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| Class Summary | |
|---|---|
| ArrayRank | Mostly copied from SchbathZScores. |
| EmpiricalZscore | Represents each word frequency by its Z-score based on the distribution of frequencies in the whole vector. |
| KmerIdUtils | |
| MsensrDoubleKcount<T extends MsensrDoubleKcount> | |
| NucleotideKcount | Provides a means for storing counts of kmers |
| NucleotideKcountTree | A spectrum implementation that maintains a live connection to a SequenceFragment so that it can rescan the sequence on demand. |
| NucleotideKtrie | Provides a means for storing trees of conditional probabilities of finding kmers |
| RonPSAAdapter | Convenience class for learning a RonPST from a SequenceFragment. |
| SchbathExpecter | Computes the expected number of words of a given ID, based on the counts of smaller words, using the method of Schbath 1995. |
| SchbathExpecter.SchbathExpectation | |
| SchbathRatio | Mostly copied from SchbathZScores. |
| SchbathZScores | |
| ZeroMarkovRatio | Mostly copied from SchbathZScores. |
| ZeroMarkovRatioTacoa | |
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