| Cbpp::SiteFrequencySpectrumMafStatistics::Categorizer | |
| ▼Cbpp::Clonable [external] | |
| ▼Cbpp::Range< size_t > [external] | |
| Cbpp::SeqRange | Coordinate 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::SequenceWithAnnotation [external] | |
| Cbpp::MafSequence | A sequence class which is used to store data from MAF files |
| ►Cbpp::CoreSequenceSymbolList< class > [external] | |
| ►Cbpp::Sequence [external] | |
| Cbpp::SequenceWithAnnotation [external] | |
| ▼Cbpp::CruxSymbolList [external] | |
| ►Cbpp::CoreSymbolList< class > [external] | |
| ►CSymbolList< int > [external] | |
| ►CEdSymbolList< int > [external] | |
| ►Cbpp::EdIntSymbolList [external] | |
| Cbpp::SequenceWithAnnotation [external] | |
| Cbpp::CoreSequenceSymbolList< class > [external] | |
| ►Cbpp::EdCoreSymbolList< class > [external] | |
| CEdSymbolList< int > [external] | |
| Cbpp::MafBlock | A synteny block data structure, the basic unit of a MAF alignement file |
| ▼Cbpp::SequenceFeature | The base interface for sequence features |
| Cbpp::BasicSequenceFeature | A very simple implementation of the SequenceFeature class |
| ▼Cbpp::Commentable [external] | |
| Cbpp::AbstractCoreSequence [external] | |
| ▼Cbpp::FeatureReader | Interface for feature readers |
| Cbpp::BedGraphFeatureReader | A simple reader for features in the BedGraph format |
| Cbpp::GffFeatureReader | A simple reader implementing the Gene Finding Feature format |
| Cbpp::GtfFeatureReader | A simple reader implementing the Gene Transfer Format |
| ▼Cbpp::IOFormat [external] | |
| ▼Cbpp::IOSequenceStream [external] | |
| ►Cbpp::ISequenceStream [external] | |
| Cbpp::Fastq | The fastq sequence file format |
| ►Cbpp::OSequenceStream [external] | |
| Cbpp::Fastq | The fastq sequence file format |
| ▼Cbpp::IterationListener | Listener which enables to catch events when parsing a Maf file |
| ▼Cbpp::AbstractStatisticsOutputIterationListener | Iteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file (partial implementation, format-independent) |
| Cbpp::CsvStatisticsOutputIterationListener | Iteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file in CSv format |
| ▼Cbpp::MafIterator | Interface to loop over maf alignment blocks |
| ▼Cbpp::AbstractMafIterator | Partial implementation of the MafIterator interface |
| ►Cbpp::AbstractFilterMafIterator | Helper class for developping filter for maf blocks |
| Cbpp::AlignmentFilter2MafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
| Cbpp::AlignmentFilterMafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
| Cbpp::BlockLengthMafIterator | Filter maf blocks to keep only the ones with a minimum number of sites |
| Cbpp::BlockMergerMafIterator | Merge blocks if some of their sequences are contiguous |
| Cbpp::BlockSizeMafIterator | Filter maf blocks to keep only the ones with a minimum number of species |
| Cbpp::ChromosomeMafIterator | Filter maf blocks to keep only the block corresponding to one chromosome (of a reference sequence) |
| Cbpp::ConcatenateMafIterator | Concatenate blocks up to a certain size |
| Cbpp::CoordinateTranslatorMafIterator | Translate features coordinates from one species to another, based on the alignment |
| Cbpp::CoordinatesOutputMafIterator | Output each sequence coordinates for each block |
| Cbpp::DuplicateFilterMafIterator | Filter maf blocks to remove duplicated blocks, according to a reference sequence) |
| Cbpp::EntropyFilterMafIterator | Filter maf blocks highly divergent regions |
| Cbpp::FeatureExtractorMafIterator | Extract alignments corresponding to sequence features given as a vector of SequenceFeature objects |
| Cbpp::FeatureFilterMafIterator | Remove from alignment all positions that fall within any feature from a list given as a SequenceFeatureSet object |
| Cbpp::FullGapFilterMafIterator | Filter maf blocks to remove in each block the positions made only of gaps |
| Cbpp::MafIteratorSynchronizer | This special iterator synchronizes two adaptors |
| Cbpp::MaskFilterMafIterator | Filter maf blocks to remove regions with masked positions |
| Cbpp::MsmcOutputMafIterator | This iterator outputs all SNPs in the format readable by MSMC |
| Cbpp::OrderFilterMafIterator | This iterator check that blocks are ordered according to a reference sequence |
| Cbpp::OrphanSequenceFilterMafIterator | Filter maf blocks to keep a the ones which display a specified combination of species |
| Cbpp::OutputAlignmentMafIterator | This iterator forward the iterator given as input after having printed its content to an alignment file. The syntax for ENSEMBL meta data is used |
| Cbpp::OutputMafIterator | This iterator forward the iterator given as input after having printed its content to a file |
| Cbpp::PlinkOutputMafIterator | This iterator outputs all biallelic SNPs in the PLINK format (ped and map files) |
| Cbpp::QualityFilterMafIterator | Filter maf blocks to remove regions with low quality |
| Cbpp::RemoveEmptySequencesMafIterator | Remove ga-only or unresolved and gap-only sequences in each block |
| Cbpp::SequenceFilterMafIterator | Filter maf blocks to keep a subset of sequences, given their name. this filter can also be used to filter block which contain a certain set of sequences |
| Cbpp::SequenceLDhotOutputMafIterator | This iterator forward the iterator given as input after having printed its content to an alignment file |
| Cbpp::SequenceStatisticsMafIterator | Compute a series of sequence statistics for each block |
| Cbpp::TableOutputMafIterator | This iterator outputs sequence states for selected species and positions |
| Cbpp::VcfOutputMafIterator | This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF) |
| Cbpp::WindowSplitMafIterator | Splits block into windows of given sizes |
| Cbpp::MafParser | MAF file parser |
| Cbpp::SequenceStreamToMafIterator | A MafIterator built from a sequence stream |
| Cbpp::TrashIteratorAdapter | |
| ▼Cbpp::MafStatistics | General interface for computing statistics based on a Maf block |
| ▼Cbpp::AbstractMafStatistics | Partial implementation of MafStatistics, for convenience |
| Cbpp::CharacterCountsMafStatistics | Compute the base frequencies of a maf block |
| Cbpp::FourSpeciesPatternCountsMafStatistics | Compute the frequency of site patterns for a quadruplet of species |
| Cbpp::PolymorphismMafStatistics | Counts number of polymorphic / fixed sites in two populations |
| Cbpp::SequenceDiversityMafStatistics | Provide estimates of sequence diversity |
| Cbpp::SiteFrequencySpectrumMafStatistics | Compute the Site Frequency Spectrum of a maf block |
| Cbpp::SiteMafStatistics | Compute a few site statistics in a maf block |
| ▼Cbpp::AbstractMafStatisticsSimple | Partial implementation of MafStatistics, for convenience |
| Cbpp::AlignmentScoreMafStatistics | Retrieves the alignment score of a maf block |
| Cbpp::BlockLengthMafStatistics | Computes the number of columns in a maf block |
| Cbpp::BlockSizeMafStatistics | Computes the number of sequences in a maf block |
| Cbpp::PairwiseDivergenceMafStatistics | Computes the pairwise divergence for a pair of sequences in a maf block |
| Cbpp::SequenceLengthMafStatistics | Retrieve the sequence length (number of nucleotides) for a given species in a maf block |
| ▼Cbpp::AbstractSpeciesMultipleSelectionMafStatistics | Partial implementation of MafStatistics for method working on multiple distinct subsets of species, in a site-wise manner |
| Cbpp::PolymorphismMafStatistics | Counts number of polymorphic / fixed sites in two populations |
| ▼Cbpp::AbstractSpeciesSelectionMafStatistics | Partial implementation of MafStatistics for method working on a subset of species, in a site-wise manner |
| Cbpp::CharacterCountsMafStatistics | Compute the base frequencies of a maf block |
| Cbpp::FourSpeciesPatternCountsMafStatistics | Compute the frequency of site patterns for a quadruplet of species |
| Cbpp::SequenceDiversityMafStatistics | Provide estimates of sequence diversity |
| Cbpp::SiteFrequencySpectrumMafStatistics | Compute the Site Frequency Spectrum of a maf block |
| Cbpp::SiteMafStatistics | Compute a few site statistics in a maf block |
| ▼Cbpp::MafStatisticsResult | General interface for storing statistical results |
| Cbpp::SimpleMafStatisticsResult | A simple maf statistics result, with only one value |
| ▼Cbpp::MafTrashIterator | Interface to loop over removed blocks of a maf alignment |
| Cbpp::AlignmentFilter2MafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
| Cbpp::AlignmentFilterMafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
| Cbpp::EntropyFilterMafIterator | Filter maf blocks highly divergent regions |
| Cbpp::FeatureFilterMafIterator | Remove from alignment all positions that fall within any feature from a list given as a SequenceFeatureSet object |
| Cbpp::MaskFilterMafIterator | Filter maf blocks to remove regions with masked positions |
| Cbpp::QualityFilterMafIterator | Filter maf blocks to remove regions with low quality |
| Cbpp::SequenceFeatureSet | A simple ensemble of sequence features |
| Cbpp::SequenceFeatureTools | |
1.9.1