Sequence Directory Reference

Directories

Files
file	Alignment.hpp [code]
	Declaration of namespace Sequence::Alignment.
file	AlignStream.hpp [code]
	declaration of virtual base class for alignment streams (Sequence::AlignStream)
file	Clustalw.hpp [code]
	Declaration of Sequence::ClustalW streams.
file	CodonTable.hpp [code]
	facility to count codons in CDS sequence, function Sequence::makeCodonUsageTable
file	Comeron95.hpp [code]
	declaration of Sequence::Comeron95 to calculate Ka/Ks
file	Comparisons.hpp [code]
	delcaration of routines for comparing DNA sequences This file declares a set of functions useful for comparing two bits of sequence data–sequences, nucleotides, etc.
file	ComplementBase.hpp [code]
	Delcaration of Sequence::ComplementBase, a function object to return the complement of a DNA nucleotide.
file	CountingOperators.hpp [code]
	Declarations of operators to add associative containers together.
file	descriptiveStats.hpp [code]
	classes and functions for calculating descriptive statistics of lists of random variables
file	Fasta.hpp [code]
	Declaration of Sequence::Fasta streams.
file	fastq.hpp [code]
	FASTQ class.
file	FST.hpp [code]
	delcaration of a class (Sequence::FST) to analyze population structure
file	Grantham.hpp [code]
	Grantham's distances (Sequence::Grantham)
file	GranthamWeights.hpp [code]
	declaration of classes to weight codons by Grantham distance (i.e. for Sequence::Comeron95). Declares Sequence::GranthamWeights2 and Sequence::GranthamWeights3
file	HKA.hpp [code]
	Calculations related to the HKA test.
file	Hudson2001.hpp [code]
file	Kimura80.hpp [code]
	declaration of Sequence::Kimura80
file	PathwayHelper.hpp [code]
	declarations of Sequence::Intermediates2 and Sequence::Intermediates3
file	phylipData.hpp [code]
	Sequence::phylipData – read in phylip alignments.
file	PolyFunctional.hpp [code]
	A collection of function objects for SNP analysis.
file	PolySIM.hpp [code]
	declaration of Sequence::PolySIM, a class to analyze coalescent simulation data
file	PolySites.hpp [code]
	Sequence::PolySites, generates polymorphism tables from data.
file	polySiteVector.hpp [code]
	Site-major variation tables in ASCII format.
file	PolySNP.hpp [code]
	declaration of Sequence::PolySNP, a class to analyze SNP data
file	PolyTable.hpp [code]
	Sequence::PolyTable, a virtual base class for polymorphism tables.
file	PolyTableFunctions.hpp [code]
	Operations on non-const Sequence::PolyTable objects.
file	PolyTableSlice.hpp [code]
file	Recombination.hpp [code]
	namespace Sequence::Recombination
file	RedundancyCom95.hpp [code]
	class Sequence::RedundancyCom95
file	Seq.hpp [code]
	class Sequence::Seq, an abstract base class for Sequences
file	SeqAlphabets.hpp [code]
file	SeqConstants.hpp [code]
file	SeqEnums.hpp [code]
	Definition of enumeration types.
file	SeqFunctors.hpp [code]
file	SeqProperties.hpp [code]
file	SeqRegexes.hpp [code]
	various useful rexex-based functions for dealing with data. Declares Sequence::basic_dna_alphabet,Sequence::full_dna_alphabet, Sequence::pep_alphabet, and the function Sequence::validSeq.
file	SeqUtilities.hpp [code]
	Declaration of Sequence::makeCountList (an alternative to Sequence::stateCounter), Sequence::internalGapCheck.
file	shortestPath.hpp [code]
	Routines to find the shortest distance between any 2 codons, using Grantham's distance. Declares the class Sequence::shortestPath, and the functions Sequence::mutsShortestPath and Sequence::diffType.
file	SimData.hpp [code]
	Declaration of Sequence::SimData, a class representing polymorphism data from coalescent simulations generated under an infinite-sites scheme.
file	SimParams.hpp [code]
	Sequence::SimParams reads in the parameters of Dick Hudon's coalescent simulation program. Used in conjunction with Sequence::SimData.
file	SimpleSNP.hpp [code]
	Declaration of Sequence::SimpleSNP, a polymorphism table stream in a "spreadsheet" format.
file	SingleSub.hpp [code]
	used by Sequence::Comeron95, class Sequence::SingleSub calculates divergence between codons that differ at one site
file	Sites.hpp [code]
	class Sequence::Sites calculates the length of a pairwise alignment between coding sequences in terms of site degeneracy. Used by Sequence::Comeron95
file	stateCounter.hpp [code]
	declaration of Sequence::stateCounter, a class to keep track of nucleotide counts either at a site in an alignment, or along a sequence
file	SummStats.hpp [code]
file	summstats.hpp [code]
	Include all summary statistic functions and types.
file	ThreeSubs.hpp [code]
	used by Sequence::Comeron95, class Sequence::ThreeSubs calculates divergence between codons that differ at three sites
file	Translate.hpp [code]
	declares Sequence::Translate,a function to translate CDS sequences into peptide sequences
file	Translate2.hpp [code]
	Deprecated header declaring routines to translate sequences. Including it includes the current header and issues a compiler warning.
file	TwoSubs.hpp [code]
	used by Sequence::Comeron95, class Sequence::TwoSubs calculates divergence between codons that differ at two sites
file	typedefs.hpp [code]
	typedefs used by libsequence
file	Unweighted.hpp [code]
	declares Sequence::Unweighted2 and Sequence::Unweighted3
file	WeightingSchemes.hpp [code]
	abstract interface to weighting schemes when codons differ at 2 positions