StochHMM::tracks Class Reference

#include <track.h>

List of all members.

Public Member Functions
void	push_back (track *)
size_t	indexOf (const std::string &)
size_t	size ()
track *	getTrack (const std::string &)
bool	isTrackDefined (const std::string &)
track *	operator[] (size_t i)
void	print ()
	Print the each track in tracks to stdout.
std::string	stringify ()

Private Attributes
std::vector< track * >	trks
std::map< std::string, size_t >	index

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Detailed Description

Definition at line 287 of file track.h.

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Member Function Documentation

track * StochHMM::tracks::getTrack

(

const std::string &

name

)

Get pointer to track from the track name

Parameters:

name	Name of the track

Returns:

pointer to track if it exists, NULL otherwise

Definition at line 542 of file track.cpp.

References index, and trks.

Referenced by StochHMM::transition::_parseLexical(), StochHMM::model::getTrack(), StochHMM::transitionFuncParam::parse(), StochHMM::emm::parse(), and StochHMM::emissionFuncParam::parse().

                                                {
        if (index.count(name)){
            return trks[index[name]];
        }
        else{
            return NULL;
        }
    }

size_t StochHMM::tracks::indexOf

(

const std::string &

name

)

Get iterator index of track by tracks name

Parameters:

name	Name of the track

Returns:

size_t Iterator to track within the tracks

-1 if track doesn't exist in tracks

Definition at line 529 of file track.cpp.

References index, and SIZE_MAX.

Referenced by StochHMM::model::getTrackIter().

                                               {
        if (index.count(name)){
            return index[name];
        }
        else{
            return SIZE_MAX;
        }
    }

bool StochHMM::tracks::isTrackDefined

(

const std::string &

name

)

Definition at line 551 of file track.cpp.

References index.

Referenced by StochHMM::emm::_processTags().

                                                    {
        if (index.count(name)){
            return true;
        }
        
        return false;
    }

track* StochHMM::tracks::operator[] ( size_t  i )

inline

Definition at line 298 of file track.h.

References trks.

{return trks[i];};

void StochHMM::tracks::print

(

)

Print the each track in tracks to stdout.

Definition at line 560 of file track.cpp.

References stringify().

                      {
        std::cout << stringify() << std::endl;
    }

void StochHMM::tracks::push_back

(

track *

tk

)

Add track to tracks container

Parameters:

tk	Pointer to track to be added

Definition at line 511 of file track.cpp.

References StochHMM::track::getName(), index, StochHMM::track::name, and trks.

Referenced by StochHMM::model::_parseTracks(), and StochHMM::model::addTrack().

                                   {
        std::string& name= tk->name;
        
        if (!index.count(name)){
            index[tk->getName()]=trks.size();
            trks.push_back(tk);
        }
        else{
            std::cerr << "Track with name: " << name << " already exists.  Cannot add tracks with the same name\n";
            exit(1);
        }
        
    }

size_t StochHMM::tracks::size ( void  )

inline

Definition at line 295 of file track.h.

References trks.

Referenced by StochHMM::model::_parseTracks(), StochHMM::model::getTrack(), StochHMM::sequences::sequences(), and StochHMM::model::track_size().

{return trks.size();};

std::string StochHMM::tracks::stringify

(

)

Get string representation of each track in tracks

Returns:

std::string String representation of tracks as in model file

Definition at line 566 of file track.cpp.

References trks.

Referenced by StochHMM::model::_stringifyTracks(), and print().

                               {
        std::string trackString;
        std::string ambigString;
        std::string lnSep(50,'=');
        trackString+="TRACK SYMBOL DEFINITIONS\n" + lnSep + "\n";
        
        for(size_t i=0;i<trks.size();i++){
            trackString+=trks[i]->stringify();
            if (trks[i]->isAmbiguousSet()){
                ambigString+=trks[i]->stringifyAmbig();
            }
        }
        if (!ambigString.empty()){
            ambigString="AMBIGUOUS SYMBOL DEFINITIONS\n" + lnSep + "\n"+ ambigString;
            trackString+="\n" + ambigString + "\n";
        }
        else{
            trackString+="\n";
        }
        
        return trackString;
    }

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Member Data Documentation

std::map<std::string,size_t> StochHMM::tracks::index

private

Definition at line 305 of file track.h.

Referenced by getTrack(), indexOf(), isTrackDefined(), and push_back().

std::vector<track*> StochHMM::tracks::trks

private

Definition at line 304 of file track.h.

Referenced by getTrack(), operator[](), push_back(), size(), and stringify().

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

• track.h
• track.cpp