AugustusGraph Class Reference

#include <graph.hh>

Inheritance diagram for AugustusGraph:

Public Member Functions
	AugustusGraph (list< Status > *states, const char *dna)
bool	exonAtGeneStart (Status *st)
bool	exonAtGeneEnd (Status *st)
bool	exonAtCodingStart (Node *st)
bool	exonAtCodingEnd (Node *st)
string	getKey (Node *n)
string	getKey (Status *st)
string	getKey (State *st)
string	getKey (ExonCandidate *exoncand)
double	getIntronScore (Status *predExon, Status *nextExon)
void	addEdgeFromHead (Status *exon)
void	addEdgeToTail (Status *exon)
bool	compatible (Node *exon1, Node *exon2)
bool	sameStrand (StateType typeA, StateType typeB)
bool	sameReadingFrame (Node *e1, Node *e2)
void	calculateBaseScores ()
double	setScore (Status *st)
int	getBasetype (Status *st, int pos)
void	printGraph (string filename)
void	printGraph2 (string filename)
bool	mergedStopcodon (Node *exon1, Node *exon2)
bool	mergedStopcodon (Status *exon1, Status *exon2)
bool	mergedStopcodon (StateType type1, StateType type2, int end1, int begin2)
void	getPoints (Status *st, double p, double *a1, double *a2, double *b1, double *b2)
float	getAvgBaseProb (Status *st)
float	getAvgBaseProb (ExonCandidate *ec)
Public Member Functions inherited from Graph
	Graph (list< Status > *states)
void	addBackEdges ()
void	addBackEdgesComp ()
void	tarjan ()
void	tarjanAlg (Node *from, stack< Node * > &S, size_t &index)
void	buildGraph ()
template<class T >
bool	alreadyProcessed (T *temp)
bool	alreadyProcessed (string key)
template<class T >
Node *	getNode (T *temp)
Node *	getNode (string key)

Public Attributes
const char *	sequence
int	seqlength
vector< double >	baseScore
bool	utr
double	alpha_e
double	alpha_i
double	x0_e
double	x0_i
double	x1_e
double	x1_i
double	y0_e
double	y0_i
double	i1_e
double	i1_i
double	i2_e
double	i2_i
double	j1_e
double	j1_i
double	j2_e
double	j2_i
double	r_be
double	r_bi
Public Attributes inherited from Graph
list< Node * >	nodelist
list< Status > *	statelist
int	min
int	max
map< string, Node * >	existingNodes
Node *	head
Node *	tail

Additional Inherited Members
Protected Member Functions inherited from Graph
bool	edgeExists (Node *e1, Node *e2)
void	addToHash (Node *n)
Node *	addExon (Status *exon, vector< Node * > &neutralLine)
void	addPair (Status *exon1, Status *exon2, vector< Node * > &neutralLine)
void	createNeutralLine (vector< Node * > &neutralLine, double weight=0.0, bool onlyComplete=false)
void	addCompatibleEdges ()
void	insertIntron (Node *exon1, Node *exon2)
int	minInQueue (queue< Node * > *q)
bool	nonneutralIncomingEdge (Node *exon)
void	printGraphToShell ()
void	getSizeNeutralLine ()
void	addWeightToEdge ()

Detailed Description

Author

Stefanie Nachtweide

Member Function Documentation

addEdgeFromHead()

void AugustusGraph::addEdgeFromHead ( Status *  exon )

virtual

Implements Graph.

addEdgeToTail()

void AugustusGraph::addEdgeToTail ( Status *  exon )

virtual

Implements Graph.

calculateBaseScores()

void AugustusGraph::calculateBaseScores ( )

virtual

Implements Graph.

compatible()

bool AugustusGraph::compatible ( Node *  exon1, Node *  exon2  )

virtual

Implements Graph.

exonAtGeneEnd()

bool AugustusGraph::exonAtGeneEnd ( Status *  st )

virtual

Implements Graph.

exonAtGeneStart()

bool AugustusGraph::exonAtGeneStart ( Status *  st )

virtual

Implements Graph.

getAvgBaseProb() [1/2]

float AugustusGraph::getAvgBaseProb ( ExonCandidate *  ec )

virtual

Implements Graph.

getAvgBaseProb() [2/2]

float AugustusGraph::getAvgBaseProb ( Status *  st )

virtual

Implements Graph.

getIntronScore()

double AugustusGraph::getIntronScore ( Status *  predExon, Status *  nextExon  )

virtual

Implements Graph.

getKey() [1/4]

string AugustusGraph::getKey ( ExonCandidate *  exoncand )

virtual

Implements Graph.

getKey() [2/4]

string AugustusGraph::getKey ( Node *  n )

virtual

Implements Graph.

getKey() [3/4]

string AugustusGraph::getKey ( State *  st )

virtual

Implements Graph.

getKey() [4/4]

string AugustusGraph::getKey ( Status *  st )

virtual

Implements Graph.

mergedStopcodon() [1/3]

bool AugustusGraph::mergedStopcodon ( Node *  exon1, Node *  exon2  )

virtual

Implements Graph.

mergedStopcodon() [2/3]

bool AugustusGraph::mergedStopcodon ( StateType  type1, StateType  type2, int  end1, int  begin2  )

virtual

Implements Graph.

mergedStopcodon() [3/3]

bool AugustusGraph::mergedStopcodon ( Status *  exon1, Status *  exon2  )

virtual

Implements Graph.

printGraph()

void AugustusGraph::printGraph ( string  filename )

virtual

Implements Graph.

printGraph2()

void AugustusGraph::printGraph2 ( string  filename )

virtual

Implements Graph.

setScore()

double AugustusGraph::setScore ( Status *  st )

virtual

Implements Graph.

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

• include/graph.hh
• src/graph.cc