ColumnFillerBasic Class Reference

#include <MatchAligner.h>

Collaboration diagram for ColumnFillerBasic:

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List of all members.

Public Member Functions

 ColumnFillerBasic (const char *p1, int p1Size, const char *p2, int p2Size, int bandExtension, const ScoreTable &scoreTable)
ScoreType operator() (PathMatrix< PathType > &matrix)

Private Attributes

const char * p1_
const char * p2_
int bandExtension_
const int bandWidth_
const int bandLength_
const int colSize_
CellFiller fillCell_
vector< ScoreType > v1_
vector< ScoreType > v2_
vector< ScoreType > * pLast_
vector< ScoreType > * pCurrent_
vector< ScoreType > * temp_
ScoreMaker getScore_
ScoreType gapScore_

Detailed Description

Definition at line 619 of file MatchAligner.h.

Constructor & Destructor Documentation

ColumnFillerBasic::ColumnFillerBasic ( const char *  p1,
int  p1Size,
const char *  p2,
int  p2Size,
int  bandExtension,
const ScoreTable &  scoreTable 
) [inline]

Definition at line 622 of file MatchAligner.h.

00625                                                    :
00626     p1_(p1), 
00627     p2_(p2), 
00628     //    bandExtension_(bandExtension),
00629     bandExtension_( (bandExtension<(p1Size/2))
00630                     ? bandExtension
00631                     : max( (p1Size/2)-1, 0 ) ), 
00632     bandWidth_(p2Size-p1Size+1),
00633     bandLength_(p1Size+1),
00634     colSize_(p2Size-p1Size+1+(2*bandExtension_)),
00635     //    scoresPossible_(3),
00636     fillCell_(),
00637     v1_(colSize_, veryBadScoreIndeed ), 
00638     v2_(colSize_, veryBadScoreIndeed ),
00639     pLast_(&v1_),
00640     pCurrent_(&v2_),
00641     getScore_(scoreTable),
00642     gapScore_(getScore_.getGapScore())
00643     {
00644       // TBD check bandExtension_ is not too big
00645     }
  ScoreType operator()( PathMatrix<PathType>& matrix );

Member Function Documentation

ScoreType ColumnFillerBasic::operator() ( PathMatrix< PathType > &  matrix  ) 

Definition at line 1002 of file MatchAligner.cpp.

References bandExtension_, bandLength_, colSize_, fillCell_, fromFinished, gapScore_, getScore_, PathMatrix< PATH_TYPE >::lastCell_, p1_, p2_, pCurrent_, pLast_, temp_, v1_, v2_, and veryBadScoreIndeed.

01003 {
01004   ScoreType lastScore;
01005   int i,j;
01006 
01007   matrix.resize(bandLength_, vector<PathType>(colSize_) );
01008 
01009   // Fill in first column
01010   matrix[0][bandExtension_]=fromFinished;
01011   v1_[bandExtension_]=0;
01012 
01013   //  cout << "doing first column" << endl;
01014   for (j= bandExtension_+1; j< colSize_ ; j++)
01015   {
01016     v1_[j] = fillCell_( matrix[0][j],
01017                         veryBadScoreIndeed,
01018                         veryBadScoreIndeed,
01019                         v1_[j-1]+gapScore_);
01020 
01021   } // ~for i
01022   //  print (v1_);
01023   pLast_    = &v1_;
01024   pCurrent_ = &v2_;
01025 
01026 
01027   // Fill in next bandExtension_ columns
01028 
01029   for ( i=1 ; i <= bandExtension_ ; i++  ) // NB <= not <
01030   {
01031     //    cout << "doing leftmost columns" << i << endl;
01032 
01033     lastScore = fillCell_( matrix[i][bandExtension_-i],
01034                                  veryBadScoreIndeed,
01035                                  (*pLast_)[bandExtension_-i+1]+gapScore_,
01036                                  veryBadScoreIndeed );
01037     (*pCurrent_)[bandExtension_-i]=lastScore;
01038     for ( j=bandExtension_-i+1; j < colSize_-1 ; j++)
01039     {
01040       lastScore = fillCell_
01041         ( matrix[i][j],
01042           (*pLast_)[j]
01043           + getScore_(p1_[i-1],p2_[j-bandExtension_+i-1]),
01044           //      + ((tolower(p1_[i-1])==tolower(p2_[j-bandExtension_+i-1])) 
01045           //         ? matchScore : mismatchScore),
01046           (*pLast_)[j+1]    + gapScore_,
01047           lastScore + gapScore_ );
01048       (*pCurrent_)[j] = lastScore;
01049     } // ~for j
01050 
01051     (*pCurrent_)[j] = fillCell_
01052       ( matrix[i][j],
01053         (*pLast_)[j]
01054         + getScore_(p1_[i-1],p2_[j-bandExtension_+i-1]),
01055         // + ((tolower(p1_[i-1])==tolower(p2_[j-bandExtension_+i-1])) ?
01056         //   matchScore : mismatchScore),
01057         veryBadScoreIndeed,
01058         lastScore + gapScore_ );
01059     //  print (*pCurrent_);
01060     temp_ = pCurrent_; pCurrent_ = pLast_; pLast_ = temp_;
01061   } // ~for i
01062 
01063 
01064   // Fill in main set of columns
01065   for ( i=(bandExtension_+1) ; 
01066         i < bandLength_ -bandExtension_; 
01067         i++ ) 
01068   {
01069     //    cout << "doing centre columns" << i << endl;
01070 
01071     lastScore = veryBadScoreIndeed;
01072 
01073     for ( j=0; j < colSize_-1 ; j++)
01074     {
01075       lastScore = fillCell_
01076         ( matrix[i][j],
01077           (*pLast_)[j]
01078           + getScore_(p1_[i-1],p2_[j-bandExtension_+i-1]),
01079           //      + ((tolower(p1_[i-1])==tolower(p2_[j-bandExtension_+i-1])) 
01080           //   ? matchScore : mismatchScore),
01081           (*pLast_)[j+1]    + gapScore_,
01082           lastScore + gapScore_ );
01083       (*pCurrent_)[j]=lastScore;
01084     } // ~for j
01085 
01086     (*pCurrent_)[j] = fillCell_
01087       ( matrix[i][j],
01088         (*pLast_)[j]
01089         + getScore_(p1_[i-1],p2_[j-bandExtension_+i-1]),
01090         //      + ((tolower(p1_[i-1])==tolower(p2_[j-bandExtension_+i-1])) 
01091         // ? matchScore : mismatchScore),
01092           veryBadScoreIndeed,
01093           lastScore + gapScore_ );
01094     //  print (*pCurrent_);
01095     temp_ = pCurrent_; pCurrent_ = pLast_; pLast_ = temp_;
01096 
01097   } // ~for i
01098 
01099   // Fill in last bandExtension_ columns;
01100 
01101 
01102   for ( i=bandLength_-bandExtension_ ; i < bandLength_ ; i++ ) 
01103   {
01104     //    cout << "doing rightmost columns" << i << endl;
01105 
01106     lastScore = veryBadScoreIndeed;
01107 
01108     for ( j=0; j < colSize_-1-i-bandExtension_+bandLength_ ; j++)
01109     {
01110       lastScore = fillCell_
01111         ( matrix[i][j], 
01112           (*pLast_)[j]
01113           + getScore_(p1_[i-1],p2_[j-bandExtension_+i-1]),
01114           //      + ((tolower(p1_[i-1])
01115           //   ==tolower(p2_[j-bandExtension_+i-1])) 
01116           // ? matchScore : mismatchScore),
01117           (*pLast_)[j+1]    + gapScore_,
01118           lastScore + gapScore_ );
01119       (*pCurrent_)[j]=lastScore;
01120     } // ~for j
01121     //  print (*pCurrent_);
01122     temp_ = pCurrent_; pCurrent_ = pLast_; pLast_ = temp_;
01123 
01124   } // ~for i
01125 
01126   // Set position of the last cell filled in ready for
01127   // the traceback
01128   matrix.lastCell_.first
01129     = matrix.end()-1;
01130   matrix.lastCell_.second
01131     = matrix.lastCell_.first->begin() + (colSize_-bandExtension_-1);
01132 
01133   return (*pLast_)[colSize_-bandExtension_-1];
01134 
01135 } // ~void ColumnFillerBasic::operator()

Member Data Documentation

const char* ColumnFillerBasic::p1_ [private]

Definition at line 648 of file MatchAligner.h.

Referenced by ColumnFiller3D::ColumnFiller3D(), and operator()().

const char* ColumnFillerBasic::p2_ [private]

Definition at line 649 of file MatchAligner.h.

Referenced by ColumnFiller3D::ColumnFiller3D(), and operator()().

int ColumnFillerBasic::bandExtension_ [private]

Definition at line 650 of file MatchAligner.h.

Referenced by operator()().

const int ColumnFillerBasic::bandWidth_ [private]

Definition at line 651 of file MatchAligner.h.

const int ColumnFillerBasic::bandLength_ [private]

Definition at line 652 of file MatchAligner.h.

Referenced by operator()().

const int ColumnFillerBasic::colSize_ [private]

Definition at line 653 of file MatchAligner.h.

Referenced by operator()().

CellFiller ColumnFillerBasic::fillCell_ [private]

Definition at line 654 of file MatchAligner.h.

Referenced by operator()().

vector<ScoreType> ColumnFillerBasic::v1_ [private]

Definition at line 656 of file MatchAligner.h.

Referenced by operator()().

vector<ScoreType> ColumnFillerBasic::v2_ [private]

Definition at line 657 of file MatchAligner.h.

Referenced by operator()().

vector<ScoreType>* ColumnFillerBasic::pLast_ [private]

Definition at line 658 of file MatchAligner.h.

Referenced by operator()().

vector<ScoreType>* ColumnFillerBasic::pCurrent_ [private]

Definition at line 659 of file MatchAligner.h.

Referenced by operator()().

vector<ScoreType>* ColumnFillerBasic::temp_ [private]

Definition at line 660 of file MatchAligner.h.

Referenced by operator()().

ScoreMaker ColumnFillerBasic::getScore_ [private]

Definition at line 661 of file MatchAligner.h.

Referenced by operator()().

ScoreType ColumnFillerBasic::gapScore_ [private]

Definition at line 662 of file MatchAligner.h.

Referenced by operator()().

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