| ▼Nbpp | |
| NIntegerTools | |
| NTextTools | |
| CBedGraphFeatureReader | A simple reader for features in the BedGraph format |
| CFeatureReader | Interface for feature readers |
| CGffFeatureReader | A simple reader implementing the Gene Finding Feature format |
| CGtfFeatureReader | A simple reader implementing the Gene Transfer Format |
| CSeqRange | Coordinate range on a sequence. Stores coordinates as a Range<size_t> object, but also keep the strand information |
| CSequenceFeature | The base interface for sequence features |
| CBasicSequenceFeature | A very simple implementation of the SequenceFeature class |
| CSequenceFeatureSet | A simple ensemble of sequence features |
| CSequenceFeatureTools | |
| CFastq | The fastq sequence file format |
| CAlignmentFilterMafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
| CAlignmentFilter2MafIterator | Filter maf blocks to remove ambiguously aligned or non-informative regions |
| CBlockLengthMafIterator | Filter maf blocks to keep only the ones with a minimum number of sites |
| CBlockMergerMafIterator | Merge blocks if some of their sequences are contiguous |
| CBlockSizeMafIterator | Filter maf blocks to keep only the ones with a minimum number of species |
| CChromosomeMafIterator | Filter maf blocks to keep only the block corresponding to one chromosome (of a reference sequence) |
| CConcatenateMafIterator | Concatenate blocks up to a certain size |
| CCoordinatesOutputMafIterator | Output each sequence coordinates for each block |
| CCoordinateTranslatorMafIterator | Translate features coordinates from one species to another, based on the alignment |
| CDuplicateFilterMafIterator | Filter maf blocks to remove duplicated blocks, according to a reference sequence) |
| CEntropyFilterMafIterator | Filter maf blocks highly divergent regions |
| CFeatureExtractorMafIterator | Extract alignments corresponding to sequence features given as a vector of SequenceFeature objects |
| CFeatureFilterMafIterator | Remove from alignment all positions that fall within any feature from a list given as a SequenceFeatureSet object |
| CFullGapFilterMafIterator | Filter maf blocks to remove in each block the positions made only of gaps |
| CIterationListener | Listener which enables to catch events when parsing a Maf file |
| CAbstractStatisticsOutputIterationListener | Iteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file (partial implementation, format-independent) |
| CCsvStatisticsOutputIterationListener | Iteration listener that works with a SequenceStatisticsMafIterator, enabling output of results in a file in CSv format |
| CMafBlock | A synteny block data structure, the basic unit of a MAF alignement file |
| CMafIterator | Interface to loop over maf alignment blocks |
| CAbstractMafIterator | Partial implementation of the MafIterator interface |
| CMafTrashIterator | Interface to loop over removed blocks of a maf alignment |
| CAbstractFilterMafIterator | Helper class for developping filter for maf blocks |
| CTrashIteratorAdapter | |
| CMafIteratorSynchronizer | This special iterator synchronizes two adaptors |
| CMafParser | MAF file parser |
| CMafSequence | A sequence class which is used to store data from MAF files |
| CMafStatisticsResult | General interface for storing statistical results |
| CSimpleMafStatisticsResult | A simple maf statistics result, with only one value |
| CMafStatistics | General interface for computing statistics based on a Maf block |
| CAbstractMafStatistics | Partial implementation of MafStatistics, for convenience |
| CAbstractMafStatisticsSimple | Partial implementation of MafStatistics, for convenience |
| CPairwiseDivergenceMafStatistics | Computes the pairwise divergence for a pair of sequences in a maf block |
| CBlockSizeMafStatistics | Computes the number of sequences in a maf block |
| CBlockLengthMafStatistics | Computes the number of columns in a maf block |
| CSequenceLengthMafStatistics | Retrieve the sequence length (number of nucleotides) for a given species in a maf block |
| CAlignmentScoreMafStatistics | Retrieves the alignment score of a maf block |
| CAbstractSpeciesSelectionMafStatistics | Partial implementation of MafStatistics for method working on a subset of species, in a site-wise manner |
| CAbstractSpeciesMultipleSelectionMafStatistics | Partial implementation of MafStatistics for method working on multiple distinct subsets of species, in a site-wise manner |
| CCharacterCountsMafStatistics | Compute the base frequencies of a maf block |
| ▼CSiteFrequencySpectrumMafStatistics | Compute the Site Frequency Spectrum of a maf block |
| CCategorizer | |
| CFourSpeciesPatternCountsMafStatistics | Compute the frequency of site patterns for a quadruplet of species |
| CSiteMafStatistics | Compute a few site statistics in a maf block |
| CPolymorphismMafStatistics | Counts number of polymorphic / fixed sites in two populations |
| CSequenceDiversityMafStatistics | Provide estimates of sequence diversity |
| CMaskFilterMafIterator | Filter maf blocks to remove regions with masked positions |
| CMsmcOutputMafIterator | This iterator outputs all SNPs in the format readable by MSMC |
| COrderFilterMafIterator | This iterator check that blocks are ordered according to a reference sequence |
| COrphanSequenceFilterMafIterator | Filter maf blocks to keep a the ones which display a specified combination of species |
| COutputAlignmentMafIterator | 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 |
| COutputMafIterator | This iterator forward the iterator given as input after having printed its content to a file |
| CPlinkOutputMafIterator | This iterator outputs all biallelic SNPs in the PLINK format (ped and map files) |
| CQualityFilterMafIterator | Filter maf blocks to remove regions with low quality |
| CRemoveEmptySequencesMafIterator | Remove ga-only or unresolved and gap-only sequences in each block |
| CSequenceFilterMafIterator | 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 |
| CSequenceLDhotOutputMafIterator | This iterator forward the iterator given as input after having printed its content to an alignment file |
| CSequenceStatisticsMafIterator | Compute a series of sequence statistics for each block |
| CSequenceStreamToMafIterator | A MafIterator built from a sequence stream |
| CTableOutputMafIterator | This iterator outputs sequence states for selected species and positions |
| CVcfOutputMafIterator | This iterator performs a simple SNP call from the MAF blocks, and outputs the results in the Variant Call Format (VCF) |
| CWindowSplitMafIterator | Splits block into windows of given sizes |
1.9.1