Uses of Package
com.biomatters.geneious.publicapi.documents.sequence
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Packages that use com.biomatters.geneious.publicapi.documents.sequence Package Description com.biomatters.geneious.publicapi.databaseservice Provides the interface and associated classes for defining a database service which is a service that appears on the left-hand side of the main Geneious window and provides the user with access to a database, for example NCBI or the local database for storing the user's documents.com.biomatters.geneious.publicapi.documents.sequence Provides interfaces specifying the types ofsequence
andalignment
documents in Geneious, together with concrete classes used by sequence documents such asSequenceAnnotation
andSequenceCharSequence
.com.biomatters.geneious.publicapi.documents.types Provides interfaces specifying the types of documents available in Geneious.com.biomatters.geneious.publicapi.implementations Provides implementations for many of the document interfaces defined in the package com.biomatters.geneious.publicapi.documents.types together with some utility classes for dealing with some of these document types.com.biomatters.geneious.publicapi.implementations.sequence ProvidesSequenceDocument
implementations for nucelotide, amino acid, and nucleotide graph (chromatogram) sequences.com.biomatters.geneious.publicapi.implementations.structure ProvidesMolecularStructureDocument
implementations for many commonly used 3D structure documents.com.biomatters.geneious.publicapi.plugin Provides theGeneiousPlugin
interface and plugin related interfaces.com.biomatters.geneious.publicapi.utilities Provides various utility methods and classes, none of which are necessary for creating a plugin, but many plugins implentations will find these methods useful. -
Classes in com.biomatters.geneious.publicapi.documents.sequence used by com.biomatters.geneious.publicapi.databaseservice Class Description SequenceDocument.Alphabet Supported sequence types. -
Classes in com.biomatters.geneious.publicapi.documents.sequence used by com.biomatters.geneious.publicapi.documents.sequence Class Description AlignmentLayout Provides information about how to layout of sequences (excluding the reference sequence) for rendering in an alignment or contig.AminoAcidSequenceDocument An interface for an Amino Acid sequence.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
.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 Specifies how to serialize the elements to disk and read them back in again.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.NucleotideGraph Optional phred-likequality information
on the residues of a sequence, and an optional chromatogram graph.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.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.SequenceAnnotationInterval.Direction The direction of a sequence annotation interval.SequenceAnnotationQualifier A named item of information (i.e.SequenceCharSequence A CharSequence that knows the length of its terminal gaps (sequences of '-') and allows for efficientinsertions
anddeletions
of subsequences.SequenceDocument Interface representing one sequence.SequenceDocument.Alphabet Supported sequence types.SequenceDocument.Transformer Provides a method for returning a new sequence which represents a transformation made to another 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.SequenceListOnDisk A list of sequences which are loaded from disk on demand rather than all stored in memory.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.SequenceListSummary.Provider An interface that lists of sequences (e.g.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 -
Classes in com.biomatters.geneious.publicapi.documents.sequence used by com.biomatters.geneious.publicapi.documents.types Class Description PairedReads Provides data about whether nucleotide sequences are paired together and their expected paired distance.SequenceAlignmentDocument An alignment or contig of sequences.SequenceListSummary.Provider An interface that lists of sequences (e.g. -
Classes in com.biomatters.geneious.publicapi.documents.sequence used by com.biomatters.geneious.publicapi.implementations Class Description 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.NucleotideGraph Optional phred-likequality information
on the residues of a sequence, and an optional chromatogram graph.PairedReads Provides data about whether nucleotide sequences are paired together and their expected paired distance.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.SequenceAnnotationInterval Immutable pair of integers with a direction, representing a directed range in the sequence annotation.SequenceCharSequence A CharSequence that knows the length of its terminal gaps (sequences of '-') and allows for efficientinsertions
anddeletions
of subsequences.SequenceDocument Interface representing one sequence.SequenceDocument.Alphabet Supported sequence types.SequenceListOnDisk 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.SequenceListSummary Provides a summary of data in a list of sequences.SequenceListSummary.Provider An interface that lists of sequences (e.g. -
Classes in com.biomatters.geneious.publicapi.documents.sequence used by com.biomatters.geneious.publicapi.implementations.sequence Class 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.ExtendedNucleotideGraph Provides an extended interface to aNucleotideGraph
.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.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.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.SequenceAnnotationInterval Immutable pair of integers with a direction, representing a directed range in the sequence annotation.SequenceAnnotationQualifier A named item of information (i.e.SequenceCharSequence A CharSequence that knows the length of its terminal gaps (sequences of '-') and allows for efficientinsertions
anddeletions
of subsequences.SequenceDocument Interface representing one sequence.SequenceDocumentWithEditableAnnotations An extension of aSequenceDocument
that allows its annotations to be changed. -
Classes in com.biomatters.geneious.publicapi.documents.sequence used by com.biomatters.geneious.publicapi.implementations.structure Class Description AminoAcidSequenceDocument An interface for an Amino Acid sequence.NucleotideSequenceDocument An interface for a nucleotide sequence.SequenceListDocument A document containing 0 or more nucleotide and 0 or more protein sequences. -
Classes in com.biomatters.geneious.publicapi.documents.sequence used by com.biomatters.geneious.publicapi.plugin Class Description AminoAcidSequenceDocument An interface for an Amino Acid sequence.ExtendedNucleotideGraph Provides an extended interface to aNucleotideGraph
.ImmutableSequence An implementation of aSequenceDocument
that is immutable and has very low memory usage.NucleotideSequenceDocument An interface for a nucleotide sequence.PairedReads Provides data about whether nucleotide sequences are paired together and their expected paired distance.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.SequenceAnnotationInterval.Direction The direction of a sequence annotation interval.SequenceAnnotationQualifier A named item of information (i.e.SequenceCharSequence A CharSequence that knows the length of its terminal gaps (sequences of '-') and allows for efficientinsertions
anddeletions
of subsequences.SequenceDocument Interface representing one sequence.SequenceDocument.Alphabet Supported sequence types.SequenceListDocument A document containing 0 or more nucleotide and 0 or more protein sequences.SequenceListSummary Provides a summary of data in a list of sequences. -
Classes in com.biomatters.geneious.publicapi.documents.sequence used by com.biomatters.geneious.publicapi.utilities Class Description EditableSequenceDocument An extensions of aSequenceDocument
that can be edited.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.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.SequenceAnnotationInterval Immutable pair of integers with a direction, representing a directed range in the sequence annotation.SequenceDocument Interface representing one sequence.SequenceDocument.Alphabet Supported sequence types.SequenceDocument.Transformer Provides a method for returning a new sequence which represents a transformation made to another sequence.