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| Graph (list< Status > *states) |
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void | addBackEdges () |
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void | addBackEdgesComp () |
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void | tarjan () |
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void | tarjanAlg (Node *from, stack< Node * > &S, size_t &index) |
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void | buildGraph () |
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template<class T > |
| bool | alreadyProcessed (T *temp) |
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bool | alreadyProcessed (string key) |
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template<class T > |
| Node * | getNode (T *temp) |
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Node * | getNode (string key) |
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list< Node * > | nodelist |
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list< Status > * | statelist |
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int | min |
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int | max |
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map< string, Node * > | existingNodes |
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Node * | head |
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Node * | tail |
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bool | edgeExists (Node *e1, Node *e2) |
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void | addToHash (Node *n) |
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Node * | addExon (Status *exon, vector< Node * > &neutralLine) |
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void | addPair (Status *exon1, Status *exon2, vector< Node * > &neutralLine) |
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void | createNeutralLine (vector< Node * > &neutralLine, double weight=0.0, bool onlyComplete=false) |
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void | addCompatibleEdges () |
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void | insertIntron (Node *exon1, Node *exon2) |
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int | minInQueue (queue< Node * > *q) |
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bool | nonneutralIncomingEdge (Node *exon) |
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void | printGraphToShell () |
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void | getSizeNeutralLine () |
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void | addWeightToEdge () |
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virtual bool | exonAtGeneStart (Status *st)=0 |
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virtual bool | exonAtGeneEnd (Status *st)=0 |
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virtual string | getKey (Node *n)=0 |
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virtual string | getKey (Status *st)=0 |
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virtual string | getKey (State *st)=0 |
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virtual string | getKey (ExonCandidate *exoncand)=0 |
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virtual double | getIntronScore (Status *predExon, Status *nextExon)=0 |
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virtual void | addEdgeFromHead (Status *exon)=0 |
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virtual void | addEdgeToTail (Status *exon)=0 |
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virtual bool | compatible (Node *exon1, Node *exon2)=0 |
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virtual double | setScore (Status *st)=0 |
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virtual void | calculateBaseScores ()=0 |
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virtual void | printGraph (string filename)=0 |
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virtual void | printGraph2 (string filename)=0 |
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virtual bool | mergedStopcodon (Node *exon1, Node *exon2)=0 |
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virtual bool | mergedStopcodon (Status *exon1, Status *exon2)=0 |
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virtual bool | mergedStopcodon (StateType type1, StateType type2, int end1, int begin2)=0 |
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virtual float | getAvgBaseProb (Status *st)=0 |
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virtual float | getAvgBaseProb (ExonCandidate *ec)=0 |
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The documentation for this class was generated from the following files:
