trainingSeqs Class Reference

#include <trainingSeq.h>

List of all members.

Public Member Functions
int	fileCount ()
bool	eof (size_t iter)
bool	good (size_t iter)
bool	is_open (size_t iter)
int	queueSize (size_t iter)
bool	openFiles (std::string &)
bool	openFiles (char **)
bool	importMask (std::string &)
bool	importMask (char **)
void	determineAlphabet (size_t iter)
void	setAlphabet (size_t, stringList &)

Private Attributes
vector< std::ifstream * >	seqFiles
std::ifstream *	maskFile
bool	masked
queue< int >	stateMask
std::vector< std::map < std::string, int > >	alphaIndex
std::vector< std::vector < std::string > >	indexAlpha
std::vector< stateInfo >	stateEmm
std::map< int, map< int, int > > transitions std::vector < trainingSeq >	seqs

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Detailed Description

Definition at line 53 of file trainingSeq.h.

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Member Function Documentation

void trainingSeqs::determineAlphabet

(

size_t

iter

)

Definition at line 184 of file trainingSeq.cpp.

References MAX_BUFFER.

                                               {
    const std::ifstream* file(seqFile[iter]);
    
    //Import a buffer full of the sequence
    std::string temp;
    std::string undigitized;
    
    while(getline(*file,temp,'\n')){
        if (temp[0]== '>'){
            continue;
        }
        else{
            undigitized+=temp;
        }
        
        if (undigitized.size() >= MAX_BUFFER){
            break;
        }
    }
    
    std::set<std::string> alphabet;
    pair<std::set<int>::iterator,bool> ret;
    
    for(size_t i=0;i<undigitized.size();i++){
        ret = alphabet.insert(undigitized[i]);
        if (ret.second()){
            indexAlpha[iter].push_back(undigitized[i]);
        }
    }
    
    for(size_t i=0;i<indexAlpha[iter].size();i++){
        string &temp= indexAlpha[iter][i];
        alphaIndex[iter][temp]=i;
    }
    
    file.seekg(0,std::ios::beg);
    file.clear();
    
    return;
}

bool trainingSeqs::eof ( size_t  iter )

inline

Definition at line 56 of file trainingSeq.h.

{return seqFiles[iter]->eof();}

int trainingSeqs::fileCount ( )

inline

Definition at line 55 of file trainingSeq.h.

{return seqFiles.size();};

bool trainingSeqs::good ( size_t  iter )

inline

Definition at line 57 of file trainingSeq.h.

{return seqFiles[iter]->good();}

bool trainingSeqs::importMask

(

std::string &

)

bool trainingSeqs::importMask

(

char **

)

bool trainingSeqs::is_open ( size_t  iter )

inline

Definition at line 58 of file trainingSeq.h.

{return seqFiles[iter]->is_open();}

bool trainingSeqs::openFiles

(

std::string &

filename

)

Definition at line 172 of file trainingSeq.cpp.

                                               {
    
}

bool trainingSeqs::openFiles

(

char **

)

int trainingSeqs::queueSize ( size_t  iter )

inline

Definition at line 61 of file trainingSeq.h.

{return seqs.size();}

void trainingSeqs::setAlphabet	(	size_t	iter,
		stringList &	lst
	)

Definition at line 225 of file trainingSeq.cpp.

References StochHMM::stringList::push_back(), and StochHMM::stringList::size().

                                                          {
    for(size_t i=0;i<lst.size();i++){
        string& temp = lst[i];
        indexAlpha[iter].push_back(temp);
        alphaIndex[iter][temp]=i;
    }
    return;
}

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Member Data Documentation

std::vector<std::map<std::string, int> > trainingSeqs::alphaIndex

private

Definition at line 78 of file trainingSeq.h.

std::vector<std::vector<std::string> > trainingSeqs::indexAlpha

private

Definition at line 79 of file trainingSeq.h.

bool trainingSeqs::masked

private

Definition at line 75 of file trainingSeq.h.

std::ifstream* trainingSeqs::maskFile

private

Definition at line 73 of file trainingSeq.h.

vector<std::ifstream*> trainingSeqs::seqFiles

private

Definition at line 72 of file trainingSeq.h.

std::map<int,map<int,int> > transitions std::vector<trainingSeq> trainingSeqs::seqs

private

Definition at line 86 of file trainingSeq.h.

std::vector<stateInfo> trainingSeqs::stateEmm

private

Definition at line 81 of file trainingSeq.h.

queue<int> trainingSeqs::stateMask

private

Definition at line 76 of file trainingSeq.h.

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

• trainingSeq.h
• trainingSeq.cpp