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| SecSequenceData (int n, const string &seq1, const string &seq2, const string &sec1, const string &sec2, const string &name1="Seq1", const string &name2="Seq2") |
| Default constructor. More...
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| SecSequenceData (const SecSequenceData &orig) |
| Copy constructor. More...
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virtual | ~SecSequenceData () |
| Destructor.
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virtual void | add (string s, int n) |
| Insert a sequence at position n of the vector.
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virtual void | calculateMatch (int i, int tbi, int j, int tbj) |
| Calculate single match positions. More...
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virtual void | clear () |
| Insert a void string in all positions of the vector.
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virtual void | copy (const SecSequenceData &orig) |
| Copy orig object to this object ("deep copy"). More...
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virtual void | copy (const AlignmentData &orig) |
| Copy orig object to this object ("deep copy"). More...
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virtual Alignment & | generateMatch (double score=0.00) |
| Generate and return an ensemble of suboptimal alignments. More...
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virtual void | getMatch () |
| Reverse the strings of the vector.
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virtual string | getSequence (int n) |
| Return the sequence at position n of the vector. More...
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virtual SecSequenceData * | newCopy () |
| Construct a new "deep copy" of this object.
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SecSequenceData & | operator= (const SecSequenceData &orig) |
| Assignment operator. More...
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virtual void | outputMatch (ostream &os, bool fasta=false) |
| Control if the strings of the vector are similar and print them. More...
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virtual void | setSequence (string s, int n) |
| Set the sequence at position n of the vector. More...
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virtual bool | similar (char a, char b) |
| Define if two residues are similar. More...
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Print alignment of two sequences considering also secondary structure.