#include <traceback_path.h>

Public Member Functions
	multiTraceback ()
	Create multiTraceback()
	~multiTraceback ()
	Destroy multiTraceback.
void	begin ()
	Set position in multiTraceback to the beginning.
void	end ()
	Set position in multiTraceback to the ending.
void	operator++ ()
	Increment the iterator to next position.
void	operator-- ()
	Decrement the iterator to previous position.
void	operator= (size_t)
void	print_path ()
void	print_label ()
void	print_gff (std::string &)
void	print_hits ()
traceback_path	path ()
	Get traceback_path at currently set index in multiTraceback.
int	counts ()
	Get the number times that traceback_path was recorded in multiple traceback.
traceback_path	operator[] (size_t)
void	assign (traceback_path &)
void	finalize ()
	Sorts the multiTraceback by the number of time a particular tracback path occurred.
void	clear ()
size_t	size ()
heatTable *	get_hit_table ()

Private Attributes
size_t	vectorIterator
size_t	maxSize
std::vector< std::map < traceback_path, int > ::iterator >	pathAccess
std::map< traceback_path, int >	paths
heatTable *	table

Detailed Description

Contains multiple tracebacks. Will store them in sorted unique list (sorted in order of number of occurances);

Definition at line 169 of file traceback_path.h.

Constructor & Destructor Documentation

StochHMM::multiTraceback::multiTraceback ( )

Create multiTraceback()

Definition at line 441 of file traceback_path.cpp.

References maxSize, and vectorIterator.

                                  {
        maxSize=0;
        vectorIterator=0;
        table=NULL;
    }

StochHMM::multiTraceback::~multiTraceback ( )

Destroy multiTraceback.

Definition at line 448 of file traceback_path.cpp.

References table.

                                   {
        if(table!=NULL){
            delete table;
        }
    }

Member Function Documentation

void StochHMM::multiTraceback::assign ( traceback_path & path )

Add traceback_path to multiTraceback

Parameters:

path	Traceback path to add

Definition at line 512 of file traceback_path.cpp.

References path(), and paths.

Referenced by StochHMM::trellis::stochastic_traceback(), and StochHMM::trellis::traceback_stoch_posterior().

                                                   {
        paths[path]++;
        return;
    }

void StochHMM::multiTraceback::begin ( )

Set position in multiTraceback to the beginning.

Definition at line 455 of file traceback_path.cpp.

References vectorIterator.

                              {
        vectorIterator=0;
        return;
    }

void StochHMM::multiTraceback::clear ( )

inline

Definition at line 200 of file traceback_path.h.

References paths.

{paths.clear();return;};

int StochHMM::multiTraceback::counts ( )

Get the number times that traceback_path was recorded in multiple traceback.

Definition at line 505 of file traceback_path.cpp.

References pathAccess, and vectorIterator.

                              {
        return (*pathAccess[vectorIterator]).second;
    }

void StochHMM::multiTraceback::end ( )

Set position in multiTraceback to the ending.

Definition at line 461 of file traceback_path.cpp.

References paths, and vectorIterator.

                            {
        vectorIterator=paths.size();
        return;
    }

void StochHMM::multiTraceback::finalize ( )

Sorts the multiTraceback by the number of time a particular tracback path occurred.

Definition at line 519 of file traceback_path.cpp.

References maxSize, pathAccess, paths, StochHMM::sortTBVec(), and vectorIterator.

Referenced by print_gff(), print_label(), print_output(), and print_path().

                                 {
        maxSize=paths.size();
        vectorIterator=0;
        
        std::map<traceback_path,int>::iterator pathsIterator;
        for(pathsIterator=paths.begin();pathsIterator!=paths.end();pathsIterator++){
            pathAccess.push_back(pathsIterator);
        }
        
        sort(pathAccess.begin(),pathAccess.end(),sortTBVec);
        return;
    }

heatTable * StochHMM::multiTraceback::get_hit_table ( )

Generate a hit table from a multiple traceback paths Hit table is 2D table describing how many times a state was called at a particular position in the sequence

Definition at line 534 of file traceback_path.cpp.

References pathAccess, paths, StochHMM::model::state_size(), and table.

Referenced by print_hits().

                                            {
        if (table!=NULL){
            delete table;
        }
        
        //Over the lenght of the sequence
        model* hmm = ((*pathAccess[0]).first).getModel();
        size_t sequenceSize=((*pathAccess[0]).first).size();
        size_t stateSize=hmm->state_size();
        
        
        std::vector<int> states(stateSize,0);
        table = new heatTable(sequenceSize,states);
        
        std::map<traceback_path,int>::iterator it;
        
        for( it =paths.begin(); it!=paths.end();it++){
            int count = (*it).second;
            for(size_t position=0;position<sequenceSize;position++){
                int tbState=(*it).first[position];
                (*table)[position][tbState]+=count;
            }
        }
        return table;
    }

void StochHMM::multiTraceback::operator++ ( )

Increment the iterator to next position.

Definition at line 467 of file traceback_path.cpp.

References maxSize, and vectorIterator.

                                   {
        if (vectorIterator<maxSize){
            vectorIterator++;
        }
        return;
    }

void StochHMM::multiTraceback::operator-- ( )

Decrement the iterator to previous position.

Definition at line 475 of file traceback_path.cpp.

References vectorIterator.

                                   {
        if (vectorIterator>0){
            vectorIterator--;
        }
        return;
    }

void StochHMM::multiTraceback::operator= ( size_t val )

Set iterator to index val

Parameters:

val	Index value to set

Definition at line 484 of file traceback_path.cpp.

References maxSize, and vectorIterator.

                                            {
        if (val<=maxSize){
            vectorIterator=val;
        }
        return;
    }

traceback_path StochHMM::multiTraceback::operator[] ( size_t val )

Get traceback_path at index position

Parameters:

val	Index position

Definition at line 494 of file traceback_path.cpp.

References pathAccess.

                                                       {
        return (*pathAccess[val]).first;
    }

traceback_path StochHMM::multiTraceback::path ( )

Get traceback_path at currently set index in multiTraceback.

Definition at line 500 of file traceback_path.cpp.

References pathAccess, and vectorIterator.

Referenced by assign().

                                       {
        return (*pathAccess[vectorIterator]).first;
    }

void StochHMM::multiTraceback::print_gff ( std::string & header )

Definition at line 604 of file traceback_path.cpp.

References finalize(), pathAccess, and size().

Referenced by print_output().

                                                   {
        this->finalize();
        for(size_t iter=0; iter<this->size(); iter++){
            std::cout << "Traceback occurred:\t " << (*pathAccess[iter]).second << std::endl;
            (*pathAccess[iter]).first.print_gff(header);
            std::cout << std::endl;
        }
        return;
    }

void StochHMM::multiTraceback::print_hits ( )

Definition at line 561 of file traceback_path.cpp.

References get_hit_table(), StochHMM::model::getStateName(), StochHMM::join(), pathAccess, and StochHMM::model::state_size().

Referenced by print_output().

                                   {
        if (table==NULL){
            get_hit_table();
        }
        
        std::string header_row = "Position";
        model* hmm = ((*pathAccess[0]).first).getModel();
        for (size_t state_iter =0; state_iter<hmm->state_size(); state_iter++){
            header_row+="\t";
            header_row+=hmm->getStateName(state_iter);
        }
        std::cout << header_row << std::endl;
        
        for(size_t position = 0; position < table->size(); position++){
            std::string line = join((*table)[position], '\t');
            std::cout << position+1 << "\t" << line << std::endl;
        }
        
        return;
    }

void StochHMM::multiTraceback::print_label ( )

Definition at line 594 of file traceback_path.cpp.

References finalize(), pathAccess, and size().

Referenced by print_output().

                                    {
        this->finalize();
        for(size_t iter=0; iter<this->size(); iter++){
            std::cout << "Traceback occurred:\t " << (*pathAccess[iter]).second << std::endl;
            (*pathAccess[iter]).first.print_label();
            std::cout << std::endl;
        }
        return;
    }

void StochHMM::multiTraceback::print_path ( )

Definition at line 584 of file traceback_path.cpp.

References finalize(), pathAccess, and size().

Referenced by print_output().

                                   {
        this->finalize();
        for(size_t iter=0; iter<this->size(); iter++){
            std::cout << "Traceback occurred:\t " << (*pathAccess[iter]).second << std::endl;
            (*pathAccess[iter]).first.print_path();
            std::cout << std::endl;
        }
        return;
    }