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| SWAlign (AlignmentData *ad, GapFunction *gf, ScoringScheme *ss) |
| Default constructor. More...
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| SWAlign (AlignmentData *ad, GapFunction *gf, ScoringScheme *ss, const vector< unsigned int > &v1, const vector< unsigned int > &v2) |
| Constructor with weighted alignment positions.
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| SWAlign (const SWAlign &orig) |
| Copy constructor.
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virtual | ~SWAlign () |
| Destructor.
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virtual void | copy (const SWAlign &orig) |
| Copy orig object to this object ("deep copy").
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virtual void | copy (const Align &orig) |
| Copy orig object to this object ("deep copy"). More...
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virtual void | doMatch (ostream &os) const |
| Output of alignment result.
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virtual void | doMatchPlusHeader (ostream &os, string headerTarget, string headerTemplate) const |
| Output of alignment result (including headers of the two sequences).
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virtual vector< Alignment > | generateMultiMatch (unsigned int num=1) |
| Generate and return an ensemble of suboptimal alignments. More...
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virtual vector< double > | generateMultiMatchScore (unsigned int num=10) |
| Generate and return scores of an ensemble of suboptimal alignments. More...
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AlignmentData * | getAlignmentData () |
| Return AlignmentData pointer.
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GapFunction * | getGapFunction () |
| Return GapFunction pointer.
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virtual vector< string > | getMatch () const |
| Return two-element array containing an alignment with maximal score.
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virtual vector< vector< int > > | getMatchSubset () |
| Return subset corresponding to match.
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virtual void | getMultiMatch () |
| Return two-element array containing an alignment with maximal score.
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virtual vector< double > | getMultiMatchScore (unsigned int num=10) |
| Return alignment scores of an ensemble of suboptimal alignments.
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virtual double | getScore () const |
| Return alignment score.
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ScoringScheme * | getScoringScheme () |
| Return ScoringScheme pointer.
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virtual SWAlign * | newCopy () |
| Construct a new "deep copy" of this object. More...
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virtual Traceback | next (const Traceback &tb) const |
| Return next Traceback element.
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SWAlign & | operator= (const SWAlign &orig) |
| Assignment operator.
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virtual void | outputMultiMatch (ostream &os, unsigned int num=10, bool fasta=false) |
| Generate and output an ensemble of suboptimal alignments.
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virtual void | pCalculateMatrix (bool update=true) |
| Update/create matrix values. More...
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virtual void | pCalculateMatrix (const vector< unsigned int > &v1, const vector< unsigned int > &v2, bool update=true) |
| Update/create weighted matrix values. More...
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void | pModifyMatrix (int i, int j) |
| Modify matrix during suboptimal alignment generation. More...
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virtual void | recalculateMatrix () |
| Recalculate the alignment matrix.
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void | setPenalties (double mul, double add) |
| Set penalties for suboptimal alignments. More...
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virtual vector< int > | shiftMatchSubset (vector< int > inputVector, int newStartPos) |
| Return vector with positions shifted depending on new position.
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Implement Smith-Waterman local alignment.