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Augustus 3.4.0
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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 |
1.9.8