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| SubstateModel (Profile &p) |
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void | initScores () |
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void | initHitSequences () |
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void | advanceScores (int base) |
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void | scoreAssOrRDss (ViterbiSubmapType &submap, bool complement, int firstBase, const Double &maxProb) |
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void | clearLowScoring (ViterbiSubmapType &submap) |
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void | clearLowScoringSubstates (ViterbiColumnType &vit) |
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double | getIntronBonus (int b, int i, int frame, bool comp) |
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int | blockCount () const |
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int | blockNoOfB (int b, bool comp) const |
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int | iBlockOfB (int b, bool comp) const |
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DistanceType | interBlockDist (int b, bool comp) const |
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int | blockSize (int b, bool comp) const |
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const Block & | getBlock (int b, bool comp) const |
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void | addHitSeqMatch (const HitSequence *hs, bool comp) |
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void | addPrefixMatch (Position ppos, int endOfLastCodon, int endOfBioExon, bool comp) |
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void | addSuffixMatch (Position ppos, int beginOfFirstCodon, int beginOfBioExon, bool comp) |
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void | addInternMatch (Position ppos, int beginOfBioExon, int endOfLastCodon, int endOfBioExon, bool comp) |
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void | appendMatchesTo (list< Match > &target) |
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static void | setStateStrands (const vector< StateType > &stateMap) |
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The documentation for this struct was generated from the following files:
