StochHMM::models Class Reference

#include <hmm.h>

List of all members.

Public Member Functions
model *	operator[] (size_t iter)
size_t	size ()
model *	getModel (size_t)
void	importModels (std::string &, StateFuncs *)
void	addModel (model *)

Private Attributes
std::vector< model * >	hmms
weights *	scaling
templates *	modelTemplates

---

Detailed Description

models is a class to store multiple models. This allows StochMM the ability, to load multiple models, then select the model that appropriate for the sequence based on a used-defined attribute. Stores multiple HMM models and contains the get functions for specific models

Definition at line 445 of file hmm.h.

---

Member Function Documentation

void StochHMM::models::addModel

(

model *

)

model * StochHMM::models::getModel

(

size_t

iter

)

Get pointer to model at index position

Parameters:

iter	Index iterator for position

Returns:

pointer to model

Definition at line 144 of file hmm.cpp.

References hmms, and size().

Referenced by StochHMM::seqTracks::loadSeqs().

                                       {
        if (iter<this->size()) {
            return hmms[iter];
        }
        else{
            return NULL;
        }
    }

void StochHMM::models::importModels	(	std::string &	modelFile,
		StateFuncs *	funcs
	)

Import multiple models

Parameters:

modelFile	Path to multiple model file
funcs	Pointer to state Functions

Definition at line 33 of file hmm.cpp.

References hmms.

                                                                    {
        std::ifstream MOD;
        MOD.open(modelFile.c_str());
        if (MOD.fail()){
            std::string info = "Model file not found: " + modelFile;
            std::cerr << info << std::endl;
            exit(1);
        }
        
        //Input is assigned to "input" & get first line
        std::string input;
        
        //Check file header for correct type
        getline(MOD, input, '\n');
#ifdef DEBUG_MODEL
        std::cout << input <<std::endl;
#endif
        if (input.compare("#STOCHHMM MODEL FILE")==0){
            MOD.close();
            model* temp= new(std::nothrow) model;
            
            if (temp==NULL){
                std::cerr << "OUT OF MEMORY\nFile" << __FILE__ << "Line:\t"<< __LINE__ << std::endl;
                exit(1);
            }
            
            hmms.push_back(temp);
            hmms[0]->import(modelFile,funcs);
        }
        else if (input.compare("#STOCHHMM MODELS")==0){
            std::vector<std::string> filenames;
            
            while (getline(MOD,input,'\n')){
#ifdef DEBUG_MODEL
                sd::cout << input <<endl;
#endif
                //Need to check input to make sure its valid;
                //cout << input <<endl;
                if (input.compare("")==0){
                    break;
                }
                else{
                    filenames.push_back(input);
                }
            }
            MOD.close();
            
            for(size_t i=0;i<filenames.size();i++){
                model* temp=new(std::nothrow) model;
                
                if (temp==NULL){
                    std::cerr << "OUT OF MEMORY\nFile" << __FILE__ << "Line:\t"<< __LINE__ << std::endl;
                    exit(1);
                }
                
                hmms.push_back(temp);
            }
            
            for(size_t i=0;i<filenames.size();i++){
                hmms[i]->import(filenames[i],funcs);
                hmms[i]->print();
            }
        }
        else{
            std::cerr << "Header for " << modelFile <<  "does not indicate that it is a StochHMM model file.\n";
            std::cerr << "Header should be:  #STOCHHMM MODEL FILE \n" << "Header given: " << input <<std::endl;
        }
        return;
    }

model* StochHMM::models::operator[] ( size_t  iter )

inline

Get model located at index

Parameters:

iter	Index iterator for model

Returns:

pointer to model

Definition at line 455 of file hmm.h.

References hmms.

                                                     {
                        if (iter>hmms.size()-1){
                                return NULL;
                        }
                        
                        return hmms[iter];
                };

size_t StochHMM::models::size ( )

inline

Get the number of model

Returns:

size_t

Definition at line 465 of file hmm.h.

References hmms.

Referenced by getModel(), and StochHMM::seqTracks::getNext().

{return hmms.size();};

---

Member Data Documentation

std::vector<model*> StochHMM::models::hmms

private

Definition at line 477 of file hmm.h.

Referenced by getModel(), importModels(), operator[](), and size().

templates* StochHMM::models::modelTemplates

private

Definition at line 479 of file hmm.h.

weights* StochHMM::models::scaling

private

Definition at line 478 of file hmm.h.

---

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

• hmm.h
• hmm.cpp