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| SeqDivergenceProfile () |
| Default constructor.
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| SeqDivergenceProfile (const SeqDivergenceProfile &orig) |
| Copy constructor.
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virtual | ~SeqDivergenceProfile () |
| Destructor.
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virtual void | copy (const SeqDivergenceProfile &orig) |
| Copy orig object to this object ("deep copy"). More...
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virtual void | copy (const Profile &orig) |
| Copy orig object to this object ("deep copy"). More...
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virtual double | getAminoFrequency (char amino, unsigned int i) |
| Return the frequency of the aminoacid amino for position i.
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virtual double | getAminoFrequencyFromCode (AminoAcidCode amino, unsigned int i) |
| Return the frequency of the aminoacid amino for position i.
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virtual char | getAminoMaxFrequency (unsigned int i) |
| Return the most frequent aminoacid for position i.
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virtual AminoAcidCode | getAminoMaxFrequencyCode (unsigned int i) |
| Return the most frequent aminoacid for position i.
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virtual string | getConsensus () |
| Return the consensus of the profile.
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virtual double | getFreqMaxAminoFrequency (unsigned int i) |
| Return the frequency of the most frequent aminoacid for position i.
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virtual unsigned int | getNumGap (unsigned int i) |
| Return the number of gaps for position i.
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virtual unsigned int | getNumSequences () |
| Return the number of sequences in the profile.
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virtual const string | getSeq () |
| Return the master sequence.
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virtual unsigned int | getSequenceLength () |
| Return the lenght of sequences in the profile.
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virtual SeqDivergenceProfile * | newCopy () |
| Construct a new "deep copy" of this object. More...
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SeqDivergenceProfile & | operator= (const SeqDivergenceProfile &orig) |
| Assignment operator. More...
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virtual void | pCalculateRawFrequency (vector< double > &freq, double &gapFreq, Alignment &ali, unsigned int i) |
| Calculate the raw (ie. unnormalized) aminoacids frequencies for position i. More...
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virtual void | pCalculateWeight (Alignment &ali) |
| Calculate alignment weights. More...
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virtual void | pConstructData (Alignment &ali) |
| Construct data from alignment. More...
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virtual void | pResetData () |
| Reset all data.
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virtual void | reverse () |
| Reverse profile.
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virtual void | setAllowGaps (bool g) |
| Set wether to include/exclude gaps in the master sequence.
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virtual void | setFrequency (double freq, AminoAcidCode amino, int i) |
| Set the frequency of the aminoacid amino for position i.
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virtual void | setFrequency (double freq, char amino, int i) |
| Set the frequency of the aminoacid amino for position i.
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virtual void | setNumGap (int numGap, int j) |
| Set the number of gaps for position i.
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virtual void | setNumSequences (int i) |
| Set the number of sequences in the profile.
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virtual void | setProfile (Alignment &ali) |
| Set the profile with or without gaps in the master sequence. More...
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virtual void | setProfile (Alignment &ali, istream &is) |
| Set the profile with or without gaps in the master sequence. More...
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virtual void | setSeq (string master) |
| Set the master sequence.
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Calculate a frequency profile or PSSM using SeqDivergence weighting scheme.
Some explanations can be found in:
Guoli Wang, Roland L. Dunbrack jr.
Scoring profile-to-profile sequence alignments.
Institute for Cancer Research, Fox Chase Cancer Center,
Philadelphia, Pennsylvania 19111, USA. March 16, 2004.