Package com.biomatters.geneious.publicapi.documents.sequence
Provides interfaces specifying the types of
sequence
and
alignment
documents in Geneious, together with concrete classes used by sequence documents
such as SequenceAnnotation
and SequenceCharSequence
.
For default implementations of the interfaces defined in this pacakage,
see the
com.biomatters.geneious.publicapi.implementations.sequence package.-
Interface Summary Interface Description AminoAcidSequenceDocument An interface for an Amino Acid sequence.ChromatogramDocument Deprecated. Check for instanceofNucleotideGraphSequenceDocument
instead.EditableNucleotideGraphSequenceDocument A mutable nucleotide sequence with residue graph.EditableSequenceDocument An extensions of aSequenceDocument
that can be edited.EditableSequenceListDocument ASequenceListDocument
that can have its internal lists of nucleotide and amino acid sequences reordered, added to, or removed from.ExtendedEditableSequenceListDocument Similar to anEditableSequenceListDocument
but also allows replacing sequences with new sequences or modifying the contents of individual sequencesExtendedNucleotideGraph Provides an extended interface to aNucleotideGraph
.ExternalSort.Serializer<T> Specifies how to serialize the elements to disk and read them back in again.NucleotideGraph Optional phred-likequality information
on the residues of a sequence, and an optional chromatogram graph.NucleotideGraph.ImmutableGraphProvider An interface a NucleotideGraph may implement to indicate it can provide an immutable instance of itself.NucleotideGraphSequenceDocument A nucleotide sequence with an underlying "graph".NucleotideSequenceDocument An interface for a nucleotide sequence.PairedReads Provides data about whether nucleotide sequences are paired together and their expected paired distance.SequenceAlignmentListDocument A document representing a list of alignments.SequenceDocument Interface representing one sequence.SequenceDocumentWithEditableAnnotations An extension of aSequenceDocument
that allows its annotations to be changed.SequenceListDocument A document containing 0 or more nucleotide and 0 or more protein sequences.SequenceListSummary.Provider An interface that lists of sequences (e.g. -
Class Summary Class Description AlignmentLayout Provides information about how to layout of sequences (excluding the reference sequence) for rendering in an alignment or contig.ByteBackedCharSequence A CharSequence whose data is stored as bytes (instead of a String) to reduce memory usage.CompactQualityOnlyGraph A memory efficient nucleotide graph that only supports quality values in the range 0->256 and does not support traces.ConstructorWrapper A wrapper around Constructor that improved performance.DefaultNucleotideGraph ANucleotideGraph
that stores its values in int[] arrays internally, and allows getting and setting those arrays.DefaultSequenceListDocument A default implementation of aSequenceListDocument
.ExternalSort<T> Sorts some objects, using temporary files on disk if necessary because the objects can't all fit in memory (e.g.GeneiousObjectInputStream An input stream to read from data previously written using aGeneiousObjectOutputStream
.GeneiousObjectOutputStream An extension toObjectOutputStream
that tries to reduce disk space and also reduce memory usage when the stream is read back in again later.ImmutableSequence An implementation of aSequenceDocument
that is immutable and has very low memory usage.ImmutableSequence.Builder Provides a system for building a list of ImmutableSequence which are even more compact than normal by analyzing patterns in the names of sequences.ImmutableSequenceImplementation Despite this class being public, it is only public for implementation reasons.SequenceAlignmentDocument An alignment or contig of sequences.SequenceAlignmentDocument.ReferencedSequence Represents a reference to the original document that a sequence in this alignment was aligned from.SequenceAnnotation Provides information on a subset of the sequence.SequenceAnnotationGroup An immutable class representing a collection of relatedSequenceAnnotation
types.SequenceAnnotationInterval Immutable pair of integers with a direction, representing a directed range in the sequence annotation.SequenceAnnotationQualifier A named item of information (i.e.SequenceBuilder Provides methods for creatingCharSequences
for use as biological sequences.SequenceCharSequence A CharSequence that knows the length of its terminal gaps (sequences of '-') and allows for efficientinsertions
anddeletions
of subsequences.SequenceDocument.Transformer Provides a method for returning a new sequence which represents a transformation made to another sequence.SequenceListOnDisk<T extends SequenceDocument> A list of sequences which are loaded from disk on demand rather than all stored in memory.SequenceListOnDisk.AlignmentData An immutable class (all of whose elements are immutable too) representing the sequences and data relevant to the sequences (excluding the reference sequence) in an alignment.SequenceListOnDisk.Builder<T extends SequenceDocument> Used for building a SequenceListOnDisk.SequenceListSummary Provides a summary of data in a list of sequences.SequenceListSummary.Coverage Represents the coverage (number of sequences covering a column in an alignment)SequenceListSummary.PairwiseSimilarity Immutable value class representing the number of identical and non-identical pairs of bases/residues in an alignment column.ValueAndFrequencyDistribution Provides a sorted distribution of longs and the frequency of each of them.ValueAndFrequencyDistribution.ValueAndFrequency Represents a value and the number of occurrences of the value -
Enum Summary Enum Description SequenceAnnotationInterval.Direction The direction of a sequence annotation interval.SequenceDocument.Alphabet Supported sequence types.