bpp-seq-omics  2.4.1
Class Hierarchy

Go to the graphical class hierarchy

This inheritance list is sorted roughly, but not completely, alphabetically:
[detail level 1234567]
 Cbpp::SiteFrequencySpectrumMafStatistics::Categorizer
 Cbpp::Clonable [external]
 Cbpp::Range< size_t > [external]
 Cbpp::SeqRangeCoordinate range on a sequence. Stores coordinates as a Range<size_t> object, but also keep the strand information
 Cbpp::CoreSequence [external]
 Cbpp::AbstractCoreSequence [external]
 Cbpp::CoreSequenceSymbolList< class > [external]
 Cbpp::CruxSymbolList [external]
 Cbpp::CoreSymbolList< class > [external]
 Cbpp::MafBlockA synteny block data structure, the basic unit of a MAF alignement file
 Cbpp::SequenceFeatureThe base interface for sequence features
 Cbpp::BasicSequenceFeatureA very simple implementation of the SequenceFeature class
 Cbpp::Commentable [external]
 Cbpp::AbstractCoreSequence [external]
 Cbpp::FeatureReaderInterface for feature readers
 Cbpp::BedGraphFeatureReaderA simple reader for features in the BedGraph format
 Cbpp::GffFeatureReaderA simple reader implementing the Gene Finding Feature format
 Cbpp::GtfFeatureReaderA simple reader implementing the Gene Transfer Format
 Cbpp::IOFormat [external]
 Cbpp::IOSequenceStream [external]
 Cbpp::ISequenceStream [external]
 Cbpp::OSequenceStream [external]
 Cbpp::IterationListenerListener which enables to catch events when parsing a Maf file
 Cbpp::AbstractStatisticsOutputIterationListenerIteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file (partial implementation, format-independent)
 Cbpp::CsvStatisticsOutputIterationListenerIteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file in CSv format
 Cbpp::MafIteratorInterface to loop over maf alignment blocks
 Cbpp::AbstractMafIteratorPartial implementation of the MafIterator interface
 Cbpp::AbstractFilterMafIteratorHelper class for developping filter for maf blocks
 Cbpp::MafParserMAF file parser
 Cbpp::SequenceStreamToMafIteratorA MafIterator built from a sequence stream
 Cbpp::TrashIteratorAdapter
 Cbpp::MafStatisticsGeneral interface for computing statistics based on a Maf block
 Cbpp::AbstractMafStatisticsPartial implementation of MafStatistics, for convenience
 Cbpp::CharacterCountsMafStatisticsCompute the base frequencies of a maf block
 Cbpp::FourSpeciesPatternCountsMafStatisticsCompute the frequency of site patterns for a quadruplet of species
 Cbpp::PolymorphismMafStatisticsCounts number of polymorphic / fixed sites in two populations
 Cbpp::SequenceDiversityMafStatisticsProvide estimates of sequence diversity
 Cbpp::SiteFrequencySpectrumMafStatisticsCompute the Site Frequency Spectrum of a maf block
 Cbpp::SiteMafStatisticsCompute a few site statistics in a maf block
 Cbpp::AbstractMafStatisticsSimplePartial implementation of MafStatistics, for convenience
 Cbpp::AlignmentScoreMafStatisticsRetrieves the alignment score of a maf block
 Cbpp::BlockLengthMafStatisticsComputes the number of columns in a maf block
 Cbpp::BlockSizeMafStatisticsComputes the number of sequences in a maf block
 Cbpp::PairwiseDivergenceMafStatisticsComputes the pairwise divergence for a pair of sequences in a maf block
 Cbpp::SequenceLengthMafStatisticsRetrieve the sequence length (number of nucleotides) for a given species in a maf block
 Cbpp::AbstractSpeciesMultipleSelectionMafStatisticsPartial implementation of MafStatistics for method working on multiple distinct subsets of species, in a site-wise manner
 Cbpp::PolymorphismMafStatisticsCounts number of polymorphic / fixed sites in two populations
 Cbpp::AbstractSpeciesSelectionMafStatisticsPartial implementation of MafStatistics for method working on a subset of species, in a site-wise manner
 Cbpp::CharacterCountsMafStatisticsCompute the base frequencies of a maf block
 Cbpp::FourSpeciesPatternCountsMafStatisticsCompute the frequency of site patterns for a quadruplet of species
 Cbpp::SequenceDiversityMafStatisticsProvide estimates of sequence diversity
 Cbpp::SiteFrequencySpectrumMafStatisticsCompute the Site Frequency Spectrum of a maf block
 Cbpp::SiteMafStatisticsCompute a few site statistics in a maf block
 Cbpp::MafStatisticsResultGeneral interface for storing statistical results
 Cbpp::SimpleMafStatisticsResultA simple maf statistics result, with only one value
 Cbpp::MafTrashIteratorInterface to loop over removed blocks of a maf alignment
 Cbpp::AlignmentFilter2MafIteratorFilter maf blocks to remove ambiguously aligned or non-informative regions
 Cbpp::AlignmentFilterMafIteratorFilter maf blocks to remove ambiguously aligned or non-informative regions
 Cbpp::EntropyFilterMafIteratorFilter maf blocks highly divergent regions
 Cbpp::FeatureFilterMafIteratorRemove from alignment all positions that fall within any feature from a list given as a SequenceFeatureSet object
 Cbpp::MaskFilterMafIteratorFilter maf blocks to remove regions with masked positions
 Cbpp::QualityFilterMafIteratorFilter maf blocks to remove regions with low quality
 Cbpp::SequenceFeatureSetA simple ensemble of sequence features
 Cbpp::SequenceFeatureTools