libsequence  1.9.5
File List
Here is a list of all documented files with brief descriptions:
 algorithm.hpp
 Alignment.hppDeclaration of namespace Sequence::Alignment
 Alignment.tcc
 AlignmentTest.ccUnit tests for fxns in namespace Sequence::Alignment
 AlignStream.hppDeclaration of virtual base class for alignment streams (Sequence::AlignStream)
 AlignStream.tcc
 AlignStreamTest.ccUnit tests for Sequence::ClustalW and Sequence::phylipData
 allele_counts.cc
 allele_counts.hppCount alleles at variable sites
 AlleleCountMatrix.cc
 AlleleCountMatrix.hpp
 alphabets.ccUnit tests for Sequence/SeqAlphabets.hpp
 auxillary.cc
 auxillary.hpp
 baseComp.cc
 classics.hpp"Classic" summaries of variation data
 Clustalw.hppDeclaration of Sequence::ClustalW streams
 Clustalw.tcc
 Coalesce.hpp
 Coalesce.tcc
 Coalescent.hppA lazy header to include the headers needed to start writing simulations. Includes: <Sequence/Coalescent/SimTypes.hpp> <Sequence/Coalescent/Coalesce.hpp> <Sequence/Coalescent/Recombination.hpp> <Sequence/Coalescent/Mutation.hpp> <Sequence/Coalescent/Initialize.hpp> <Sequence/Coalescent/DemographicModels.hpp> <Sequence/Coalescent/FragmentsRescaling.hpp>
 CoalescentCoalesce.cc
 CoalescentFragmentsRescaling.cc
 CoalescentInitialize.cc
 CoalescentMutation.cc
 CoalescentRecombination.cc
 CoalescentSimTypes.cc
 CoalescentTreeOperations.cc
 codons.cc
 CodonTable.cc
 CodonTable.hppFacility to count codons in CDS sequence, function Sequence::makeCodonUsageTable
 col_view_iterator.hpp
 Comeron95.cc
 Comeron95.hppDeclaration of Sequence::Comeron95 to calculate Ka/Ks
 Comparisons.cc
 Comparisons.hppDelcaration of routines for comparing DNA sequences This file declares a set of functions useful for comparing two bits of sequence data–sequences, nucleotides, etc
 ComparisonsTest.cc
 ComplementBase.cc
 ComplementBase.hppDelcaration of Sequence::ComplementBase, a function object to return the complement of a DNA nucleotide
 config.h
 correlations.cc
 CountingOperators.cc
 CountingOperators.hppDeclarations of operators to add associative containers together
 CountingOperators.tcc
 DemographicModels.hpp
 DemographicModels.tcc
 descriptiveStats.hppClasses and functions for calculating descriptive statistics of lists of random variables
 descriptiveStats.tcc
 Fasta.cc
 Fasta.hppDeclaration of Sequence::Fasta streams
 FastaConstructors.cc
 FastaExplicitIO.cc
 FastaIO.cc
 FastaOperations.cc
 fastq.cc
 fastq.hppFASTQ class
 fastqConstructors.cc
 fastqIO.cc
 faywuh.cc
 filtering.cc
 filtering.hpp
 FragmentsRescaling.hppHelper functions for simulating partially linked fragments One often wants to simulate partially linked fragments under neutral models. An efficient way to do this is to simulate a contiguous fragment, but with the recombination rate varying along the region (to represent the variable genetic distances between fragments). This header file declares functions that make this task easier, particularly the operations of rescaling the positions of mutations/marginal trees from the genetic map back to the physical map
 fst.cc
 FST.cc
 FST.hppDelcaration of a class (Sequence::FST) to analyze population structure
 garud.cc
 Garud.cc
 garud.hppH1, H12, and H2/H1 stats
 Garud.hpp
 generic.cc
 generic.hppGeneric utilities for calculating summary statistics
 Grantham.cc
 Grantham.hppGrantham's distances (Sequence::Grantham)
 GranthamWeights.cc
 GranthamWeights.hppDeclaration of classes to weight codons by Grantham distance (i.e. for Sequence::Comeron95). Declares Sequence::GranthamWeights2 and Sequence::GranthamWeights3
 haplotype_statistics.cc
 HKA.cc
 HKA.hppCalculations related to the HKA test
 hprime.cc
 hprime_faywuh_aggregator.hpp
 Hudson2001.hpp
 Initialize.hpp
 int_handler.cc
 int_handler.hpp
 Kimura80.cc
 Kimura80.hppDeclaration of Sequence::Kimura80
 ld.cc
 ld.hpp
 lHaf.cc
 lHaf.hpp
 libseq_unit_tests.cc
 libsequenceConfig.cc
 ms_to_VariantMatrix.cc
 msformat.hpp
 msstats.cc
 Mutation.hpp
 Mutation.tcc
 NeutralSample.hpp
 nsl.cc
 nSL.cc
 nsl.hppNSL and iHS
 nSL.hpp
 nSL_from_ms.cc
 nvariablesites.cc
 nvariablesites.hppCalculate total numbers of polymorphisms
 pairwiseld.cc
 PathwayHelper.cc
 PathwayHelper.hppDeclarations of Sequence::Intermediates2 and Sequence::Intermediates3
 phylipData.hppSequence::phylipData – read in phylip alignments
 phylipData.tcc
 PolyFunctional.hppA collection of function objects for SNP analysis
 PolySIM.cc
 PolySIM.hppDeclaration of Sequence::PolySIM, a class to analyze coalescent simulation data
 PolySIMtest.cc
 PolySites.cc
 PolySites.hppSequence::PolySites, generates polymorphism tables from data
 PolySites.tcc
 PolySitesIO.cc
 polySiteVector.cc
 polySiteVector.hppSite-major variation tables in ASCII format
 polySiteVector_test.ccExamples of using Sequence::polySiteVector
 polySiteVectorTest.ccUnit tests for Sequence::polySiteVector
 PolySNP.cc
 PolySNP.hppDeclaration of Sequence::PolySNP, a class to analyze SNP data
 PolySNPimpl.hpp
 PolySNPtest.cc
 PolyTable.cc
 PolyTable.hppSequence::PolyTable, a virtual base class for polymorphism tables
 PolyTable.tcc
 PolyTableBadBehavior.ccUnit test for really bad things
 PolyTableConversions.cc
 PolyTableFunctions.cc
 PolyTableFunctions.hppOperations on non-const Sequence::PolyTable objects
 PolyTableFunctions.tcc
 PolyTableIterators.cc
 PolyTableManip.cc
 PolyTableSlice.hpp
 PolyTableSlice.tcc
 PolyTableSliceTest.ccTests for Sequence/PolyTableSlice.hpp
 PolyTableTweaking.cc
 Recombination.cc
 Coalescent/Recombination.hpp
 Recombination.hppNamespace Sequence::Recombination
 Recombination.tcc
 RedundancyCom95.cc
 RedundancyCom95.hppClass Sequence::RedundancyCom95
 RedundancyCom95test.cc
 rmin.cc
 Seq.cc
 Seq.hppClass Sequence::Seq, an abstract base class for Sequences
 Seq8test.ccUnit tests for Sequence/Seq.hpp
 SeqAlphabets.cc
 SeqAlphabets.hpp
 SeqConstants.cc
 SeqConstants.hpp
 SeqConversions.cc
 SeqEnums.hppDefinition of enumeration types
 SeqFunctors.hpp
 SeqProperties.hpp
 SeqRegexes.hppVarious 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
 SeqUtilities.hppDeclaration of Sequence::makeCountList (an alternative to Sequence::stateCounter), Sequence::internalGapCheck
 shortestPath.cc
 shortestPath.hppRoutines 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
 SimData.cc
 SimData.hppDeclaration of Sequence::SimData, a class representing polymorphism data from coalescent simulations generated under an infinite-sites scheme
 SimParams.cc
 SimParams.hppSequence::SimParams reads in the parameters of Dick Hudon's coalescent simulation program. Used in conjunction with Sequence::SimData
 SimpleSNP.cc
 SimpleSNP.hppDeclaration of Sequence::SimpleSNP, a polymorphism table stream in a "spreadsheet" format
 SimpleSNPIO.cc
 SimTypes.hppDeclaration of types for coalescent simulation
 SingleSub.cc
 SingleSub.hppUsed by Sequence::Comeron95, class Sequence::SingleSub calculates divergence between codons that differ at one site
 Sites.cc
 Sites.hppClass Sequence::Sites calculates the length of a pairwise alignment between coding sequences in terms of site degeneracy. Used by Sequence::Comeron95
 slidingWindow.cc
 slidingWindow2.cc
 Snn.cc
 Snn.hpp
 Snn.tcc
 Specializations.ccDefinitions of template specializations for library functions
 stateCounter.cc
 stateCounter.hppDeclaration of Sequence::stateCounter, a class to keep track of nucleotide counts either at a site in an alignment, or along a sequence
 stateCounterTest.cc
 StateCounts.cc
 StateCounts.hpp
 SummStats.cc
 summstats.hppInclude all summary statistic functions and types
 SummStats.hpp
 tajd.cc
 test_SimDataIO.cc
 testAlleleCountMatrix.ccTests for Sequence/VariantMatrix.hpp
 testClassicSummstats.ccUnit tests for pop gen summary statistics
 testClassicSummstatsEmptyVariantMatrix.ccUnit tests for pop gen summary statistics
 testGarudStatistics.ccUnit tests for H1, H12, H2/H1 stats
 testLD.ccUnit tests for LD-related calculations
 thetah.hppFay and Wu's $\hat\theta_H$
 thetah_thetal.cc
 thetal.hppZeng et al. $\hat\theta_L$
 thetapi.cc
 thetapi.hpp
 thetaw.cc
 thetaw.hppWatterson's theta
 ThreeSubs.cc
 ThreeSubs.hppUsed by Sequence::Comeron95, class Sequence::ThreeSubs calculates divergence between codons that differ at three sites
 Trajectories.hpp
 Trajectories.tcc
 Translate.cc
 Translate.hppDeclares Sequence::Translate,a function to translate CDS sequences into peptide sequences
 Translate2.hppDeprecated header declaring routines to translate sequences. Including it includes the current header and issues a compiler warning
 translateTest.cc
 TreeOperations.hpp
 TwoSubs.cc
 TwoSubs.hppUsed by Sequence::Comeron95, class Sequence::TwoSubs calculates divergence between codons that differ at two sites
 typedefs.hppTypedefs used by libsequence
 ufs.cc
 Unweighted.cc
 Unweighted.hppDeclares Sequence::Unweighted2 and Sequence::Unweighted3
 util.hppHelper functions for implementing summary statistics
 valid_dna.cc
 variant_matrix_views_internal.hpp
 VariantMatrix.cc
 VariantMatrix.hpp
 VariantMatrixFixture.hpp
 VariantMatrixTest.ccTests for Sequence/VariantMatrix.hpp
 VariantMatrixViews.cc
 VariantMatrixViews.hpp
 WeightingSchemes.hppAbstract interface to weighting schemes when codons differ at 2 positions
 windows.cc
 windows.hpp