StochHMM::alignment Class Reference

#include <alignment.h>

List of all members.

Public Member Functions
	alignment ()
double	align (alignment_type typ)
double	align (sequence &target, sequence &query, alignment_type typ)
double	align (sequence &target, sequence &query, alignment_type typ, double match, double mismatch, double gap, double gapext)
double	align (sequence &target, sequence &query, alignment_type typ, const mmMatrix &, double gap, double gapext)
double	calcLambda (std::vector< double > &)
double	estimateLambda ()
double	calc_pvalue ()
void	setMatrix (mmMatrix &)
void	setMatch (double)
void	setMismatch (double)
void	setGap (double value)
void	setGapExt (double value)
void	setTarget (sequence &)
void	setQuery (sequence &)
int	getHighScore ()
size_t	getAlignmentSize ()
std::string	getAlignment ()
void	printAlignment ()
void	printTrellis ()
std::string	traceback ()
std::string	stochasticTraceback ()

Private Member Functions
void	_reset ()
void	_resetSeqs ()
double	_getGapScore (size_t, size_t, tracebackDirection)
void	_initTrellis (size_t, size_t)

Private Attributes
sequence *	target
sequence *	query
track *	tr
std::vector< std::vector< cell > > *	trellis
std::vector< std::vector < double > > *	mMatrix
double	gap
double	gap_ext
double	high_score
size_t	start_position
size_t	end_position

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Detailed Description

Definition at line 46 of file alignment.h.

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Constructor & Destructor Documentation

StochHMM::alignment::alignment

(

)

Definition at line 19 of file alignment.cpp.

                        :gap(0),gap_ext(0),high_score(0),start_position(0),target(NULL),query(NULL),tr(NULL){
        
    
    }

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Member Function Documentation

double StochHMM::alignment::_getGapScore ( size_t  queryIndex, size_t  targetIndex, tracebackDirection  dir  )

private

Definition at line 167 of file alignment.cpp.

References gap, gap_ext, StochHMM::LEFT, and StochHMM::UP.

Referenced by align().

                                                                                               {
        if (gap == gap_ext){
            return gap;
        }
        else{
            if (dir == LEFT){
                if ( (*trellis)[queryIndex][targetIndex].getTraceback() == LEFT){
                    return gap_ext;
                }
                else{
                    return gap;
                }
            }
            else{
                if ( (*trellis)[queryIndex][targetIndex].getTraceback() == UP){
                    return gap_ext;
                }
                else{
                    return gap;
                }
            }
        }
    }

void StochHMM::alignment::_initTrellis ( size_t  rows, size_t  columns  )

private

Definition at line 192 of file alignment.cpp.

References gap, gap_ext, StochHMM::LEFT, StochHMM::NONE, StochHMM::cell::setDiag(), StochHMM::cell::setLeft(), StochHMM::cell::setScore(), StochHMM::cell::setTraceback(), StochHMM::cell::setUp(), trellis, and StochHMM::UP.

Referenced by align().

                                                           {
        if (trellis!=NULL){
            delete trellis;
            trellis=NULL;
        }
        
        cell x;
        x.setTraceback(NONE);
        x.setScore(0.0);
        x.setDiag(0.0);
        x.setLeft(0.0);
        x.setUp(0.0);
        std::vector<cell> row (columns+1,x);
        trellis= new std::vector<std::vector<cell> > (rows+1, row);
        
        (*trellis)[0][0].setTraceback(NONE);
        (*trellis)[0][1].setScore(gap);
        (*trellis)[0][1].setTraceback(LEFT);
        (*trellis)[1][0].setScore(gap);
        (*trellis)[1][0].setTraceback(UP);
        
        for(size_t i=2;i<=columns;i++){
            (*trellis)[0][i].setScore((*trellis)[0][i-1].getScore()+gap_ext);
            (*trellis)[0][i].setTraceback(LEFT);
        }
        
        for(size_t j=2;j<=rows;j++){
            (*trellis)[j][0].setScore((*trellis)[j-1][0].getScore()+gap_ext);
            (*trellis)[j][0].setTraceback(UP);
        }
        return;
    }

void StochHMM::alignment::_reset ( )

private

Definition at line 24 of file alignment.cpp.

References end_position, gap, gap_ext, high_score, mMatrix, query, start_position, target, and tr.

                          {
        target=NULL;
        query=NULL;
        tr=NULL;
        delete mMatrix;
        mMatrix=NULL;
        gap=0;
        gap_ext=0;
        high_score=0;
        start_position=0;
        end_position=0;
        return;
    }

void StochHMM::alignment::_resetSeqs ( )

private

Definition at line 38 of file alignment.cpp.

References end_position, high_score, mMatrix, query, start_position, and target.

Referenced by setQuery(), and setTarget().

                              {
        target=NULL;
        query=NULL;
        delete mMatrix;
        mMatrix=NULL;
        high_score=0;
        start_position=0;
        end_position=0;
    }

double StochHMM::alignment::align

(

alignment_type

typ

)

Definition at line 247 of file alignment.cpp.

References _getGapScore(), _initTrellis(), StochHMM::cGlobal, StochHMM::cLocal, StochHMM::DIAGONAL, StochHMM::sequence::getSymbol(), StochHMM::LEFT, printTrellis(), query, StochHMM::sequence::seqValue(), StochHMM::sequence::size(), target, and StochHMM::UP.

Referenced by align(), and calc_pvalue().

                                              {  //(sequence &top, sequence &side, double gap, double mismatch, double match){
        
        int top_size=target->size();
        int side_size=query->size();
        
        _initTrellis(side_size, top_size);
        double max_score(-INFINITY);
        size_t max_row_index(0);
        size_t max_col_index(0);
                
        //Fill
        for(size_t top_index=1;top_index<=top_size;top_index++){
            for(size_t side_index=1;side_index<=side_size;side_index++){
                //table[side_index-1][top_index-1].setDiag();
                
                short targetLetter = query->seqValue(side_index-1);
                short queryLetter =  target->seqValue(top_index-1);
                
                double diagonal_score = (*trellis)[side_index-1][top_index-1].getScore() + (*mMatrix)[queryLetter][targetLetter];
                
                
                
                double left_score=(*trellis)[side_index][top_index-1].getScore()+_getGapScore(side_index, top_index-1, LEFT);
                
                
                double up_score=(*trellis)[side_index-1][top_index].getScore()+_getGapScore(side_index-1, top_index, UP);
                
                
                
                if (typ == cLocal){
                    if (diagonal_score<0.0){
                        diagonal_score=0.0;
                    }
                    else if (diagonal_score>max_score){
                        max_score = diagonal_score;
                        max_row_index=side_index;
                        max_col_index=top_index;
                    }
                    
                    if (left_score<0.0){
                        left_score=0.0;
                    }
                    else if (left_score>max_score){
                        max_score = left_score;
                        max_row_index=side_index;
                        max_col_index=top_index;
                    }
                    
                    if (up_score<0.0){
                        up_score=0.0;
                    }
                    else if (up_score>max_score){
                        max_score = up_score;
                        max_row_index=side_index;
                        max_col_index=top_index;
                    }
                }
                
                
                if (diagonal_score>=up_score && diagonal_score >= left_score){
                    (*trellis)[side_index][top_index].setScore(diagonal_score);
                    (*trellis)[side_index][top_index].setTraceback(DIAGONAL);
                                    }
                else if(up_score>=left_score){
                    (*trellis)[side_index][top_index].setScore(up_score);
                    (*trellis)[side_index][top_index].setTraceback(UP);
                }
                else{
                    (*trellis)[side_index][top_index].setScore(left_score);
                    (*trellis)[side_index][top_index].setTraceback(LEFT);
                }
            }
        }
        
        std::string align_top;
        std::string align_side;
        std::string align_status;
        
        size_t top_iter;
        size_t side_iter;
        
        if (typ == cGlobal){
            top_iter=top_size;
            side_iter=side_size;
        }
        else if (typ == cLocal){
            top_iter=max_col_index;
            side_iter=max_row_index;
        }
        
        
        while (top_iter!=0 || side_iter!=0){
            
            std::cout << side_iter << "," << top_iter << "\t" << (*trellis)[side_iter][top_iter].getScore() << std::endl;
            
            switch ((*trellis)[side_iter][top_iter].getTraceback()){
                case DIAGONAL:
                    align_side+=query->getSymbol(--side_iter);
                    align_top+=target->getSymbol(--top_iter);
                    align_status+= (query->seqValue(side_iter) != target->seqValue(top_iter)) ? ' ' : '|';
                    break;
                case UP:                    
                    align_side+=query->getSymbol(--side_iter);
                    align_top+="-";
                    align_status+=" ";
                    break;
                case LEFT:
                    //cout << "Case LEFT:" << side_size << "\t" << top_size << endl;
                    
                    align_top+=target->getSymbol(--top_iter);
                    align_side+="-";
                    align_status+=" ";
                    break;
                default:
                    //cout << "We have a problem Houston\n" << endl;
                    break;
            }
            
            
            if (typ == cLocal && fabs((*trellis)[side_iter][top_iter].getScore())<0.001){
                break;
            }
        }
        
        std::reverse(align_top.begin(), align_top.end());
        std::reverse(align_side.begin(), align_side.end());
        std::reverse(align_status.begin(), align_status.end());
        
        std::cout << align_top << std::endl << align_status << std::endl << align_side << std::endl;

        printTrellis();
        return (*trellis)[side_size][top_size].getScore();
    }

double StochHMM::alignment::align	(	sequence &	target,
		sequence &	query,
		alignment_type	typ
	)

double StochHMM::alignment::align	(	sequence &	target,
		sequence &	query,
		alignment_type	typ,
		double	match,
		double	mismatch,
		double	gap,
		double	gapext
	)

Definition at line 235 of file alignment.cpp.

References align(), setGap(), setGapExt(), setMatch(), setMismatch(), setQuery(), and setTarget().

                                                                                                                                 {
        setTarget(tgt);
        setQuery(qu);
        setMatch(mtch);
        setMismatch(mismtch);
        setGap(gp);
        setGapExt(gp_ext);
        return align(typ);
    }

double StochHMM::alignment::align	(	sequence &	target,
		sequence &	query,
		alignment_type	typ,
		const mmMatrix &	,
		double	gap,
		double	gapext
	)

double StochHMM::alignment::calc_pvalue

(

)

Definition at line 400 of file alignment.cpp.

References align(), StochHMM::cGlobal, query, and setQuery().

                                 {
        std::vector<double> scores;
        
        for(int i=0;i<100;++i){
            sequence* oldQuery=query;
            sequence shuffled=shuffle(query);
            setQuery(shuffled);
            double score = align(cGlobal);
            scores.push_back(score);
            std::cout<< score << std::endl;
            query=oldQuery;
        }
        
        return 0.0;
    }

double StochHMM::alignment::calcLambda

(

std::vector< double > &

frequencies

)

Definition at line 382 of file alignment.cpp.

                                                              {
        
        return 0;
    }

double StochHMM::alignment::estimateLambda

(

)

Definition at line 387 of file alignment.cpp.

References mMatrix.

                                    {
        size_t alphaSize = mMatrix->size();
        double estimatedFreq= 1/static_cast<double>(alphaSize);
        
        double expectedScore(0);
        for ( size_t row=0; row<alphaSize; ++row){
            for ( size_t col=0; col<alphaSize; ++col){
                
            }
        }
    }

std::string StochHMM::alignment::getAlignment

(

)

size_t StochHMM::alignment::getAlignmentSize ( )

inline

Definition at line 72 of file alignment.h.

References end_position, and start_position.

                                        {
            if (end_position!=0) return end_position-start_position+1; 
            return 0;
        }

int StochHMM::alignment::getHighScore ( )

inline

Definition at line 70 of file alignment.h.

References high_score.

{return high_score;}

void StochHMM::alignment::printAlignment

(

)

void StochHMM::alignment::printTrellis

(

)

Definition at line 226 of file alignment.cpp.

Referenced by align().

                                {
        for (size_t row=0;row<trellis->size();++row){
            for (size_t col = 0; col<(*trellis)[row].size();++col){
                std::cout << (*trellis)[row][col].getScore() << " " << (*trellis)[row][col].getTraceback() << "\t";
            }
            std::cout << std::endl;
        }
    }

void StochHMM::alignment::setGap ( double  value )

inline

Definition at line 64 of file alignment.h.

Referenced by align().

{gap = value;}

void StochHMM::alignment::setGapExt ( double  value )

inline

Definition at line 65 of file alignment.h.

References gap_ext.

Referenced by align().

{gap_ext = value;}

void StochHMM::alignment::setMatch

(

double

value

)

Definition at line 48 of file alignment.cpp.

References mMatrix, query, StochHMM::sequence::size(), and target.

Referenced by align().

                                        {
        if (target==NULL && query==NULL){
            std::cerr << "Either target or query sequence must be set before defining match matrix" << std::endl;
            return;
        }
        else{
            size_t alphaSize=(target!=NULL) ? target->size() : query->size();
            if (mMatrix==NULL){
                std::vector<double> row (alphaSize, 0.0);
                mMatrix = new mmMatrix;
                mMatrix->insert(mMatrix->begin(),alphaSize,row);
                //std::cout << mMatrix->size() <<std::endl;
                //std::cout << (*mMatrix)[0].size();
            }
            else if (mMatrix->size()!=alphaSize){
                delete mMatrix;
                mMatrix=NULL;
                std::vector<double> row (alphaSize,0.0);
                mMatrix = new mmMatrix;
                mMatrix->insert(mMatrix->begin(),alphaSize,row);
            }
            
            for(size_t i=0;i<alphaSize;++i){
                (*mMatrix)[i][i]=value;
            }
            
        }
        return;
    }

void StochHMM::alignment::setMatrix

(

mmMatrix &

matrix

)

Definition at line 78 of file alignment.cpp.

References mMatrix, query, StochHMM::sequence::size(), and target.

                                             {
        if (target==NULL && query==NULL){
            std::cerr << "Either target or query sequence must be set before defining match matrix" << std::endl;
            return;
        }
        else{
            size_t alphaSize=(target!=NULL) ? target->size() : query->size();
            if (mMatrix==NULL){
                mMatrix=&matrix;
            }
            else{
                delete mMatrix;
                mMatrix=&matrix;
            }
        }
        return;
    }

void StochHMM::alignment::setMismatch

(

double

value

)

Definition at line 96 of file alignment.cpp.

References mMatrix, query, StochHMM::sequence::size(), and target.

Referenced by align().

                                           {
        if (target==NULL && query==NULL){
            std::cerr << "Either target or query sequence must be set before defining match matrix" << std::endl;
            return;
        }
        else{
            size_t alphaSize=(target!=NULL) ? target->size() : query->size();
            if (mMatrix==NULL){
                std::vector<double> row (0.0,alphaSize);
                mMatrix = new mmMatrix;
                mMatrix->insert(mMatrix->begin(),alphaSize,row);
            }
            else if (mMatrix->size()!=alphaSize){
                delete mMatrix;
                mMatrix=NULL;
                std::vector<double> row (0.0,alphaSize);
                mMatrix = new mmMatrix;
                mMatrix->insert(mMatrix->begin(),alphaSize,row);
            }
            
            for(size_t row=0;row<alphaSize;++row){
                for(size_t col=0;col<alphaSize;++col){
                    if (row!=col){
                        (*mMatrix)[row][col]=value;
                    }
                }
            }
        }
        return;
    }

void StochHMM::alignment::setQuery

(

sequence &

seq

)

Definition at line 147 of file alignment.cpp.

References _resetSeqs(), end_position, StochHMM::sequence::getTrack(), high_score, query, start_position, and tr.

Referenced by align(), and calc_pvalue().

                                          {
        track* temp = seq.getTrack();
        if (tr==temp){
            query= &seq;
            high_score=0;
            start_position=0;
            end_position=0;
        }
        else if (tr==NULL){
            query = &seq;
            tr=temp;
        }
        else{
            _resetSeqs();
            query = &seq;
            tr=temp;
        }
        return;
    }

void StochHMM::alignment::setTarget

(

sequence &

seq

)

Definition at line 127 of file alignment.cpp.

References _resetSeqs(), end_position, StochHMM::sequence::getTrack(), high_score, start_position, target, and tr.

Referenced by align().

                                          {
        track* temp = seq.getTrack();
        if (tr==temp){
            target= &seq;
            high_score=0;
            start_position=0;
            end_position=0;
        }
        else if (tr==NULL){
            target = &seq;
            tr=temp;
        }
        else{
            _resetSeqs();
            target = &seq;
            tr=temp;
        }
        return;
    }

std::string StochHMM::alignment::stochasticTraceback

(

)

std::string StochHMM::alignment::traceback

(

)

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Member Data Documentation

size_t StochHMM::alignment::end_position

private

Definition at line 101 of file alignment.h.

Referenced by _reset(), _resetSeqs(), getAlignmentSize(), setQuery(), and setTarget().

double StochHMM::alignment::gap

private

Definition at line 96 of file alignment.h.

Referenced by _getGapScore(), _initTrellis(), and _reset().

double StochHMM::alignment::gap_ext

private

Definition at line 97 of file alignment.h.

Referenced by _getGapScore(), _initTrellis(), _reset(), and setGapExt().

double StochHMM::alignment::high_score

private

Definition at line 99 of file alignment.h.

Referenced by _reset(), _resetSeqs(), getHighScore(), setQuery(), and setTarget().

std::vector<std::vector<double> >* StochHMM::alignment::mMatrix

private

Definition at line 94 of file alignment.h.

Referenced by _reset(), _resetSeqs(), estimateLambda(), setMatch(), setMatrix(), and setMismatch().

sequence* StochHMM::alignment::query

private

Definition at line 89 of file alignment.h.

Referenced by _reset(), _resetSeqs(), align(), calc_pvalue(), setMatch(), setMatrix(), setMismatch(), and setQuery().

size_t StochHMM::alignment::start_position

private

Definition at line 100 of file alignment.h.

Referenced by _reset(), _resetSeqs(), getAlignmentSize(), setQuery(), and setTarget().

sequence* StochHMM::alignment::target

private

Definition at line 88 of file alignment.h.

Referenced by _reset(), _resetSeqs(), align(), setMatch(), setMatrix(), setMismatch(), and setTarget().

track* StochHMM::alignment::tr

private

Definition at line 91 of file alignment.h.

Referenced by _reset(), setQuery(), and setTarget().

std::vector<std::vector<cell> >* StochHMM::alignment::trellis

private

Definition at line 93 of file alignment.h.

Referenced by _initTrellis().

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

• alignment.h
• alignment.cpp