This is the complete list of members for SequenceFeatureCollection, including all inherited members.

addFeature(Feature f) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
checkGroupConsistency(AnnoSequence *seq) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
cleanRedundantFeatures() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
collection (defined in SequenceFeatureCollection)	SequenceFeatureCollection
computeHintedSites(const char *dna) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
computeIndices() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
createPredictionScheme(list< AltGene > *genes) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
cumCovCDSpartMinus (defined in SequenceFeatureCollection)	SequenceFeatureCollection
cumCovCDSpartPlus (defined in SequenceFeatureCollection)	SequenceFeatureCollection
cumCovExonpartMinus (defined in SequenceFeatureCollection)	SequenceFeatureCollection
cumCovExonpartPlus (defined in SequenceFeatureCollection)	SequenceFeatureCollection
cumCovUTRpartMinus (defined in SequenceFeatureCollection)	SequenceFeatureCollection
cumCovUTRpartPlus (defined in SequenceFeatureCollection)	SequenceFeatureCollection
deleteEqualElements(list< Feature > &list) (defined in SequenceFeatureCollection)	SequenceFeatureCollection	static
deleteFeatureAt(FeatureType type, int endPosition, Strand strand) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
determineInterGroupRelations() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
emptyTrash() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
featureLists (defined in SequenceFeatureCollection)	SequenceFeatureCollection
findGenicGaps() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
findGroupGaps() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
firstEnd (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getAllActiveFeatures(FeatureType type) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getCausingGroups(PredictionRun &pr) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getExonListInRange(int startPosition, int endPosition, Strand strand, int seqRelFrame=-1) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getExonListOvlpingRange(int startPosition, int endPosition, Strand strand, int seqRelFrame=-1) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getFeatureAt(FeatureType type, int endPosition, Strand strand) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getFeatureList(FeatureType type) (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
getFeatureListAt(FeatureType type, int endPosition, Strand strand) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getFeatureListBeginningInRange(FeatureType type, int startPosition, int endPosition, Strand strand, int seqRelFrame=-1) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getFeatureListContaining(Bitmask featuretypes, int position, Strand strand) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getFeatureListInRange(FeatureType type, int startPosition, int endPosition, Strand strand, int seqRelFrame=-1) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getFeatureListOvlpingRange(FeatureType type, int startPosition, int endPosition, Strand strand) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getFeatureListOvlpingRange(Bitmask featuretypes, int startPosition, int endPosition, Strand strand) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getPosFirstEndAtOrAfter(int type, int e) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
getPosStartAfter(int type, int s) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
groupGaps (defined in SequenceFeatureCollection)	SequenceFeatureCollection
groupList (defined in SequenceFeatureCollection)	SequenceFeatureCollection
groupsSorted (defined in SequenceFeatureCollection)	SequenceFeatureCollection
hasLocalSSmalus (defined in SequenceFeatureCollection)	SequenceFeatureCollection
hintedSites (defined in SequenceFeatureCollection)	SequenceFeatureCollection
initHintedSplicesites(string ssList) (defined in SequenceFeatureCollection)	SequenceFeatureCollection	static
isHintedASS(int pos, Strand strand) const (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
isHintedDSS(int pos, Strand strand) const (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
joinGenesFromPredRuns(list< list< AltGene > * > *genesOfRuns, int maxtracks, bool uniqueCDS) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
K (defined in SequenceFeatureCollection)	SequenceFeatureCollection
lastStart (defined in SequenceFeatureCollection)	SequenceFeatureCollection
localSSMalus(FeatureType type, int pos, Strand strand) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
makeGroups() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
numZeroCov(int start, int end, int type, Strand strand) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
predictionScheme (defined in SequenceFeatureCollection)	SequenceFeatureCollection
prepare(AnnoSequence *annoseq, bool print, bool withEvidence=true) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
prepareLocalMalus(const char *dna) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
printFeatures(ostream &out) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
printGroups() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
rescaleBoniByConformance() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
resetConformance() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
seqlen (defined in SequenceFeatureCollection)	SequenceFeatureCollection
SequenceFeatureCollection(FeatureCollection *collection) (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
SequenceFeatureCollection(SequenceFeatureCollection &other, int from, int to, bool rc=false) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
setActiveFlag(list< HintGroup * > *groups, bool flag) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
setSeqLen(int len) (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
shift(int offset) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
sorted (defined in SequenceFeatureCollection)	SequenceFeatureCollection
sortFeatureLists() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
sortIncompGroupsOfGroups() (defined in SequenceFeatureCollection)	SequenceFeatureCollection
validASS (defined in SequenceFeatureCollection)	SequenceFeatureCollection	static
validASSPattern(const char *dna) const (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
validDSS (defined in SequenceFeatureCollection)	SequenceFeatureCollection	static
validDSSPattern(const char *dna) const (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
validHintedSites (defined in SequenceFeatureCollection)	SequenceFeatureCollection	static
validRASSPattern(const char *dna) const (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
validRDSSPattern(const char *dna) const (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
validRSplicePattern(string s) const (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
validSplicePattern(string s) const (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline
warnInconsistentHints(AnnoSequence *seq) (defined in SequenceFeatureCollection)	SequenceFeatureCollection
~SequenceFeatureCollection() (defined in SequenceFeatureCollection)	SequenceFeatureCollection	inline