StochHMM::seqJob Class Reference

#include <seqTracks.h>

List of all members.

Public Member Functions
	seqJob (size_t)
	Create a seqJob.
	~seqJob ()
	Destroy a seqJob.
void	evaluateFunctions ()
size_t	size ()
model *	getModel ()
sequences *	getSeqs ()
std::string	getHeader ()
bool	evaluated ()
void	printModel ()
void	printSeq ()
traceback_path *	getPath ()
double	getSeqAttrib ()
std::string	getSeqFilename (size_t iter)
void	setSeqFilename (std::string &filename)
void	printFilenames ()

Private Attributes
model *	hmm
sequences *	set
std::vector< std::string >	seqFilename
double	attrib
bool	funcEvaluated
TrackFuncs *	functions
bool	decodingPerformed
traceback_path *	path

Friends
class	seqTracks

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Detailed Description

*Stores the model and sequence information for each job

Definition at line 242 of file seqTracks.h.

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Constructor & Destructor Documentation

StochHMM::seqJob::seqJob

(

size_t

sz

)

Create a seqJob.

Definition at line 33 of file seqJobs.cpp.

References attrib, decodingPerformed, hmm, and path.

                           {
        decodingPerformed=false;
        attrib=-INFINITY;
        hmm=NULL;
        set=new sequences(sz);
        path=NULL;
    }

StochHMM::seqJob::~seqJob

(

)

Destroy a seqJob.

Definition at line 42 of file seqJobs.cpp.

References hmm, and path.

                   {
        hmm=NULL;
        delete path;
        delete set;
        path=NULL;
        set=NULL;
    }

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Member Function Documentation

bool StochHMM::seqJob::evaluated ( )

inline

Definition at line 265 of file seqTracks.h.

References funcEvaluated.

{return funcEvaluated;};

void StochHMM::seqJob::evaluateFunctions

(

)

std::string StochHMM::seqJob::getHeader ( )

inline

Definition at line 263 of file seqTracks.h.

{return set->getHeader();};

model* StochHMM::seqJob::getModel ( )

inline

Definition at line 260 of file seqTracks.h.

References hmm.

Referenced by main().

{return hmm;};

traceback_path* StochHMM::seqJob::getPath ( )

inline

Definition at line 272 of file seqTracks.h.

References decodingPerformed, and path.

{if (decodingPerformed) return path;else return NULL;};

double StochHMM::seqJob::getSeqAttrib ( )

inline

Definition at line 274 of file seqTracks.h.

References attrib.

{return attrib;};

std::string StochHMM::seqJob::getSeqFilename ( size_t  iter )

inline

Definition at line 276 of file seqTracks.h.

References seqFilename.

{return seqFilename[iter];};

sequences* StochHMM::seqJob::getSeqs ( )

inline

Definition at line 261 of file seqTracks.h.

Referenced by main().

{return set;};

void StochHMM::seqJob::printFilenames ( )

inline

Definition at line 278 of file seqTracks.h.

References seqFilename.

{for(size_t i=0;i<seqFilename.size();i++){ std::cout << seqFilename[i] << std::endl;}};

void StochHMM::seqJob::printModel ( )

inline

Definition at line 268 of file seqTracks.h.

References hmm, and StochHMM::model::print().

{if(hmm) hmm->print();};

void StochHMM::seqJob::printSeq ( )

inline

Definition at line 270 of file seqTracks.h.

{set->print();};

void StochHMM::seqJob::setSeqFilename ( std::string &  filename )

inline

Definition at line 277 of file seqTracks.h.

References seqFilename.

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

{seqFilename.push_back(filename); return;};

size_t StochHMM::seqJob::size ( void  )

inline

Definition at line 258 of file seqTracks.h.

{return set->getLength();};

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Friends And Related Function Documentation

friend class seqTracks

friend

Definition at line 250 of file seqTracks.h.

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Member Data Documentation

double StochHMM::seqJob::attrib

private

Definition at line 286 of file seqTracks.h.

Referenced by getSeqAttrib(), and seqJob().

bool StochHMM::seqJob::decodingPerformed

private

Definition at line 291 of file seqTracks.h.

Referenced by getPath(), and seqJob().

bool StochHMM::seqJob::funcEvaluated

private

Definition at line 287 of file seqTracks.h.

Referenced by evaluated().

TrackFuncs* StochHMM::seqJob::functions

private

Definition at line 289 of file seqTracks.h.

model* StochHMM::seqJob::hmm

private

Definition at line 278 of file seqTracks.h.

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

traceback_path* StochHMM::seqJob::path

private

Definition at line 292 of file seqTracks.h.

Referenced by getPath(), seqJob(), and ~seqJob().

std::vector< std::string> StochHMM::seqJob::seqFilename

private

Definition at line 284 of file seqTracks.h.

Referenced by getSeqFilename(), printFilenames(), and setSeqFilename().

sequences* StochHMM::seqJob::set

private

Definition at line 282 of file seqTracks.h.

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

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

• seqTracks.h
• seqJobs.cpp