statistics Namespace Reference

Namespace containing all classes related to statistics handling. More...

Classes
class	Consistency
	Class to calculate the consistency between several MSA containing the same sequences, differently aligned. Using this statistics, the class is able to select the most consistent alignment between all alignments provided. It is possible to forcefully select an alignment, but to calculate the statistics for latter use. After selecting an alignment (most consistent or manually selected), it is possible to use this statistic to trim the alignment, removing columns that are not consistent enough with the other alignments. More...
class	Gaps
	Class to handle gaps statistics. More...
class	Manager
	Class to handle the interaction with Alignment and statistics objects. It serves as a wrapper or intermediate between the alignment and each specific stat. It also encapsulates the similarityMatrix. More...
class	Mold
	Currently not in use Class to serve as a mold to multiple stats. This would help to maintain coherence and to ease the understanding of each of the stats. As the number of stats grows, this standarization will become more valuable. More...
class	Similarity
	Class to handle the calculation relative to similarity. This class is narrowly connected to similarityMatrix, as the latter contains the information to calculate the similarity of the alignment. More...
class	similarityMatrix
	Class that contains information of similarity matrices. These are used to calculate the similarity between residues on the same column. Default matrices for AA, NT and DEG NT are provided, along with method for loading custom matrices. More...

Detailed Description

Namespace containing all classes related to statistics handling.