#include <pwm.h>

Public Member Functions
	matrixPosition ()
	~matrixPosition ()
bool	parse (std::string &txt, track *trk, stringList &names)
float	getEmissionValue (sequences *, size_t)
float	getEmissionValue (sequence *, size_t)
emm *	getEmission ()
void	addTransition (emm *trans)
std::vector< std::string > &	getTransitionNames ()
void	setThreshold (float thresh)
float *	getThresholdPtr ()
float	getThreshold ()
size_t	transitionsSize ()
bool	isThresholdSet ()
std::string	stringify ()

Private Attributes
emm *	positionMatrix
bool	thresholdSet
float	threshold
std::vector< emm * >	transitions
std::vector< std::string >	transition_names
std::string	name

Detailed Description

Stores weight information for a position in the position weight matrix

Definition at line 122 of file pwm.h.

Constructor & Destructor Documentation

StochHMM::matrixPosition::matrixPosition ( )

Definition at line 217 of file pwm.cpp.

References positionMatrix, threshold, and thresholdSet.

                                      {
                positionMatrix  = NULL;
                thresholdSet    = false;
                threshold               = -INFINITY;
        }

StochHMM::matrixPosition::~matrixPosition ( )

Definition at line 223 of file pwm.cpp.

References positionMatrix.

                                       {
                delete positionMatrix;
                positionMatrix = NULL;
        }

Member Function Documentation

void StochHMM::matrixPosition::addTransition ( emm * trans )

inline

Definition at line 130 of file pwm.h.

References transitions.

{transitions.push_back(trans);}

emm* StochHMM::matrixPosition::getEmission ( )

inline

Definition at line 129 of file pwm.h.

References positionMatrix.

{return positionMatrix;};

float StochHMM::matrixPosition::getEmissionValue	(	sequences *	seqs,
		size_t	pos
	)

Definition at line 397 of file pwm.cpp.

References StochHMM::emm::get_emission(), and positionMatrix.

                                                                         {
                return positionMatrix->get_emission(*seqs, pos);
        }

float StochHMM::matrixPosition::getEmissionValue	(	sequence *	seq,
		size_t	pos
	)

Definition at line 401 of file pwm.cpp.

References StochHMM::emm::get_emission(), and positionMatrix.

                                                                       {
                return positionMatrix->get_emission(*seq, pos);
        }

float StochHMM::matrixPosition::getThreshold ( )

inline

Definition at line 134 of file pwm.h.

References threshold.

{return threshold;}

float* StochHMM::matrixPosition::getThresholdPtr ( )

inline

Definition at line 133 of file pwm.h.

References threshold.

{return &threshold;}

std::vector<std::string>& StochHMM::matrixPosition::getTransitionNames ( )

inline

Definition at line 131 of file pwm.h.

References transition_names.

{return transition_names;}

bool StochHMM::matrixPosition::isThresholdSet ( )

inline

Definition at line 136 of file pwm.h.

References thresholdSet.

{return thresholdSet;}

bool StochHMM::matrixPosition::parse	(	std::string &	txt,
		track *	trk,
		stringList &	names
	)

Parses the emission for each position from a string

Parameters:

txt	String representation of emissions
names	stringList of all state names defined in the model
trks	Tracks defined in the model
wts	Weight defined of the model
funcs	StateFunction defined for the model

Definition at line 235 of file pwm.cpp.

References StochHMM::clear_whitespace(), name, StochHMM::emm::parse(), positionMatrix, StochHMM::stringList::size(), StochHMM::stringList::splitND(), StochHMM::stringList::splitString(), threshold, thresholdSet, and transition_names.

Referenced by StochHMM::PWM::_parsePositions().

                                                                           {
                
                size_t nameHeader = txt.find("NAME:");
                size_t transHeader = txt.find("TRANSITION:");
                size_t thresholdHeader = txt.find("THRESHOLD:");
                //size_t emmHeader = txt.find("EMISSION:");
                size_t end = txt.find("//END");
                
                if (end != std::string::npos){
                        txt = txt.substr(0,end);
                }
                
                //Parse Name
                if (nameHeader != std::string::npos){
                        size_t endline = txt.find("\n",nameHeader);
                        std::string temp_name = txt.substr(nameHeader,endline-nameHeader);
                        stringList tmp;
                        tmp.splitString(temp_name, ":");
                        clear_whitespace(tmp[1], "\t\n ");
                        name = tmp[1];
                }
                else{
                        std::cerr << "Position is missing NAME definition\n"<< txt << std::endl;
                        exit(2);
                }
                
                
                //Parse Transitions
                if (transHeader != std::string::npos){
                        std::string temp;
                        size_t endline = txt.find("\n",transHeader);
                        temp = txt.substr(transHeader, endline - transHeader);
                        stringList transi;
                        transi.splitString(temp,":,");
                        for(size_t i = 1; i < transi.size(); i++){
                                clear_whitespace(transi[i], " \t\n");
                                transition_names.push_back(transi[i]);
                        }
                }
                
                
                //Parse Thresholds
                if (thresholdHeader != std::string::npos){
                        size_t endline = txt.find("\n",thresholdHeader);
                        std::string temp = txt.substr(thresholdHeader, endline-thresholdHeader);
                        stringList tmp;
                        tmp.splitString(temp, ":");
                        clear_whitespace(tmp[1], "\t\n ");
                        threshold = atof(tmp[1].c_str());
                        thresholdSet = true;
                }
                
                
        stringList lst;
        lst.splitND(txt,"EMISSION:");
        
                emm* temp_emm = new(std::nothrow) emm;
                
                if (temp_emm==NULL){
                        std::cerr << "OUT OF MEMORY\nFile" << __FILE__ << "Line:\t"<< __LINE__ << std::endl;
                        exit(1);
                }
                
                if (!temp_emm->parse(lst[0],trk)){
                        return false;
                }
                
                positionMatrix = temp_emm;
        
        return true;
    }

void StochHMM::matrixPosition::setThreshold ( float thresh )

inline

Definition at line 132 of file pwm.h.

References threshold.

{threshold = thresh;}

std::string StochHMM::matrixPosition::stringify ( )

Definition at line 353 of file pwm.cpp.

References StochHMM::double_to_string(), StochHMM::join(), name, positionMatrix, StochHMM::emm::stringify(), threshold, thresholdSet, and transition_names.

                                           {
                std::string mat;
                mat = "NAME:\t" + name + "\n";
                
                if (thresholdSet){
                        mat+= "THRESHOLD:\t" + double_to_string(threshold) + "\n";
                }
                
                if (transition_names.size() > 0){
                        mat += "TRANSITIONS:" + join(transition_names, ',') + "\n";
                }
                
                mat += positionMatrix->stringify();
                return mat;
        }