << " " <<
                          adjacentStart << " " <<
                          adjacentStart + adjacentBases -1 << " " <<
                          adjacentStart + lastHit->diff << " " <<
                          adjacentStart + lastHit->diff + adjacentBases -1 );

            
            addMatch(     lastHit->subjectNum,
                          adjacentBases,
                          adjacentStart,
                          adjacentStart + adjacentBases -1,
                          adjacentStart + lastHit->diff,
                          adjacentStart + lastHit->diff + adjacentBases -1 );
          }
          adjacentStart = i->queryPos;
          adjacentBases = wordLength_;
        } // ~else
      }
      else
      {
        if( adjacentBases>=minToProcess_)
          {
            DEBUG_L2(lastHit->subjectNum << " " << 
                          adjacentBases << " " <<
                          adjacentStart << " " <<
                          adjacentStart + adjacentBases -1 << " " <<
                          adjacentStart + lastHit->diff << " " <<
                          adjacentStart + lastHit->diff + adjacentBases -1 );
          
                addMatch(         lastHit->subjectNum,
                          adjacentBases,
                          adjacentStart,
                          adjacentStart + adjacentBases -1,
                          adjacentStart + lastHit->diff,
                          adjacentStart + lastHit->diff + adjacentBases -1 );
          }
           adjacentStart = i->queryPos;
           adjacentBases = wordLength_;

      } // ~else
      ++lastHit;
    } // ~for
    if (adjacentBases>=minToProcess_)
      {
            DEBUG_L2(lastHit->subjectNum << " " << 
                          adjacentBases << " " <<
                          adjacentStart << " " <<
                          adjacentStart + adjacentBases -1 << " " <<
                          adjacentStart + lastHit->diff << " " <<
                          adjacentStart + lastHit->diff + adjacentBases -1 );

        addMatch(                 lastHit->subjectNum,
                          adjacentBases,
                          adjacentStart,
                          adjacentStart + adjacentBases -1,
                          adjacentStart + lastHit->diff,
                          adjacentStart + lastHit->diff + adjacentBases -1 );
      }
    return;

  } // ~findMatch

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Member Data Documentation

int MatchAlgorithmUngapped::minToProcess_ [private]

Definition at line 72 of file MatchStoreUngapped.h.

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

• QueryManager/MatchStoreUngapped.h
• QueryManager/MatchStoreUngapped.cpp

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