  theplu::yat::statistics::averager_base< Averager > | |
  theplu::yat::statistics::averager_base2< Averager > | |
  theplu::yat::statistics::Averager | Class to calculate simple (first and second moments) averages |
| theplu::yat::statistics::averager_base< Averager1 > | |
| theplu::yat::statistics::Averager1 | Class to calculate mean |
| theplu::yat::statistics::averager_base< Averager3 > | |
| theplu::yat::statistics::averager_base2< Averager3 > | |
| theplu::yat::statistics::averager_base3< Averager3 > | |
| theplu::yat::statistics::Averager3 | Class to calculate 1st, 2nd, and 3rd central moments |
| theplu::yat::statistics::averager_base< Averager4 > | |
| theplu::yat::statistics::averager_base2< Averager4 > | |
| theplu::yat::statistics::averager_base3< Averager4 > | |
| theplu::yat::statistics::averager_base4< Averager4 > | |
| theplu::yat::statistics::Averager4 | Class to calculate 1st, 2nd, 3rd, and 4th central moments |
| Assignable | |
 theplu::yat::classifier::NeighborWeightingConcept< T > | Concept check for a Neighbor Weighting Method |
| theplu::yat::utility::TrivialIterator< T > | Concept check for Trivial Iterator |
| CopyConstructible | |
| theplu::yat::utility::DistanceConcept< T > | Concept check for a Distance |
| DefaultConstructible | |
| theplu::yat::classifier::NeighborWeightingConcept< T > | Concept check for a Neighbor Weighting Method |
| theplu::yat::utility::TrivialIterator< T > | Concept check for Trivial Iterator |
| EqualityComparable | |
| theplu::yat::utility::TrivialIterator< T > | Concept check for Trivial Iterator |
| function_output_iterator | |
| theplu::yat::omic::BamWriteIterator | Output iterator for bam file |
| theplu::yat::utility::OstreamIterator< T > | |
| iterator_adaptor | |
| theplu::yat::utility::DataIterator< Base > | DataIterator |
| theplu::yat::utility::StrideIterator< RandomAccessIterator > | Adaptor using a stride on underlying iterator |
| theplu::yat::utility::WeightIterator< Base > | WeightIterator |
| iterator_facade | |
| theplu::yat::utility::CigarIterator< const uint32_t * > | |
| theplu::yat::omic::BamPairIterator< Base > | |
| theplu::yat::omic::BamReadIterator | Class to iterate through a InBamFile |
| theplu::yat::utility::CigarIterator< BASE > | Iterator over a CIGAR |
| theplu::yat::utility::Container2DIterator< Container, value, reference > | Iterator for a Container2D |
| theplu::yat::utility::GetlineIterator | Read from std::istream with std::getline |
| theplu::yat::utility::MergeIterator< Base, Compare > | Iterate over several ranges as if ranges have been merged |
| theplu::yat::utility::WeightedIterator< DataIterator, WeightIterator > | WeightedIterator |
| theplu::yat::utility::WeightedIteratorArchetype< AccessCategory, TraversalCategory > | |
| noncopyable | |
| theplu::yat::omic::BamFile< InBamFile > | |
| theplu::yat::omic::InBamFile | |
| theplu::yat::omic::BamFile< OutBamFile > | |
| theplu::yat::omic::OutBamFile | |
| theplu::yat::omic::BamFile< Derived > | |
| operators | |
| theplu::yat::omic::DNA | |
| theplu::yat::omic::GenomicPosition | |
| theplu::yat::statistics::Distance< EuclideanDistance > | |
| theplu::yat::statistics::EuclideanDistance | Calculates the Euclidean distance between elements of two ranges |
| theplu::yat::utility::PriorityQueue< JobPtr, LowerPriority > | |
| theplu::yat::utility::Queue< JobPtr > | |
| theplu::yat::utility::SegmentTree< std::map< Segment< T, Compare >, Tp, SegmentCompare< T, Compare > >, Compare, PairFirst< const std::pair< const Segment< T, Compare >, Tp > > > | |
| theplu::yat::utility::SegmentMap< T, Tp, Compare > | Map of Segments |
| theplu::yat::utility::SegmentTree< std::set< Segment< T, Compare >, SegmentCompare< T, Compare > >, Compare, Identity< const Segment< T, Compare > & > > | |
| theplu::yat::utility::SegmentSet< T, Compare > | Set of Segments |
| theplu::yat::utility::SmartPtr< const std::vector< size_t > > | |
| binary_function | |
| theplu::yat::omic::AminoAcidEqual | Functor comparing if two Codons translate to the same amino acid |
| theplu::yat::omic::BamLessEnd | |
| theplu::yat::omic::BamLessName | |
| theplu::yat::omic::BamLessPos | |
| theplu::yat::utility::compose_f_gx_hy< F, G, H > | |
| theplu::yat::utility::compose_f_gxy< F, G > | |
| theplu::yat::utility::less_nan< T > | Functor that behaves like std::less with the exception that it treats NaN as a number larger than infinity |
| theplu::yat::utility::less_nan< DataWeight > | Specialization for DataWeight |
| theplu::yat::utility::SegmentCompare< T, Compare > | Functor using compare |
| runtime_error | |
| theplu::yat::utility::runtime_error | Class used for all runtime error detected within yat library |
| theplu::yat::utility::cmd_error | Class used for error reported from Commandline or Option |
| theplu::yat::utility::errno_error | Class that contains information reported via global variable errno |
| theplu::yat::utility::get_error< Key > | Error class used in get(const std::map<Key, Tp, Compare, Alloc>& m, const Key& k) |
| theplu::yat::utility::GSL_error | Class for errors reported from underlying GSL calls |
| theplu::yat::utility::IO_error | Class to report errors associated with IO operations |
| theplu::yat::omic::OutBamFile::error | Error thrown from OutBamFile::write(const BamRead&) at failure |
| unary_function | |
| theplu::yat::omic::BamReadFilter | Filter bam reads |
| theplu::yat::omic::BamWriter | |
| theplu::yat::random::DiscreteUniform | Discrete uniform distribution |
| theplu::yat::utility::abs< T > | |
| theplu::yat::utility::compose_f_gx< F, G > | |
| theplu::yat::utility::compose_f_gx_hx< F, G, H > | |
| theplu::yat::utility::Dereferencer< Pointer > | Adaptor between pointer and pointee interface |
| theplu::yat::utility::detail::OstreamIteratorFunc< T > | |
| theplu::yat::utility::Exp< T > | |
| theplu::yat::utility::Identity< T > | Identity functor that returns its argument |
| theplu::yat::utility::Log< T > | |
| theplu::yat::classifier::ConsensusInputRanker | Robust algorithm to rank rows in a data matrix versus a target vector |
| theplu::yat::classifier::DataLookup1D | Class for general vector view |
| theplu::yat::classifier::DataLookupWeighted1D | Class for general weighted vector view |
| theplu::yat::classifier::EnsembleBuilder< Classifier, Data > | Class for ensembles of supervised classifiers |
| theplu::yat::classifier::FeatureSelector | Interface class for FeatureSelection |
| theplu::yat::classifier::FeatureSelectorIR | FeatureSelector using an InputRanker |
| theplu::yat::classifier::FeatureSelectorRandom | Class for selection features by random |
| theplu::yat::classifier::IGP< Distance > | Class for In Group Proportions (IGP) |
| theplu::yat::classifier::InputRanker | Class for ranking rows in a matrix, using a Score and a target vector |
| theplu::yat::classifier::IRRetrieve | Interface class for retrieving information from a InputRanker to build a ConsensusInputRanker |
| theplu::yat::classifier::IRRank | Functor retrieving minus rank from a InputRanker to build a ConsensusInputRanker |
| theplu::yat::classifier::Kernel | Interface Class for Kernels |
| theplu::yat::classifier::Kernel_MEV | Memory Efficient Kernel |
| theplu::yat::classifier::Kernel_SEV | Speed Efficient Kernel |
| theplu::yat::classifier::KernelFunction | Interface class calculating elements in Kernel |
| theplu::yat::classifier::GaussianKernelFunction | Class for Gaussian kernel calculations |
| theplu::yat::classifier::PolynomialKernelFunction | Class for polynomial kernel calculations |
| theplu::yat::classifier::KernelLookup | Lookup into Kernel |
| theplu::yat::classifier::KNN_ReciprocalDistance | A model of the concept Neighbor Weighting Method to be used with KNN to weight the votes of the k nearest neighbors of a sample |
| theplu::yat::classifier::KNN_ReciprocalRank | A model of the concept Neighbor Weighting Method to be used with KNN to weight the votes of the k nearest neighbors of a sample |
| theplu::yat::classifier::KNN_Uniform | A model of the concept Neighbor Weighting Method to be used with KNN to weight the votes of the k nearest neighbors of a sample |
| theplu::yat::classifier::MatrixLookup | General view into utility::Matrix |
| theplu::yat::classifier::MatrixLookupWeighted | General view into utility::MatrixWeighted |
| theplu::yat::classifier::Sampler | Interface class for dividing samples into training and validation |
| theplu::yat::classifier::BootstrapSampler | Class creating trainingset and validationset using bootstrapping |
| theplu::yat::classifier::CrossValidationSampler | Class splitting a set into training set and validation set in a crossvalidation manner |
| theplu::yat::classifier::SubsetGenerator< Data > | Class splitting Data into training and validation set |
| theplu::yat::classifier::SupervisedClassifier | Interface class for supervised classifiers that use data in a matrix format |
| theplu::yat::classifier::KNN< Distance, NeighborWeighting > | Nearest Neighbor Classifier |
| theplu::yat::classifier::NBC | Naive Bayesian Classifier |
| theplu::yat::classifier::NCC< Distance > | Nearest Centroid Classifier |
| theplu::yat::classifier::SVindex | |
| theplu::yat::classifier::SVM | Support Vector Machine |
| theplu::yat::classifier::SvmMultiClass | Support Vector Machine for more than two classes |
| theplu::yat::classifier::Target | Class for containing sample labels |
| theplu::yat::normalizer::Centralizer< UnaryFunction > | Centralize a range |
| theplu::yat::normalizer::ColumnNormalizer< T > | Using a functor T to normalize each column |
| theplu::yat::normalizer::Gauss | Gaussian Normalizer |
| theplu::yat::normalizer::qQuantileNormalizer | Perform Q-quantile normalization |
| theplu::yat::normalizer::QuantileNormalizer | Perform quantile normalization |
| theplu::yat::normalizer::RowNormalizer< T > | Using a functor T to normalize each column |
| theplu::yat::normalizer::Spearman | Replace elements with normalized rank |
| theplu::yat::normalizer::Zscore | Zero mean and unity variance |
| theplu::yat::omic::BamHeader | Wrapper around bam_hdr_t struct |
| theplu::yat::omic::BamPair | |
| theplu::yat::omic::BamPairProxy | |
| theplu::yat::omic::BamRead | Class holding a bam query |
| theplu::yat::omic::Codon | |
| theplu::yat::omic::DnaComplementer | Functor that calculates genomic complement |
| theplu::yat::omic::Fasta | Wrapper class around struct faidx_t in libhts |
| theplu::yat::omic::Fasta::Sequence | |
| theplu::yat::omic::GFF | |
| theplu::yat::omic::GFF2 | |
| theplu::yat::omic::GFF3 | |
| theplu::yat::omic::Pileup< Iterator > | |
| theplu::yat::omic::Pileup< Iterator >::Entry | |
| theplu::yat::random::Continuous | Continuous random number distributions |
| theplu::yat::random::ContinuousGeneral | Generates numbers from a histogram in a continuous manner |
| theplu::yat::random::ContinuousUniform | Uniform distribution |
| theplu::yat::random::Exponential | Generator of random numbers from an exponential distribution |
| theplu::yat::random::Gaussian | Gaussian distribution |
| theplu::yat::random::Discrete | Discrete random number distributions |
| theplu::yat::random::Binomial | Binomial distribution |
| theplu::yat::random::DiscreteGeneral | General |
| theplu::yat::random::DiscreteUniform | Discrete uniform distribution |
| theplu::yat::random::Geometric | Geomtric Distribution |
| theplu::yat::random::HyperGeometric | |
| theplu::yat::random::NegativeHyperGeometric | |
| theplu::yat::random::Poisson | Poisson Distribution |
| theplu::yat::random::RNG | Random Number Generator |
| theplu::yat::random::RNG_state | Class holding state of a random generator |
| theplu::yat::regression::GSLInterpolation | Base class for interfacing GSL interpolation |
| theplu::yat::regression::AkimaInterpolation | Non-rounded Akima spline with natural boundary conditions |
| theplu::yat::regression::AkimaPeriodicInterpolation | AkimaPeriodic interpolation |
| theplu::yat::regression::CSplineInterpolation | Cubic spline with natural boundary conditions |
| theplu::yat::regression::CSplinePeriodicInterpolation | Cubic spline with periodic boundary conditions |
| theplu::yat::regression::LinearInterpolation | Linear interpolation |
| theplu::yat::regression::PolynomialInterpolation | Polynomial interpolation |
| theplu::yat::regression::Kernel | Interface Class for calculating the weights in a more general way than classical rectangular windows |
| theplu::yat::regression::KernelBox | Class for KernelBox a.k.a. rectangular window |
| theplu::yat::regression::KernelTriCube | Class for TriCubal kernel |
| theplu::yat::regression::TukeyBiweight | |
| theplu::yat::regression::Local | Class for Locally weighted regression |
| theplu::yat::regression::MultiDimensional | MultiDimesional fitting |
| theplu::yat::regression::MultiDimensionalWeighted | MultiDimesional fitting |
| theplu::yat::regression::OneDimensional | Interface Class for One Dimensional fitting |
| theplu::yat::regression::Linear | Linear regression |
| theplu::yat::regression::Naive | Naive Regression |
| theplu::yat::regression::Polynomial | Polynomial regression |
| theplu::yat::regression::OneDimensionalWeighted | Interface Class for One Dimensional fitting in a weighted fashion |
| theplu::yat::regression::LinearWeighted | Linear regression |
| theplu::yat::regression::NaiveWeighted | Naive fitting |
| theplu::yat::regression::PolynomialWeighted | Polynomial Regression in weighted fashion |
| theplu::yat::statistics::Average | Functor to take average of a range |
| theplu::yat::statistics::averager< Iterator > | |
| theplu::yat::statistics::averager_base< Derived > | Base class for averager classes |
| theplu::yat::statistics::averager_base2< Derived > | Base class for averagers calculating mean and variance |
| theplu::yat::statistics::averager_base3< Derived > | |
| theplu::yat::statistics::averager_base4< Derived > | |
| theplu::yat::statistics::averager_pair< Iterator1, Iterator2 > | |
| theplu::yat::statistics::averager_traits< T > | |
| theplu::yat::statistics::averager_traits< utility::unweighted_iterator_tag > | |
| theplu::yat::statistics::averager_traits< utility::weighted_iterator_tag > | |
| theplu::yat::statistics::AveragerPair | Class for taking care of mean and covariance of two variables |
| theplu::yat::statistics::AveragerPairWeighted | Class for taking care of mean and covariance of two variables in a weighted manner |
| theplu::yat::statistics::AveragerWeighted | Class to calulate averages with weights |
| theplu::yat::statistics::Distance< Derived > | A convenience class to implement Distance |
| theplu::yat::statistics::Fisher | Fisher's exact test |
| theplu::yat::statistics::Histogram | Histograms provide a convenient way of presenting the distribution of a set of data |
| theplu::yat::statistics::Kendall | Kendall's tau rank coefficient |
| theplu::yat::statistics::KolmogorovSmirnov | Kolmogorov Smirnov Test |
| theplu::yat::statistics::KolmogorovSmirnov::Element | |
| theplu::yat::statistics::KolmogorovSmirnovOneSample | Kolmogorov Smirnov Test for one class |
| theplu::yat::statistics::LikelihoodRatioTestBinomial | Likelihood-ratio test for binomial data |
| theplu::yat::statistics::PearsonCorrelation | Class for calculating Pearson correlation |
| theplu::yat::statistics::PearsonDistance | Calculates the Pearson correlation distance between two points given by elements of ranges |
| theplu::yat::statistics::Percentiler | Functor to calculate percentile of a range |
| theplu::yat::statistics::ROC | Reciever Operating Characteristic |
| theplu::yat::statistics::Score | Interface Class for score classes |
| theplu::yat::statistics::AUC | Area Under ROC Curve |
| theplu::yat::statistics::FoldChange | Score given by the difference by the group means |
| theplu::yat::statistics::Pearson | Class for calculating Pearson correlation |
| theplu::yat::statistics::SAMScore | Class for score used in Significance Analysis of Microarrays (SAM) |
| theplu::yat::statistics::SNRScore | Class for score based on signal-to-noise ratio (SNRScore) |
| theplu::yat::statistics::tScore | Class for Fisher's t-test |
| theplu::yat::statistics::WilcoxonFoldChange | WilcoxonFoldChange |
| theplu::yat::statistics::Smoother | Estimating a distribution in a smooth fashion |
| theplu::yat::statistics::Spearman | Spearman rank correlation coefficient |
| theplu::yat::statistics::tTest | Class for Student's t-test |
| theplu::yat::statistics::TukeyBiweightEstimator | Tukey's Biweight Estimator |
| theplu::yat::statistics::VectorFunction | Interface Class for vector functors |
| theplu::yat::statistics::Max | Larget element |
| theplu::yat::statistics::Mean | Mean element |
| theplu::yat::statistics::Median | Median element |
| theplu::yat::statistics::Min | Smallest element |
| theplu::yat::statistics::Nth_Element | |
| theplu::yat::utility::Aligner | Aligning two sequences |
| theplu::yat::utility::Aligner::Cigar | Compact Idiosyncratic Gapped Alignment Report |
| theplu::yat::utility::BasicStreamRedirect< charT, traits > | Redirect a stream to another stream |
| theplu::yat::utility::ColumnStream | |
| theplu::yat::utility::CommandLine | Class for parsing the command line |
| theplu::yat::utility::Container2D< T > | Concept check for Container2D |
| theplu::yat::utility::Mutable_Container2D< T > | Concept check for Mutable Container2D |
| theplu::yat::utility::DataIteratorConcept< T > | Concept check for Data Iterator |
| theplu::yat::utility::DataWeight | Holds a pair of data and associated weight |
| theplu::yat::utility::DataWeightProxy< DataIterator, WeightIterator > | Proxy class for DataWeight |
| theplu::yat::utility::Deleter | Functor that deletes an object |
| theplu::yat::utility::detail::weighted_iterator::Traversal< DataIterator, WeightIterator > | |
| theplu::yat::utility::FileUtil | Checking file/directory existence and access permissions |
| theplu::yat::utility::Index | Class for storing indices of, e.g., a MatrixLookup |
| theplu::yat::utility::iterator_traits< Iter > | |
| theplu::yat::utility::KernelMatrix< RandomAccessRange1, RandomAccessRange2, BinaryFunctor > | A KernelMatrix is a Container2D |
| theplu::yat::utility::KernelPCA | Principal Component Analysis on a Kernel Matrix |
| theplu::yat::utility::Matrix | Interface to GSL matrix |
| theplu::yat::utility::MatrixWeighted | Weighted Matrix |
| theplu::yat::utility::NNI | Interface class for nearest neighbour imputation (NNI) algorithms |
| theplu::yat::utility::kNNI | KNNimpute |
| theplu::yat::utility::WeNNI | Weighted Nearest Neighbour Imputation |
| theplu::yat::utility::Option | Container of variables for an option |
| theplu::yat::utility::OptionArg< std::string > | |
| theplu::yat::utility::OptionFile | Class for file related options |
| theplu::yat::utility::OptionInFile | Class for file related options |
| theplu::yat::utility::OptionOutFile | Class for file related options |
| theplu::yat::utility::OptionArg< T > | Option with argument |
| theplu::yat::utility::OptionSwitch | Class for switch option |
| theplu::yat::utility::OptionHelp | Class for help option |
| theplu::yat::utility::pair_value_compare< T1, T2 > | Functor comparing pairs using second |
| theplu::yat::utility::PairFirst< Pair > | Functor that return std::pair.first |
| theplu::yat::utility::PairSecond< Pair > | Functor that return std::pair.second |
| theplu::yat::utility::PCA | Principal Component Analysis |
| theplu::yat::utility::PriorityQueue< T, Compare > | Multi-thread safe priority queue |
| theplu::yat::utility::Queue< T > | Multi-thread safe queue |
| theplu::yat::utility::Range< T > | A class for storing a shallow copy of a Range |
| theplu::yat::utility::Scheduler | Handle a number of jobs and send them to threads |
| theplu::yat::utility::Scheduler::Job | |
| theplu::yat::utility::Segment< T, Compare > | Class for a Segment or Interval |
| theplu::yat::utility::SegmentTree< Container, Compare, Value2Key > | Base Class for SegmentSet and SegmentMap |
| theplu::yat::utility::SmartPtr< T > | |
| theplu::yat::utility::SmithWaterman | |
| theplu::yat::utility::SVD | Singular Value Decomposition |
| theplu::yat::utility::TypeInfo | Wrapper class for storing std::type_info |
| theplu::yat::utility::unweighted_iterator_tag | |
| theplu::yat::utility::VectorBase | This is the yat interface to GSL vector |
| theplu::yat::utility::VectorConstView | Read-only view |
| theplu::yat::utility::VectorMutable | This is the mutable interface to GSL vector |
| theplu::yat::utility::Vector | This is the yat interface to GSL vector |
| theplu::yat::utility::VectorView | This is the yat interface to gsl_vector_view |
| theplu::yat::utility::weighted_if_any2< T1, T2 > | |
| theplu::yat::utility::weighted_if_any3< T1, T2, T3 > | |
| theplu::yat::utility::weighted_iterator_tag | |
| theplu::yat::utility::weighted_iterator_traits< Iterator > | |
| theplu::yat::utility::WeightedIteratorArchetype_ctor_arg | |
1.8.5