UtrModel Member List
This is the complete list of members for UtrModel, including all inherited members.
| activeWinLen (defined in StateModel) | StateModel | protectedstatic |
| ancestor (defined in StateModel) | StateModel | protected |
| buildModel(const AnnoSequence *annoseq, int parIndex) | UtrModel | virtual |
| clearSegProbs() (defined in UtrModel) | UtrModel | static |
| computeEmiFromPat(const vector< Double > &patprobs, vector< Double > &emiprobs, Integer k) (defined in StateModel) | StateModel | static |
| computeTtsProbs(int from, int to) (defined in UtrModel) | UtrModel | static |
| countEnd (defined in StateModel) | StateModel | protectedstatic |
| countStart (defined in StateModel) | StateModel | protectedstatic |
| cs (defined in StateModel) | StateModel | protectedstatic |
| determineShortPatterns(const vector< Integer > &patcounts, int k, int minCount) (defined in StateModel) | StateModel | static |
| dnalen (defined in StateModel) | StateModel | protectedstatic |
| emiProbUnderModel(int begin, int end) const (defined in UtrModel) | UtrModel | virtual |
| endPartEmiProb(int begin, int end, int endOfBioExon) const (defined in UtrModel) | UtrModel | |
| gcIdx (defined in StateModel) | StateModel | protectedstatic |
| getActiveWindowStart(int) (defined in StateModel) | StateModel | static |
| getEndPositions(int end, int &beginOfEndPart, int &endOfBioExon) const (defined in UtrModel) | UtrModel | |
| getGCIdx(int at) (defined in StateModel) | StateModel | inlinestatic |
| getStateType() const (defined in UtrModel) | UtrModel | inlinevirtual |
| init() (defined in UtrModel) | UtrModel | static |
| initAlgorithms(Matrix< Double > &, int) (defined in UtrModel) | UtrModel | virtual |
| initPredecessors(Matrix< Double > &, int self) (defined in StateModel) | StateModel | |
| isPossibleASS(int pos) (defined in StateModel) | StateModel | inlinestatic |
| isPossibleDSS(int pos) (defined in StateModel) | StateModel | inlinestatic |
| isPossibleRASS(int pos) (defined in StateModel) | StateModel | inlinestatic |
| isPossibleRDSS(int pos) (defined in StateModel) | StateModel | inlinestatic |
| makeProbsFromCounts(vector< Double > &patprobs, const vector< Integer > &patcounts, int k, Double pseudocount, Boolean shorten=false) (defined in StateModel) | StateModel | static |
| newStateModelPtr(const char *path) | StateModel | static |
| notEndPartEmiProb(int begin, int end, int endOfBioExon, Feature *exonparts) const (defined in UtrModel) | UtrModel | |
| prepareViterbi(const char *dna, int len, const vector< StateType > &stateMap) (defined in StateModel) | StateModel | static |
| printProbabilities(int zusNumber, BaseCount *bc, const char *suffix=NULL) | UtrModel | virtual |
| process3InitialExon(const State *exon, bool withLen=true) (defined in UtrModel) | UtrModel | |
| process3InternalExon(const State *exon) (defined in UtrModel) | UtrModel | |
| process3Intron(int begin, int end) (defined in UtrModel) | UtrModel | |
| process3SingleExon(const State *exon, bool withLen=true) (defined in UtrModel) | UtrModel | |
| process3TerminalExon(const State *exon, bool withLen) (defined in UtrModel) | UtrModel | |
| process5InitialExon(const State *exon, bool withLen=true) (defined in UtrModel) | UtrModel | |
| process5InternalExon(const State *exon) (defined in UtrModel) | UtrModel | |
| process5Intron(int begin, int end) (defined in UtrModel) | UtrModel | |
| process5SingleExon(const State *exon, bool withLen=true) (defined in UtrModel) | UtrModel | |
| process5TerminalExon(const State *exon) (defined in UtrModel) | UtrModel | |
| processStates(const Gene *gene) (defined in UtrModel) | UtrModel | |
| profileModel (defined in StateModel) | StateModel | protectedstatic |
| readAllParameters() (defined in UtrModel) | UtrModel | static |
| readProbabilities(int zusNumber) (defined in UtrModel) | UtrModel | static |
| registerPars(Parameters *parameters) (defined in UtrModel) | UtrModel | virtual |
| resetModelCount() (defined in UtrModel) | UtrModel | inlinestatic |
| resetModelCounts() (defined in StateModel) | StateModel | static |
| resetPars() (defined in UtrModel) | UtrModel | inlinestatic |
| seqFeatColl (defined in StateModel) | StateModel | protectedstatic |
| sequence (defined in StateModel) | StateModel | protectedstatic |
| setContentStairs(ContentStairs *stairs) (defined in StateModel) | StateModel | inlinestatic |
| setCountRegion(int from, int to) (defined in StateModel) | StateModel | inlinestatic |
| setGCIdx(int idx) (defined in StateModel) | StateModel | inlinestatic |
| setPP(PP::SubstateModel *mdl) (defined in StateModel) | StateModel | inlinestatic |
| setSFC(SequenceFeatureCollection *psfc) (defined in StateModel) | StateModel | inlinestatic |
| setTtsSpacing(int spacing) (defined in UtrModel) | UtrModel | inlinestatic |
| shortpattern (defined in StateModel) | StateModel | protectedstatic |
| stateMap (defined in StateModel) | StateModel | protectedstatic |
| StateModel() (defined in StateModel) | StateModel | inlineprotected |
| storeGCPars(int idx) (defined in UtrModel) | UtrModel | static |
| tssProb(int left) const (defined in UtrModel) | UtrModel | |
| tssupSeqProb(int left, int right, bool reverse) const (defined in UtrModel) | UtrModel | |
| updateToLocalGC(int from=-1, int to=-1) (defined in UtrModel) | UtrModel | static |
| updateToLocalGC(int idx, int from=-1, int to=-1) (defined in StateModel) | StateModel | static |
| updateToLocalGCEach(Matrix< Double > &trans, int cur) (defined in StateModel) | StateModel | inlinevirtual |
| UtrModel() (defined in UtrModel) | UtrModel | |
| viterbiForwardAndSampling(ViterbiMatrixType &, ViterbiMatrixType &, int, int, AlgorithmVariant, OptionListItem &) (defined in UtrModel) | UtrModel | virtual |
| ~StateModel() (defined in StateModel) | StateModel | inlinevirtual |
| ~UtrModel() (defined in UtrModel) | UtrModel |
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