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Augustus 3.4.0
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This is the complete list of members for PP::SubstateModel, including all inherited members.
| addHitSeqMatch(const HitSequence *hs, bool comp) (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| addInternMatch(Position ppos, int beginOfBioExon, int endOfLastCodon, int endOfBioExon, bool comp) (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| addPrefixMatch(Position ppos, int endOfLastCodon, int endOfBioExon, bool comp) (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| addSuffixMatch(Position ppos, int beginOfFirstCodon, int beginOfBioExon, bool comp) (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| advanceScores(int base) (defined in PP::SubstateModel) | PP::SubstateModel | |
| allow_truncated (defined in PP::SubstateModel) | PP::SubstateModel | |
| appendMatchesTo(list< Match > &target) (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| blockCount() const (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| blockNoOfB(int b, bool comp) const (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| blockScores (defined in PP::SubstateModel) | PP::SubstateModel | |
| blockSize(int b, bool comp) const (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| clearLowScoring(ViterbiSubmapType &submap) (defined in PP::SubstateModel) | PP::SubstateModel | |
| clearLowScoringSubstates(ViterbiColumnType &vit) (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| currentResult (defined in PP::SubstateModel) | PP::SubstateModel | |
| exhaustive_substates (defined in PP::SubstateModel) | PP::SubstateModel | |
| getBlock(int b, bool comp) const (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| getIntronBonus(int b, int i, int frame, bool comp) (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| hitSeqColl (defined in PP::SubstateModel) | PP::SubstateModel | |
| iBlockOfB(int b, bool comp) const (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| initHitSequences() (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| initScores() (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| interBlockDist(int b, bool comp) const (defined in PP::SubstateModel) | PP::SubstateModel | inline |
| maxBlockSize (defined in PP::SubstateModel) | PP::SubstateModel | |
| prfl (defined in PP::SubstateModel) | PP::SubstateModel | |
| scoreAssOrRDss(ViterbiSubmapType &submap, bool complement, int firstBase, const Double &maxProb) (defined in PP::SubstateModel) | PP::SubstateModel | |
| setStateStrands(const vector< StateType > &stateMap) (defined in PP::SubstateModel) | PP::SubstateModel | inlinestatic |
| SubstateModel(Profile &p) (defined in PP::SubstateModel) | PP::SubstateModel |
1.9.8