orthologous graphs for comparative gene prediction More...

Public Member Functions
void	linkToOEs (list< OrthoExon > &oes)

double	dualdecomp (list< OrthoExon > &all_orthoex, ExonEvo &evo, vector< list< Transcript * > * > &genelist, int gr_ID, int T, vector< double > &c)

double	treeMAPInf (list< OrthoExon > &all_orthoex, ExonEvo &evo, int &numInconsistent)

double	globalPathSearch ()

double	getStepSize (int r, double c, int t, int v, int numInconsistent, double current_dual, double best_primal, double best_dual)

double	makeConsistent (list< OrthoExon > &all_orthoex, ExonEvo &evo)

double	init (list< OrthoExon > &all_orthoex, ExonEvo &evo, int &numInconsistent)

void	buildGeneList (vector< list< Transcript * > * > &genelist)

void	filterGeneList (vector< list< Transcript * > * > &genelist, vector< int > &geneid)

void	printGenelist (vector< ofstream * > &filestreams)

void	outputGenes (vector< ofstream * > &filestreams, vector< int > &geneid)

void	createOrthoGenes (const GeneMSA *geneRange)

void	printOrthoGenes ()

Static Public Member Functions
static void	setStepRule (const char *r)

Public Attributes
vector< SpeciesGraph * >	graphs

vector< list< Transcript * > * >	ptrs_to_alltranscripts

vector< SequenceFeatureCollection * >	sfcs

vector< list< AltGene > * >	geneLists

list< OrthoGene >	all_orthogenes

Detailed Description

orthologous graphs for comparative gene prediction

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

Public Member Functions