bpp Namespace Reference

Classes
class	AbstractFilterMafIterator
	Helper class for developping filter for maf blocks. More...
class	AbstractMafIterator
	Partial implementation of the MafIterator interface. More...
class	AbstractMafStatistics
	Partial implementation of MafStatistics, for convenience. More...
class	AbstractMafStatisticsSimple
	Partial implementation of MafStatistics, for convenience. More...
class	AbstractSpeciesMultipleSelectionMafStatistics
	Partial implementation of MafStatistics for method working on multiple distinct subsets of species, in a site-wise manner. More...
class	AbstractSpeciesSelectionMafStatistics
	Partial implementation of MafStatistics for method working on a subset of species, in a site-wise manner. More...
class	AbstractStatisticsOutputIterationListener
	Iteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file (partial implementation, format-independent) More...
class	AlignmentFilter2MafIterator
	Filter maf blocks to remove ambiguously aligned or non-informative regions. More...
class	AlignmentFilterMafIterator
	Filter maf blocks to remove ambiguously aligned or non-informative regions. More...
class	AlignmentScoreMafStatistics
	Retrieves the alignment score of a maf block. More...
class	BasicSequenceFeature
	A very simple implementation of the SequenceFeature class. More...
class	BlockLengthMafIterator
	Filter maf blocks to keep only the ones with a minimum number of sites. More...
class	BlockLengthMafStatistics
	Computes the number of columns in a maf block. More...
class	BlockMergerMafIterator
	Merge blocks if some of their sequences are contiguous. More...
class	BlockSizeMafIterator
	Filter maf blocks to keep only the ones with a minimum number of species. More...
class	BlockSizeMafStatistics
	Computes the number of sequences in a maf block. More...
class	CharacterCountsMafStatistics
	Compute the base frequencies of a maf block. More...
class	ChromosomeMafIterator
	Filter maf blocks to keep only the block corresponding to one chromosome (of a reference sequence). More...
class	ConcatenateMafIterator
	Concatenate blocks up to a certain size. More...
class	CoordinatesOutputMafIterator
	Output each sequence coordinates for each block. More...
class	CsvStatisticsOutputIterationListener
	Iteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file in CSv format. More...
class	DuplicateFilterMafIterator
	Filter maf blocks to remove duplicated blocks, according to a reference sequence). More...
class	EntropyFilterMafIterator
	Filter maf blocks highly divergent regions. More...
class	Fastq
	The fastq sequence file format. More...
class	FeatureExtractor
	Extract alignments corresponding to sequence features given as a vector of SequenceFeature objects. More...
class	FeatureFilterMafIterator
	Remove from alignment all positions that fall within any feature from a list given as a SequenceFeatureSet object. More...
class	FeatureReader
	Interface for feature readers. More...
class	FourSpeciesPatternCountsMafStatistics
	Compute the frequency of site patterns for a quadruplet of species. More...
class	FullGapFilterMafIterator
	Filter maf blocks to remove in each block the positions made only of gaps. More...
class	GffFeatureReader
	A simple reader implementing the Gene Finding Feature format. More...
class	GtfFeatureReader
	A simple reader implementing the Gene Transfer Format. More...
class	IterationListener
	Listener which enable to catch events when parsing a Maf file. More...
class	MafBlock
	A synteny block data structure, the basic unit of a MAF alignement file. More...
class	MafIterator
	Interface to loop over maf alignment blocks. More...
class	MafIteratorSynchronizer
	This special iterator synchronizes two adaptors. More...
class	MafParser
	MAF file parser. More...
class	MafSequence
	A sequence class which is used to store data from MAF files. More...
class	MafStatistics
	General interface for computing statistics based on a Maf block. More...
class	MafStatisticsResult
	General interface for storing statistical results. More...
class	MafTrashIterator
	Interface to loop over removed blocks of a maf alignment. More...
class	MaskFilterMafIterator
	Filter maf blocks to remove regions with masked positions. More...
class	OrphanSequenceFilterMafIterator
	Filter maf blocks to keep a the ones which display a specified combination of species. More...
class	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. More...
class	OutputMafIterator
	This iterator forward the iterator given as input after having printed its content to a file. More...
class	PairwiseDivergenceMafStatistics
	Computes the pairwise divergence for a pair of sequences in a maf block. More...
class	PolymorphismMafStatistics
	Counts number of polymorphic / fixed sites in two populations. More...
class	QualityFilterMafIterator
	Filter maf blocks to remove regions with low quality. More...
class	SeqRange
	a coordinate range on a sequence. Stores coordinates as a Range<size_t> object, but also keep the strand information. More...
class	SequenceDiversityMafStatistics
	Provide estimates of sequence diversity. More...
class	SequenceFeature
	The base interface for sequence features. More...
class	SequenceFeatureSet
	A simple ensemble of sequence features. More...
class	SequenceFeatureTools
class	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. More...
class	SequenceLengthMafStatistics
	Retrieve the sequence length (number of nucleotides) for a given species in a maf block. More...
class	SequenceStatisticsMafIterator
	Compute a series of sequence statistics for each block. More...
class	SequenceStreamToMafIterator
	A MafIterator built from a sequence stream. More...
class	SimpleMafStatisticsResult
	A simple maf statistics result, with only one value. More...
class	SiteFrequencySpectrumMafStatistics
	Compute the Site Frequency Spectrum of a maf block. More...
class	SiteMafStatistics
	Compute a few site statistics in a maf block. More...
class	TrashIteratorAdapter
class	VcfOutputMafIterator
	This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF). More...
class	WindowSplitMafIterator
	Splits block into windows of given sizes. More...