SpeciesGraph Member List
This is the complete list of members for SpeciesGraph, including all inherited members.
| addBackEdges() (defined in Graph) | Graph | |
| addBackEdgesComp() (defined in Graph) | Graph | |
| addCompatibleEdges() (defined in Graph) | Graph | protected |
| addEdgeFromHead(Status *exon) (defined in AugustusGraph) | AugustusGraph | virtual |
| addEdgeToTail(Status *exon) (defined in AugustusGraph) | AugustusGraph | virtual |
| addExon(Status *exon, vector< Node * > &neutralLine) (defined in Graph) | Graph | protected |
| addPair(Status *exon1, Status *exon2, vector< Node * > &neutralLine) (defined in Graph) | Graph | protected |
| addToHash(Node *n) (defined in Graph) | Graph | inlineprotected |
| addWeightToEdge() (defined in Graph) | Graph | protected |
| alpha_e (defined in AugustusGraph) | AugustusGraph | |
| alpha_i (defined in AugustusGraph) | AugustusGraph | |
| alreadyProcessed(T *temp) (defined in Graph) | Graph | inline |
| alreadyProcessed(string key) (defined in Graph) | Graph | inline |
| AugustusGraph(list< Status > *states, const char *dna) (defined in AugustusGraph) | AugustusGraph | inline |
| baseScore (defined in AugustusGraph) | AugustusGraph | |
| buildGraph(double meanIntrLen=numeric_limits< double >::max()) (defined in SpeciesGraph) | SpeciesGraph | |
| buildGraph() (defined in Graph) | Graph | |
| calculateBaseScores() (defined in AugustusGraph) | AugustusGraph | virtual |
| compatible(Node *exon1, Node *exon2) (defined in AugustusGraph) | AugustusGraph | virtual |
| createNeutralLine(vector< Node * > &neutralLine, double weight=0.0, bool onlyComplete=false) (defined in Graph) | Graph | protected |
| dfs(Node *node) (defined in SpeciesGraph) | SpeciesGraph | |
| ec_thold (defined in SpeciesGraph) | SpeciesGraph | static |
| edgeExists(Node *e1, Node *e2) (defined in Graph) | Graph | protected |
| existingNodes (defined in Graph) | Graph | |
| exonAtCodingEnd(Node *st) (defined in AugustusGraph) | AugustusGraph | |
| exonAtCodingStart(Node *st) (defined in AugustusGraph) | AugustusGraph | |
| exonAtGeneEnd(Status *st) (defined in AugustusGraph) | AugustusGraph | virtual |
| exonAtGeneStart(Status *st) (defined in AugustusGraph) | AugustusGraph | virtual |
| getAnnoSeq() const (defined in SpeciesGraph) | SpeciesGraph | inline |
| getAvgBaseProb(Status *st) (defined in AugustusGraph) | AugustusGraph | virtual |
| getAvgBaseProb(ExonCandidate *ec) (defined in AugustusGraph) | AugustusGraph | virtual |
| getBasetype(Status *st, int pos) (defined in AugustusGraph) | AugustusGraph | |
| getIntronScore(Status *predExon, Status *nextExon) (defined in AugustusGraph) | AugustusGraph | virtual |
| getKey(Node *n) (defined in SpeciesGraph) | SpeciesGraph | virtual |
| getKey(Status *st) (defined in SpeciesGraph) | SpeciesGraph | virtual |
| getKey(State *st) (defined in SpeciesGraph) | SpeciesGraph | virtual |
| getKey(ExonCandidate *exoncand) (defined in SpeciesGraph) | SpeciesGraph | virtual |
| getNode(T *temp) (defined in Graph) | Graph | inline |
| getNode(string key) (defined in Graph) | Graph | inline |
| getPoints(Status *st, double p, double *a1, double *a2, double *b1, double *b2) (defined in AugustusGraph) | AugustusGraph | |
| getSeqID() const (defined in SpeciesGraph) | SpeciesGraph | inline |
| getSeqLength() const (defined in SpeciesGraph) | SpeciesGraph | inline |
| getSeqOffset() const (defined in SpeciesGraph) | SpeciesGraph | inline |
| getSeqStrand() const (defined in SpeciesGraph) | SpeciesGraph | inline |
| getSequence() const (defined in SpeciesGraph) | SpeciesGraph | inline |
| getSizeNeutralLine() (defined in Graph) | Graph | protected |
| getSpeciesname() const (defined in SpeciesGraph) | SpeciesGraph | inline |
| Graph(list< Status > *states) (defined in Graph) | Graph | inline |
| head (defined in Graph) | Graph | |
| i1_e (defined in AugustusGraph) | AugustusGraph | |
| i1_i (defined in AugustusGraph) | AugustusGraph | |
| i2_e (defined in AugustusGraph) | AugustusGraph | |
| i2_i (defined in AugustusGraph) | AugustusGraph | |
| ic_thold (defined in SpeciesGraph) | SpeciesGraph | static |
| insertIntron(Node *exon1, Node *exon2) (defined in Graph) | Graph | protected |
| j1_e (defined in AugustusGraph) | AugustusGraph | |
| j1_i (defined in AugustusGraph) | AugustusGraph | |
| j2_e (defined in AugustusGraph) | AugustusGraph | |
| j2_i (defined in AugustusGraph) | AugustusGraph | |
| max (defined in Graph) | Graph | |
| maxCostOfExonLoss (defined in SpeciesGraph) | SpeciesGraph | static |
| mergedStopcodon(Node *exon1, Node *exon2) (defined in AugustusGraph) | AugustusGraph | virtual |
| mergedStopcodon(Status *exon1, Status *exon2) (defined in AugustusGraph) | AugustusGraph | virtual |
| mergedStopcodon(StateType type1, StateType type2, int end1, int begin2) (defined in AugustusGraph) | AugustusGraph | virtual |
| min (defined in Graph) | Graph | |
| minInQueue(queue< Node * > *q) (defined in Graph) | Graph | protected |
| nodelist (defined in Graph) | Graph | |
| nonneutralIncomingEdge(Node *exon) (defined in Graph) | Graph | protected |
| printCurrentPath() (defined in SpeciesGraph) | SpeciesGraph | |
| printGF(ExonCandidate *ec, double score=0.0, float avgBaseProb=0.0) (defined in SpeciesGraph) | SpeciesGraph | |
| printGraph(string filename) (defined in SpeciesGraph) | SpeciesGraph | virtual |
| printGraph2(string filename) (defined in AugustusGraph) | AugustusGraph | virtual |
| printGraphToShell() (defined in Graph) | Graph | protected |
| printSampledGF(Status *st, double score=0) (defined in SpeciesGraph) | SpeciesGraph | |
| printWeights() (defined in SpeciesGraph) | SpeciesGraph | static |
| r_be (defined in AugustusGraph) | AugustusGraph | |
| r_bi (defined in AugustusGraph) | AugustusGraph | |
| relax() (defined in SpeciesGraph) | SpeciesGraph | |
| sameReadingFrame(Node *e1, Node *e2) (defined in AugustusGraph) | AugustusGraph | |
| sameStrand(StateType typeA, StateType typeB) (defined in AugustusGraph) | AugustusGraph | |
| seqlength (defined in AugustusGraph) | AugustusGraph | |
| sequence (defined in AugustusGraph) | AugustusGraph | |
| setECThold(double t) (defined in SpeciesGraph) | SpeciesGraph | inlinestatic |
| setICThold(double t) (defined in SpeciesGraph) | SpeciesGraph | inlinestatic |
| setScore(Status *st) (defined in AugustusGraph) | AugustusGraph | virtual |
| SpeciesGraph(list< Status > *states, AnnoSequence *seq, list< ExonCandidate * > *addEx, string name, Strand s, bool u, bool o, ofstream *gf, bool ov=false) (defined in SpeciesGraph) | SpeciesGraph | inline |
| statelist (defined in Graph) | Graph | |
| tail (defined in Graph) | Graph | |
| tarjan() (defined in Graph) | Graph | |
| tarjanAlg(Node *from, stack< Node * > &S, size_t &index) (defined in Graph) | Graph | |
| topSort() (defined in SpeciesGraph) | SpeciesGraph | |
| utr (defined in AugustusGraph) | AugustusGraph | |
| x0_e (defined in AugustusGraph) | AugustusGraph | |
| x0_i (defined in AugustusGraph) | AugustusGraph | |
| x1_e (defined in AugustusGraph) | AugustusGraph | |
| x1_i (defined in AugustusGraph) | AugustusGraph | |
| y0_e (defined in AugustusGraph) | AugustusGraph | |
| y0_i (defined in AugustusGraph) | AugustusGraph | |
| ~Graph() (defined in Graph) | Graph | virtual |
| ~SpeciesGraph() (defined in SpeciesGraph) | SpeciesGraph | inline |
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