Package net.maizegenetics.analysis.gbs.neobio

Interface Summary

Interface	Description
Matrix	This interface defines a minimal set of operations that a matrix must implement. This interface is used by the class Smawk class to provide a general services regardless of how the matrix is actually stored.

Class Summary

Class	Description
AlignmentBlock	This class is used by the class CrochemoreLandauZivUkelson algorithm to store the information of an alignment block. All fields are public (but final) in order to simplify the access to the data.
BasicScoringScheme	This class implements a basic scoring scheme. At least three parameters must be provided to the constructor: the reward for a match (a substitution of equal characters), the penalty for a mismatch (a substitution of different characters) and the cost of a gap (an insertion or deletion of a character). Note that it only supports an additive gap cost function.
CharSequence	This class implements a sequence of characters stored as an array that provides random access to any position in constant time.
CrochemoreLandauZivUkelson	This abstract class is the superclass of both global and local sequence alignment algorithms (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).
CrochemoreLandauZivUkelsonGlobalAlignment	This class implements the global pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).
CrochemoreLandauZivUkelsonLocalAlignment	This class implements the local pairwise sequence alignment algorithm (with linear gap penalty function) due to Maxime Crochemore, Gad Landau and Michal Ziv-Ukelson (2002).
Factor	This class is used by class FactorSequence to create a linked list of factors of a text as induced by its Lempel-Ziv (LZ78) factorisation.
FactorSequence	This class builds a list of factors of a character sequence as induced by its Lempel-Ziv (LZ78) factorisation. Each factor is enconded as the longest factor previously seen plus one character.
LocalAlignmentBlock	This class is used by the class CrochemoreLandauZivUkelsonLocalAlignment algorithm to store the information of an alignment block. All fields are public (but final) in order to simplify the access to the data.
NeedlemanWunsch	This class implements the classic global alignment algorithm (with linear gap penalty function) due to S.B.Needleman and C.D.Wunsch (1970).
OutMatrix	Implements an interface to the OUT matrix of a block. This class is used by the class CrochemoreLandauZivUkelson and subclasses to enconde the OUT matrix from the input border and DIST matrix of an class AlignmentBlock.
PairwiseAlignment	This class is the product of a pairwise alignment, generated by one subclasses of class PairwiseAlignmentAlgorithm. It contains the two sequences strings with gaps, a score tag line, and a score value. It is typically displayed in three rows as in the following example of an alignment between parts of two protein sequences: MDEIHQLEDMFTVDSETLRKVVKHFILPHD-----MRTTKHQEELWSFIAELDSLKDFMVEQE // sequence 1 M +I E +FTV +ETL+ V KHFILP D MRTT++ +ELW FIA DSLK F+ EQ // score tag line MQQIENFEKIFTVPTETLQAVTKHFILP-DATETLMRTTQNPDELWEFIA--DSLKAFIDEQF // sequence 2
PairwiseAlignmentAlgorithm	This abstract class is the superclass of all classes implementing pairwise sequence alignment algorithms. Subclasses are required to provide methods to build a high scoring alignment between two sequences and compute its score with a given scoring scheme.
ScoringMatrix	This class implements a scoring scheme based on a substitution matrix. It is useful to represent PAM and BLOSUM family of amino acids scoring matrices. Its constructor loads such matrices from a file (or any other character stream). The following is an extract of a BLOSUM62 scoring matrix file: A R N D C Q E G H I L K M F P S T W Y V B Z X * A 4 -1 -2 -2 0 -1 -1 0 -2 -1 -1 -1 -1 -2 -1 1 0 -3 -2 0 -2 -1 0 -4 R -1 5 0 -2 -3 1 0 -2 0 -3 -2 2 -1 -3 -2 -1 -1 -3 -2 -3 -1 0 -1 -4 ... B -2 -1 3 4 -3 0 1 -1 0 -3 -4 0 -3 -3 -2 0 -1 -4 -3 -3 4 1 -1 -4 Z -1 0 0 1 -3 3 4 -2 0 -3 -3 1 -1 -3 -1 0 -1 -3 -2 -2 1 4 -1 -4 X 0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2 0 0 -2 -1 -1 -1 -1 -1 -4 * -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 1
ScoringScheme	This abstract class is the superclass of all scoring schemes. It defines basic operations that must be provided by all subclasses. Scoring schemes are used by sequence alignment algorithms to compute the score of an alignment.
Smawk	This class implement the SMAWK algorithm to compute column maxima on a totally monotone matrix as described.
SmithWaterman	This class implement the classic local alignment algorithm (with linear gap penalty function) due to T.F.Smith and M.S.Waterman (1981).
Trie	This class implements a trie, or a digital search tree. A trie is a multiway tree (each node can have multiple children) that represents a set of strings.

Exception Summary

Exception	Description
IncompatibleScoringSchemeException	Signals that an scoring scheme is not compatible with the sequences being aligned.
InvalidScoringMatrixException	Signals that the substitution matrix does not comply with the specification (see class ScoringMatrix for details).
InvalidSequenceException	Signals that the sequence does not comply with the specification (see class CharSequence or class FactorSequence for details).