holds all extrinsic feature information for one sequence More...

#include <extrinsicinfo.hh>

Public Member Functions
	SequenceFeatureCollection (FeatureCollection *collection)

	SequenceFeatureCollection (SequenceFeatureCollection &other, int from, int to, bool rc=false)

void	addFeature (Feature f)

void	printFeatures (ostream &out)

void	sortFeatureLists ()

void	checkGroupConsistency (AnnoSequence *seq)

void	warnInconsistentHints (AnnoSequence *seq)

list< Feature >	getFeatureList (FeatureType type)

Feature *	getFeatureAt (FeatureType type, int endPosition, Strand strand)

Feature *	getFeatureListAt (FeatureType type, int endPosition, Strand strand)

Feature *	getAllActiveFeatures (FeatureType type)

Feature *	getFeatureListInRange (FeatureType type, int startPosition, int endPosition, Strand strand, int seqRelFrame=-1)

Feature *	getFeatureListBeginningInRange (FeatureType type, int startPosition, int endPosition, Strand strand, int seqRelFrame=-1)

Feature *	getFeatureListOvlpingRange (FeatureType type, int startPosition, int endPosition, Strand strand)

Feature *	getFeatureListOvlpingRange (Bitmask featuretypes, int startPosition, int endPosition, Strand strand)

Feature *	getFeatureListContaining (Bitmask featuretypes, int position, Strand strand)

Feature *	getExonListInRange (int startPosition, int endPosition, Strand strand, int seqRelFrame=-1)

Feature *	getExonListOvlpingRange (int startPosition, int endPosition, Strand strand, int seqRelFrame=-1)

double	localSSMalus (FeatureType type, int pos, Strand strand)

void	shift (int offset)

void	computeHintedSites (const char *dna)

bool	validDSSPattern (const char *dna) const

bool	validRDSSPattern (const char *dna) const

bool	validASSPattern (const char *dna) const

bool	validRASSPattern (const char *dna) const

bool	validSplicePattern (string s) const

bool	validRSplicePattern (string s) const

bool	isHintedDSS (int pos, Strand strand) const

bool	isHintedASS (int pos, Strand strand) const

void	deleteFeatureAt (FeatureType type, int endPosition, Strand strand)

void	cleanRedundantFeatures ()

void	setSeqLen (int len)

void	makeGroups ()

void	printGroups ()

void	findGenicGaps ()

void	findGroupGaps ()

void	determineInterGroupRelations ()

void	resetConformance ()

void	emptyTrash ()

void	computeIndices ()

list< Feature >::iterator	getPosFirstEndAtOrAfter (int type, int e)

list< Feature >::iterator	getPosStartAfter (int type, int s)

void	rescaleBoniByConformance ()

void	createPredictionScheme (list< AltGene > *genes)

void	setActiveFlag (list< HintGroup * > *groups, bool flag)

list< AltGene > *	joinGenesFromPredRuns (list< list< AltGene > * > *genesOfRuns, int maxtracks, bool uniqueCDS)

void	sortIncompGroupsOfGroups ()

set< HintGroup * > *	getCausingGroups (PredictionRun &pr)

void	prepare (AnnoSequence *annoseq, bool print, bool withEvidence=true)

void	prepareLocalMalus (const char *dna)

int	numZeroCov (int start, int end, int type, Strand strand)

Static Public Member Functions
static void	deleteEqualElements (list< Feature > &list)

static void	initHintedSplicesites (string ssList)

Public Attributes
FeatureCollection *	collection

list< Feature > *	featureLists

list< HintGroup > *	groupList

list< Feature > *	groupGaps

bool	groupsSorted

PredictionScheme *	predictionScheme

bool	sorted

Bitmask *	hintedSites

Bitmask *	hasLocalSSmalus

int	seqlen

int	K

list< Feature >::iterator **	firstEnd

list< Feature >::iterator **	lastStart

vector< int >	cumCovUTRpartPlus

vector< int >	cumCovUTRpartMinus

vector< int >	cumCovCDSpartPlus

vector< int >	cumCovCDSpartMinus

vector< int >	cumCovExonpartPlus

vector< int >	cumCovExonpartMinus

Static Public Attributes
static Bitmask	validDSS = A_SET_FLAG(Seq2Int(2)("gt")) \| A_SET_FLAG(Seq2Int(2)("gc"))

static Bitmask	validASS = A_SET_FLAG(Seq2Int(2)("ag"))

static set< string >	validHintedSites

Detailed Description

holds all extrinsic feature information for one sequence

Author: Mario Stanke

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

include/extrinsicinfo.hh
src/extrinsicinfo.cc

Public Member Functions

Static Public Member Functions

Public Attributes

Static Public Attributes

Detailed Description