builds a directed acyclic graph from a set of sampled genes. More...

#include <speciesgraph.hh>

Inheritance diagram for SpeciesGraph:

Public Member Functions
	SpeciesGraph (list< Status > states, AnnoSequence seq, list< ExonCandidate * > addEx, string name, Strand s, bool u, bool o, ofstream gf, bool ov=false)

void	buildGraph (double meanIntrLen=numeric_limits< double >::max())

string	getKey (Node *n)

void	printGraph (string filename)

void	printSampledGF (Status *st, double score=0)

void	printGF (ExonCandidate *ec, double score=0.0, float avgBaseProb=0.0)

string	getSpeciesname () const

char *	getSequence () const

char *	getSeqID () const

int	getSeqOffset () const

int	getSeqLength () const

Strand	getSeqStrand () const

AnnoSequence *	getAnnoSeq () const

void	printCurrentPath ()

void	topSort ()

void	dfs (Node *node)

double	relax ()

string	getKey (Node *n)

string	getKey (Status *st)

string	getKey (State *st)

string	getKey (ExonCandidate *exoncand)

Public Member Functions inherited from AugustusGraph
	AugustusGraph (list< Status > states, const char dna)

bool	exonAtGeneStart (Status *st)

bool	exonAtGeneEnd (Status *st)

bool	exonAtCodingStart (Node *st)

bool	exonAtCodingEnd (Node *st)

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	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)

Static Public Member Functions
static void	setECThold (double t)

static void	setICThold (double t)

static void	printWeights ()

Static Public Attributes
static double	ec_thold = 0.0

static double	ic_thold = 0.0

static double	maxCostOfExonLoss = 0.0

Additional Inherited Members
Public Attributes inherited from AugustusGraph
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

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

builds a directed acyclic graph from a set of sampled genes.

The underlying auxiliary structure of the graph consists of seven neutral lines each representing a type of non-coding segment. In comparative gene prediction for each species an object of this class is created.

Author: Stefanie König

Member Function Documentation

◆ getKey() [1/5]

string AugustusGraph::getKey ( ExonCandidate * exoncand )

virtual

Reimplemented from AugustusGraph.

◆ getKey() [2/5]

string AugustusGraph::getKey ( Node * n )

virtual

Reimplemented from AugustusGraph.

◆ getKey() [3/5]

string SpeciesGraph::getKey ( Node * n )

virtual

Reimplemented from AugustusGraph.

◆ getKey() [4/5]

string AugustusGraph::getKey ( State * st )

virtual

Reimplemented from AugustusGraph.

◆ getKey() [5/5]

string AugustusGraph::getKey ( Status * st )

virtual

Reimplemented from AugustusGraph.

◆ printGraph()

void SpeciesGraph::printGraph ( string filename )

virtual

Reimplemented from AugustusGraph.

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

include/speciesgraph.hh
src/speciesgraph.cc

Public Member Functions

Static Public Member Functions

Static Public Attributes

Additional Inherited Members

Detailed Description

Member Function Documentation

◆ getKey() [1/5]

◆ getKey() [2/5]

◆ getKey() [3/5]

◆ getKey() [4/5]

◆ getKey() [5/5]

◆ printGraph()