Object Model (`pyncbitk.objects`)#

General (`pyncbitk.objects.general`)#

`ObjectId`	A basic identifier for any NCBI Toolkit object.
`DBTag`	A database cross-reference.

A biological sequence.

`SeqInst`	Abstract base class for declaring the contents of a sequence.
`VirtualInst`	An instance corresponding to a sequence with no data.
`ContinuousInst`	An instance corresponding to a single continuous sequence.
`SegmentedInst`	An instance corresponding to a segmented sequence.
`ConstructedInst`	An instance corresponding to a constructed sequence.
`RefInst`	An instance corresponding to a reference to another sequence.
`ConsensusInst`	An instance corresponding to a consensus sequence.
`MapInst`	An instance corresponding to an ordered mapping.
`DeltaInst`	An instance corresponding to changed applied to other sequences.

`SeqData`	An abstract base storage of sequence data.
`SeqAaData`	An abstract base storage of amino-acid sequence data.
`SeqNaData`	An abstract base storage of nucleotide sequence data.
`IupacNaData`	Nucleotide sequence data stored as a IUPAC nucleotide string.
`Ncbi2NaData`	Nucleotide sequence data stored with 2-bit encoding.
`Ncbi4NaData`	Nucleotide sequence data stored with 4-bit encoding.
`Ncbi8NaData`
`NcbiPNaData`	Nucleotide sequence data storing probabilities for each position.
`IupacAaData`	Nucleotide sequence data stored in a IUPAC-UBI amino-acid string.
`Ncbi8AaData`	Amino-acid sequence data with support for modified residues.
`NcbiEAaData`	Amino-acid sequence data storing an NCBI-extended string.
`NcbiPAaData`	Amino-acid sequence data storing probabilities for each position.
`NcbiStdAa`	Amino-acid sequence data stored as ordinal encoding.
`GapData`	A virtual sequence data storage representing a gap.

`SeqId`	An abstract base class for defining a sequence identifier.
`LocalId`	A local identifier for naming privately maintained data.
`RefSeqId`	A sequence identifier from the NCBI Reference Sequence project.
`GenBankId`	A sequence identifier from the NCBI GenBank database.
`ProteinDataBankId`	A sequence identifier from the Protein Data Bank.
`GeneralId`	A sequence identifier from a database.
`OtherId`	A sequence identifier for other databases.
`TextSeqId`	A text identifier.

`SeqDesc`	An abstract base storage of sequence description.
`NameDesc`	A description storing the name of a sequence.
`TitleDesc`	A description storing the title of a sequence.
`RegionDesc`
`SeqDescSet`	A set of sequence descriptions.

`SeqLoc`	An abstract base class for defining a location in a `BioSeq`.
`NullLoc`	A region of unknown length for which no data exists.
`EmptySeqLoc`	A gap of unknown size inside an alignment.
`WholeSeqLoc`	A reference to an entire `BioSeq`.
`SeqIntervalLoc`	A reference to an interval on a `BioSeq`.
`PackedSeqLoc`	A reference to a series of intervals on a `BioSeq`.
`PointLoc`	A reference to a single point on a `BioSeq`.
`PackedPointsLoc`	A reference to a series of points on a `BioSeq`.
`MixLoc`	An arbitrarily complex location.
`EquivalentLoc`	A set of equivalent locations.
`BondLoc`	A chemical bond between two residues.
`FeatureLoc`	A location indirectly referenced through a feature.

`SeqAlign`	A sequence alignment, mapping the coordinates of a `BioSeq` to others.
`GlobalSeqAlign`	A global alignment over the complete lengths of several `BioSeq`.
`DiagonalSeqAlign`
`PartialSeqAlign`
`DiscontinuousSeqAlign`
`AlignSegments`
`DenseSegments`
`DenseSegmentsData`
`SeqAlignSet`	A set of sequence alignments.
`AlignRow`
`SeqAlignScore`