Uses of Interface
com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument

Packages that use SequenceDocument

Package	Description
com.biomatters.geneious.publicapi.documents	Provides interfaces and classes for defining documents in Geneious and related interfaces and classes for dealing with XMLSerialization.
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.
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	Provides SequenceDocument implementations for nucelotide, amino acid, and nucleotide graph (chromatogram) sequences.
com.biomatters.geneious.publicapi.plugin	Provides the GeneiousPlugin 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.

Uses of SequenceDocument in com.biomatters.geneious.publicapi.documents

Methods in com.biomatters.geneious.publicapi.documents that return SequenceDocument

Modifier and Type	Method	Description
SequenceDocument	UrnWithSequenceRegions.getSequence(boolean throwDocumentOperationExceptionIfApdHasChanged, boolean throwDocumentOperationExceptionIfPluginDocumentHasChanged)	Gets the SequenceDocument referred to by this UrnWithSequenceRegions

Uses of SequenceDocument in com.biomatters.geneious.publicapi.documents.sequence

Classes in com.biomatters.geneious.publicapi.documents.sequence with type parameters of type SequenceDocument

Modifier and Type	Class	Description
class	SequenceListOnDisk<T extends SequenceDocument>	A list of sequences which are loaded from disk on demand rather than all stored in memory.
static class	SequenceListOnDisk.Builder<T extends SequenceDocument>	Used for building a SequenceListOnDisk.

Subinterfaces of SequenceDocument in com.biomatters.geneious.publicapi.documents.sequence

Modifier and Type	Interface	Description
interface	AminoAcidSequenceDocument	An interface for an Amino Acid sequence.
interface	ChromatogramDocument	Deprecated. Check for instanceof NucleotideGraphSequenceDocument instead.
interface	EditableNucleotideGraphSequenceDocument	A mutable nucleotide sequence with residue graph.
interface	EditableSequenceDocument	An extensions of a SequenceDocument that can be edited.
interface	NucleotideGraphSequenceDocument	A nucleotide sequence with an underlying "graph".
interface	NucleotideSequenceDocument	An interface for a nucleotide sequence.
interface	SequenceDocumentWithEditableAnnotations	An extension of a SequenceDocument that allows its annotations to be changed.

Classes in com.biomatters.geneious.publicapi.documents.sequence that implement SequenceDocument

Modifier and Type	Class	Description
class	ImmutableSequence	An implementation of a SequenceDocument that is immutable and has very low memory usage.
class	ImmutableSequenceImplementation	Despite this class being public, it is only public for implementation reasons.

Methods in com.biomatters.geneious.publicapi.documents.sequence with type parameters of type SequenceDocument

Modifier and Type	Method	Description
static <T extends SequenceDocument> SequenceListOnDisk<T>	SequenceListOnDisk.create(java.util.List<T> sequences, boolean tryCompressingSequences, jebl.util.ProgressListener progressListener)	Creates a new SequenceListOnDisk from an existing list of ungapped sequences.
static <T extends SequenceDocument> SequenceListOnDisk<T>	SequenceListOnDisk.createInterlaced(SequenceListOnDisk<T> sequences1, SequenceListOnDisk<T> sequences2, jebl.util.ProgressListener progressListener)	Creates a new SequenceListOnDisk by interlacing a pair of existing SequenceListOnDisks.

Methods in com.biomatters.geneious.publicapi.documents.sequence that return SequenceDocument

Modifier and Type	Method	Description
abstract SequenceDocument	SequenceAlignmentDocument.getSequence(int index)	Gets one row from the alignment as a SequenceDocument.
default SequenceDocument	SequenceListDocument.getSequence(int sequenceIndex)	Gets a nucleotide or amino acid sequence from this list document.
static SequenceDocument	SequenceAlignmentDocument.ReferencedSequence.getSequenceDocument(SequenceAlignmentDocument.ReferencedSequence referencedSequence, SequenceDocument.Alphabet alphabet)	Get the sequence document referenced by a ReferencedSequence (if it references a SequenceDocument or SequenceListDocument)
SequenceDocument	SequenceAlignmentDocument.ReferencedSequence.getSequenceDocument(SequenceDocument.Alphabet alphabet)	Get the sequence document referenced by this ReferencedSequence (if it references a SequenceDocument or SequenceListDocument)
SequenceDocument	GeneiousObjectInputStream.readSequence()	Reads a sequence from this input stream that was previously written using GeneiousObjectOutputStream.writeSequence(SequenceDocument, jebl.util.ProgressListener)
abstract SequenceDocument	SequenceDocument.Transformer.transformSequence(SequenceDocument sequence)	Transforms a sequence

Methods in com.biomatters.geneious.publicapi.documents.sequence that return types with arguments of type SequenceDocument

Modifier and Type	Method	Description
java.util.List<SequenceDocument>	SequenceAlignmentDocument.getSequences()	Get the alignment as a list of sequences (Convenience function).
SequenceListOnDisk<SequenceDocument>	SequenceListOnDisk.AlignmentData.getSequences()	Gets the sequences for this data
java.util.List<SequenceDocument>	SequenceAlignmentDocument.getSequencesInImmutableList()	Gets an immutable list (whose elements will not change after returning from this method).

Methods in com.biomatters.geneious.publicapi.documents.sequence with parameters of type SequenceDocument

Modifier and Type	Method	Description
void	SequenceListOnDisk.Builder.addAlignmentReferenceSequence(SequenceDocument referenceSequence, jebl.util.ProgressListener progressListener)	Adds a reference sequence when building an alignment.
void	SequenceAlignmentDocument.addSequence(SequenceDocument sequence)	Add a sequence to the end of the alignment.
void	SequenceListOnDisk.Builder.addSequence(SequenceDocument sequence, jebl.util.ProgressListener progressListener)	Adds a new unpaired sequence.
void	SequenceListSummary.addSequence(SequenceDocument sequence)	Adds a new sequence for this summary.
void	SequenceListOnDisk.Builder.addSequenceWithMate(SequenceDocument sequence, SequenceDocument mateSequence, int expectedDistance1, int expectedDistance2, jebl.util.ProgressListener progressListener)	Similar to addSequence but this version adds 2 sequences which are paired
ImmutableSequence	ImmutableSequence.Builder.createCopyOf(SequenceDocument sequenceToCopy, boolean createCopyEvenIfItDiscardsInformation)	Creates a ImmutableSequence copy of a given sequence.
static ImmutableSequence	ImmutableSequence.createImmutableSequence(SequenceDocument sequence)	Creates an ImmutableSequence copy of another sequence if possible.
static ImmutableSequence	ImmutableSequence.createImmutableSequence(SequenceDocument sequence, boolean failIfContainsNonStorableData)	Creates an ImmutableSequence copy of another sequence.
static DefaultSequenceListDocument	DefaultSequenceListDocument.forBothSequenceTypes(SequenceDocument... sequences)	Construct a new DefaultSequenceListDocument.
static java.lang.String	SequenceAnnotation.getTranslation(AnnotatedPluginDocument document, SequenceDocument sequence, SequenceAnnotation annotation)	Returns the translation (if applicable) for the given annotation.
abstract SequenceDocument	SequenceDocument.Transformer.transformSequence(SequenceDocument sequence)	Transforms a sequence
void	GeneiousObjectOutputStream.writeSequence(SequenceDocument sequence, jebl.util.ProgressListener progressListener)	Writes a sequence to this output stream which can be read back using GeneiousObjectInputStream.readSequence()

Method parameters in com.biomatters.geneious.publicapi.documents.sequence with type arguments of type SequenceDocument

Modifier and Type	Method	Description
static DefaultSequenceListDocument	DefaultSequenceListDocument.forBothSequenceTypes(java.util.List<? extends SequenceDocument> sequences, jebl.util.ProgressListener progressListener)	Construct a new DefaultSequenceListDocument.

Constructor parameters in com.biomatters.geneious.publicapi.documents.sequence with type arguments of type SequenceDocument

Constructor	Description
SequenceListSummary(java.util.List<SequenceDocument> sequences, boolean allowGaps, jebl.util.ProgressListener progressListener)	A convenience constructor which just calls SequenceListSummary.addSequence(SequenceDocument) for each sequence in the list and then calls SequenceListSummary.finishedAddingSequences(jebl.util.ProgressListener)

Uses of SequenceDocument in com.biomatters.geneious.publicapi.implementations

Methods in com.biomatters.geneious.publicapi.implementations that return SequenceDocument

Modifier and Type	Method	Description
static SequenceDocument	SequenceExtractionUtilities.extract(SequenceDocument sourceDocument, SequenceExtractionUtilities.ExtractionOptions extractionOptions)	Extracts one or more intervals from a sequence as a new sequence document.
static SequenceDocument	SequenceExtractionUtilities.extractOrThrow(SequenceDocument sourceDocument, SequenceExtractionUtilities.ExtractionOptions extractionOptions)	Extracts one or more intervals from a sequence as a new sequence document.
SequenceDocument	DefaultAlignmentDocument.getSequence(int index)
static SequenceDocument	SequenceExtractionUtilities.getTruncatedSequenceByHardTrimmingSoftTrimmedRegions(SequenceDocument sequence)	Returns a sequence with any soft trimmed regions or end gaps removed.
static SequenceDocument	SequenceExtractionUtilities.removeGaps(SequenceDocument sequence)	Equivalent to calling removeGaps(sequence, true)
static SequenceDocument	SequenceExtractionUtilities.removeGaps(SequenceDocument sequence, boolean mustGeneratedDefaultSequenceDocument)	creates a sequence the same as the given sequence but with gap characters removed.

Methods in com.biomatters.geneious.publicapi.implementations that return types with arguments of type SequenceDocument

Modifier and Type	Method	Description
java.util.List<SequenceDocument>	DefaultAlignmentDocument.getSequences()
java.util.List<SequenceDocument>	DefaultAlignmentDocument.getSequencesInImmutableList()

Methods in com.biomatters.geneious.publicapi.implementations with parameters of type SequenceDocument

Modifier and Type	Method	Description
void	DefaultAlignmentDocument.addContigReferenceSequence(SequenceDocument referenceSequence)	Adds a sequence as the contig reference sequence {see @link #getContigReferenceSequenceIndex()}.
void	DefaultAlignmentDocument.addSequence(SequenceDocument sequence)
void	DefaultPhylogenyDocument.addSequence(SequenceDocument sequence)
static java.util.List<SequenceAnnotation>	SequenceExtractionUtilities.adjustAnnotationsForGapRemoval(SequenceDocument sequenceWithGaps, java.util.List<SequenceAnnotation> annotations)	Creates a new list of annotations by adjusting their locations to compensate for removing all the gaps in the sequence.
static java.util.List<SequenceAnnotation>	SequenceExtractionUtilities.adjustAnnotationsForGaps(SequenceDocument sequenceWithGaps, java.util.List<SequenceAnnotation> annotations)	Creates a new list of annotations by adjusting their locations to compensate for adding gaps into the sequence.
static void	SequenceExtractionUtilities.copyAllDocumentFields(SequenceDocument source, DefaultSequenceDocument target)	Copy all document fields (such as organism, taxonomy and common name) from any SequenceDocument to a DefaultSequenceDocument.
static void	SequenceExtractionUtilities.copyDocumentFields(SequenceDocument source, DefaultSequenceDocument target, boolean isTranslation)	Copy important document fields (such as organism, taxonomy and common name) from any SequenceDocument to any DefaultSequenceDocument
static SequenceDocument	SequenceExtractionUtilities.extract(SequenceDocument sourceDocument, SequenceExtractionUtilities.ExtractionOptions extractionOptions)	Extracts one or more intervals from a sequence as a new sequence document.
static DefaultSequenceDocument	SequenceExtractionUtilities.extractIntervals(SequenceDocument sequence, SequenceAnnotationInterval... intervalsToExtract)	A convenience method for extracting intervals from a sequence.
static DefaultSequenceDocument	SequenceExtractionUtilities.extractIntervals(SequenceDocument sourceDocument, SequenceExtractionUtilities.ExtractionOptions extractionOptions)	Extracts one or more intervals from a sequence as a new sequence document.
static DefaultSequenceDocument	SequenceExtractionUtilities.extractIntervals(SequenceDocument sequence, Interval... intervalsToExtract)	A convenience method for extracting intervals from a sequence.
static DefaultSequenceDocument	SequenceExtractionUtilities.extractIntervals(SequenceDocument sourceDocument, java.lang.String overrideName, jebl.evolution.sequences.GeneticCode geneticCode, int translationFrame, boolean residuesOnly, java.util.List<SequenceAnnotationInterval> intervals, boolean allowReverseComplement, boolean removeGaps)	Deprecated. use SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions) instead.
static DefaultSequenceDocument	SequenceExtractionUtilities.extractIntervalsOrThrow(SequenceDocument sourceDocument, SequenceExtractionUtilities.ExtractionOptions extractionOptions)	Extracts one or more intervals from a sequence as a new sequence document.
static SequenceDocument	SequenceExtractionUtilities.extractOrThrow(SequenceDocument sourceDocument, SequenceExtractionUtilities.ExtractionOptions extractionOptions)	Extracts one or more intervals from a sequence as a new sequence document.
static SequenceGapInformation	SequenceGapInformation.forSequenceDocument(SequenceDocument sequence)	Get SequenceGapInformation for the given sequence.
static java.util.List<DocumentNote>	SequenceExtractionUtilities.getNotesFromFieldValues(SequenceDocument sequenceDocument)	Retrieve any document field values for note types as notes.
static SequenceDocument	SequenceExtractionUtilities.getTruncatedSequenceByHardTrimmingSoftTrimmedRegions(SequenceDocument sequence)	Returns a sequence with any soft trimmed regions or end gaps removed.
static boolean	SequenceExtractionUtilities.isReversedSequence(SequenceDocument sequence)	Determines if a SequenceDocument is reversed or not based on whether its name ends with SequenceExtractionUtilities.REVERSED_NAME_SUFFIX or not.
static SequenceDocument	SequenceExtractionUtilities.removeGaps(SequenceDocument sequence)	Equivalent to calling removeGaps(sequence, true)
static SequenceDocument	SequenceExtractionUtilities.removeGaps(SequenceDocument sequence, boolean mustGeneratedDefaultSequenceDocument)	creates a sequence the same as the given sequence but with gap characters removed.
static DefaultSequenceDocument	SequenceExtractionUtilities.reverseComplement(SequenceDocument sequenceToReverse)	Convenience method for calling reverseComplement(sequenceToReverse,true).
static DefaultSequenceDocument	SequenceExtractionUtilities.reverseComplement(SequenceDocument sequenceToReverse, boolean appendReversedToName)	Create a sequence that is the reverse complement another sequence.
static DefaultNucleotideSequence	SequenceExtractionUtilities.reverseComplement(SequenceDocument sequenceToReverse, boolean appendReversedToName, boolean includeOriginalBaseNumbersAnnotation)	Create a sequence that is the reverse complement another sequence.
static java.lang.String	SequenceExtractionUtilities.translate(SequenceDocument sequence, SequenceAnnotation annotation)	Deprecated. use SequenceExtractionUtilities.extractIntervals(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, com.biomatters.geneious.publicapi.implementations.SequenceExtractionUtilities.ExtractionOptions) instead.

Method parameters in com.biomatters.geneious.publicapi.implementations with type arguments of type SequenceDocument

Modifier and Type	Method	Description
EndGapsManager	EndGapsManager.Builder.toEndGapsManager(SequenceListOnDisk<? extends SequenceDocument> associatedSequences)	Creates an EndGapsManager from this builder

Constructors in com.biomatters.geneious.publicapi.implementations with parameters of type SequenceDocument

Constructor	Description
DefaultAlignmentDocument(SequenceDocument[] unalignedSequences, AnnotatedPluginDocument[] referencedDocuments, java.lang.CharSequence[] alignedSequenceCharacters, java.lang.String alignmentOptions, java.lang.Double alignmentScore, java.lang.String proposedName)	This is the constructor that should be used in most situations.
DefaultAlignmentDocument(SequenceDocument[] unalignedSequences, java.lang.CharSequence[] alignedSequenceCharacters, java.lang.String alignmentOptions, java.lang.Double alignmentScore, java.lang.String proposedName, jebl.util.ProgressListener progressListener)	Constructs an alignment without any references back to the original sequences.
DefaultAlignmentDocument(SequenceDocument[] alignedSequences, java.lang.String alignmentOptions, java.lang.Double alignmentScore, java.lang.String name)	Deprecated. use DefaultAlignmentDocument(String, com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument...) instead.
DefaultAlignmentDocument(SequenceDocument[] unalignedSequences, java.util.List<SequenceAlignmentDocument.ReferencedSequence> referencedSequences, java.lang.CharSequence[] alignedSequenceCharacters, java.lang.String alignmentOptions, java.lang.Double alignmentScore, java.lang.String proposedName, jebl.util.ProgressListener progressListener)	This is the constructor that should be used in most situations.
DefaultAlignmentDocument(java.lang.String name, SequenceDocument... alignedSequences)	Constructs alignment document with no references to original sequence documents.

Constructor parameters in com.biomatters.geneious.publicapi.implementations with type arguments of type SequenceDocument

Constructor	Description
EndGapsManager(org.jdom.Element element, SequenceListOnDisk<SequenceDocument> associatedSequences)	Recreates an EndGapsManager from XML.

Uses of SequenceDocument in com.biomatters.geneious.publicapi.implementations.sequence

Classes in com.biomatters.geneious.publicapi.implementations.sequence that implement SequenceDocument

Modifier and Type	Class	Description
class	CombinedAlignmentAndAminoAcidSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
class	CombinedAlignmentAndNucleotideGraphSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
class	CombinedAlignmentAndNucleotideSequenceDocument	See documentation at CombinedAlignmentAndSequenceDocument
class	CombinedAlignmentAndSequenceDocument	A wrapper to both an alignment and a stand-alone sequence that appears as a single EditableSequenceDocument.
class	DefaultAminoAcidSequence	A plugin document holding one amino acid sequence.
class	DefaultNucleotideGraphSequence	An implementation of an editable chromatogram.
class	DefaultNucleotideSequence	A plugin document holding one nucleotide sequence.
class	DefaultSequenceDocument	A default implementation of a sequence document.
class	OligoSequenceDocument	A sequence document which represents an olgionucleotide such as a Primer or DNA probe.

Methods in com.biomatters.geneious.publicapi.implementations.sequence that return SequenceDocument

Modifier and Type	Method	Description
static SequenceDocument	OligoSequenceDocument.createExtensionForPrimerAnnotation(SequenceAnnotation primerAnnotation)	Deprecated. this method no longer works and there is no replacement in the API.
SequenceDocument	CombinedAlignmentAndSequenceDocument.getSequence(int index)

Methods in com.biomatters.geneious.publicapi.implementations.sequence that return types with arguments of type SequenceDocument

Modifier and Type	Method	Description
java.util.List<SequenceDocument>	CombinedAlignmentAndSequenceDocument.getSequences()

Methods in com.biomatters.geneious.publicapi.implementations.sequence with parameters of type SequenceDocument

Modifier and Type	Method	Description
void	CombinedAlignmentAndSequenceDocument.addSequence(SequenceDocument sequence)
void	DefaultSequenceDocument.copySequenceTracksFrom(SequenceDocument sourceSequence)	Copies all SequenceTracks (if any) from the source sequence on to this sequence.
static SequenceTrack	SequenceTrack.getTrack(SequenceDocument sequence, java.lang.String trackName)	Gets a track by name from a sequence
static SequenceTrack.Manager	SequenceTrack.getTrackManager(SequenceDocument sequenceDocument)	Equivalent to getTrackManager(sequenceDocument, true)
static SequenceTrack.Manager	SequenceTrack.getTrackManager(SequenceDocument sequenceDocument, boolean mayReturnNullIfNoTracks)	Gets the track manager (if any) for a sequence.
static java.util.List<SequenceTrack>	SequenceTrack.getTracks(SequenceDocument sequence)	Gets all tracks from a sequence
void	NucleotideCounter.incrementFor(SequenceDocument sequenceDocument)	Increments the AT and GC counts by the nucleotides in this sequence

Constructors in com.biomatters.geneious.publicapi.implementations.sequence with parameters of type SequenceDocument

Constructor	Description
DefaultSequenceDocument(SequenceDocument sequence, java.util.Date created)	Construct a new DefaultSequenceDocument from an existing SequenceDocument.

Uses of SequenceDocument in com.biomatters.geneious.publicapi.plugin

Fields in com.biomatters.geneious.publicapi.plugin with type parameters of type SequenceDocument

Modifier and Type	Field	Description
static DocumentType<SequenceDocument>	DocumentType.SEQUENCE_TYPE	SequenceDocument document type

Methods in com.biomatters.geneious.publicapi.plugin that return SequenceDocument

Modifier and Type	Method	Description
SequenceDocument	SequenceAnnotationGenerator.AnnotationGeneratorResult.createNewSequenceWhenAppliedTo(SequenceDocument sourceSequence)	Returns the results of applying this annotation generator result to the given sequence.
abstract SequenceDocument	SequenceViewerExtension.PropertyRetrieverAndEditor.getOriginalSequenceDocument(int sequenceIndex)	WARNING: Use with care as this doesn't include any edits the user has made while the viewer has been open.
SequenceDocument	SequenceSelection.SelectionInterval.getSequence()	Deprecated. use SequenceSelection.SelectionInterval.getSequenceIndex() and SequenceSelection.SequenceIndex.getSequence(java.util.List) instead.
SequenceDocument	SequenceSelection.SequenceIndex.getSequence(java.util.List<AnnotatedPluginDocument> selectedDocuments)	Gets the selected sequence corresponding to this sequence index for these documents
SequenceDocument	SequenceSelection.SequenceIndex.getSequenceFromPluginDocuments(java.util.List<PluginDocument> selectedDocuments)	Gets the selected sequence corresponding to this sequence index for these documents

Methods in com.biomatters.geneious.publicapi.plugin that return types with arguments of type SequenceDocument

Modifier and Type	Method	Description
java.util.Set<SequenceDocument>	SequenceSelection.getSelectedSequences()	Deprecated. use SequenceSelection.getSelectedSequenceIndices()
java.util.List<SequenceDocument>	SequenceSelectionWithDocuments.getSequences()	Returns the sequences referred to by this object's SequenceSelection for its List of AnnotatedPluginDocument, as a List of SequenceDocument, applying the given ExtractionStrategy in order to extract sequences.

Methods in com.biomatters.geneious.publicapi.plugin with parameters of type SequenceDocument

Modifier and Type	Method	Description
Interval	SequenceSelection.SelectionInterval.clipToSequenceAppropriateRange(java.util.List<AnnotatedPluginDocument> documents, SequenceDocument sequenceDocument)	Clips a SelectionInterval into the actual range of the sequence/s it is selecting.
SequenceDocument	SequenceAnnotationGenerator.AnnotationGeneratorResult.createNewSequenceWhenAppliedTo(SequenceDocument sourceSequence)	Returns the results of applying this annotation generator result to the given sequence.
static SequenceViewerExtension.PropertyRetrieverAndEditor	SequenceViewerExtension.PropertyRetrieverAndEditor.forSequences(SequenceDocument... sequences)	Creates a SequencePropertyRetriever for a list of sequences.
static SequenceViewerExtension.PropertyRetrieverAndEditor	SequenceViewerExtension.PropertyRetrieverAndEditor.forSequences(SequenceViewerExtension.StatisticsMethod statisticsMethod, SequenceDocument... sequences)	Like SequenceViewerExtension.PropertyRetrieverAndEditor.forSequences(SequenceDocument...) but allows the statistics method to be specified, unlike the other variant which always uses SequenceViewerExtension.StatisticsMethod.Mean

Method parameters in com.biomatters.geneious.publicapi.plugin with type arguments of type SequenceDocument

Modifier and Type	Method	Description
static SequenceAlignmentDocument	PluginUtilities.doAlignment(java.util.List<SequenceDocument> sequences, jebl.util.ProgressListener progressListener)	Prompts the user to perform an alignment using any of the available alignment plugins.
static SequenceViewerExtension.StateFrequencies<jebl.evolution.sequences.AminoAcidState>	SequenceViewerExtension.StateFrequencies.forAminoAcidSequences(java.util.List<SequenceDocument> sequences)
static SequenceViewerExtension.StateFrequencies<jebl.evolution.sequences.NucleotideState>	SequenceViewerExtension.StateFrequencies.forNucleotideSequences(java.util.List<SequenceDocument> sequences)

Constructors in com.biomatters.geneious.publicapi.plugin with parameters of type SequenceDocument

Constructor	Description
SelectionInterval(int fromResidue, int toResidue, SequenceDocument sequence)	Deprecated. use SelectionInterval(SequenceIndex, int, int) instead
SelectionInterval(Interval residueInterval, SequenceDocument sequence)	Deprecated. use SelectionInterval(SequenceIndex, com.biomatters.geneious.publicapi.utilities.Interval) instead
SequenceSelection(SequenceDocument sequence, SequenceAnnotation annotation)	Deprecated. use SequenceSelection(com.biomatters.geneious.publicapi.plugin.SequenceSelection.SequenceIndex, com.biomatters.geneious.publicapi.documents.sequence.SequenceAnnotation) instead

Uses of SequenceDocument in com.biomatters.geneious.publicapi.utilities

Methods in com.biomatters.geneious.publicapi.utilities that return SequenceDocument

Modifier and Type	Method	Description
static SequenceDocument	SequenceUtilities.concatenateSequences(java.util.List<? extends SequenceDocument> sequences, boolean circular, int indexOfDocumentToUseForOrigin, jebl.util.ProgressListener progressListener)	Concatenate a list of sequence documents.
static SequenceDocument	SequenceUtilities.createSequenceCopy(SequenceDocument original)	Creates a copy of the original sequence if necessary.
static SequenceDocument	SequenceUtilities.createSequenceCopyAdjustedForGapInsertion(SequenceDocument sequenceDocument, java.lang.CharSequence gappedSequenceCharacters)	Creates a copy of the given sequence with annotations, sequence residues, and chromatogram values adjusted to account for gap insertion.
static SequenceDocument	SequenceUtilities.createSequenceCopyAdjustedForGapInsertion(SequenceDocument sequenceDocument, java.lang.CharSequence gappedSequenceCharacters, boolean includeTracks)	Creates a copy of the given sequence with annotations, sequence residues, and chromatogram values adjusted to account for gap insertion.
static SequenceDocument	SequenceUtilities.generateConsensus(SequenceAlignmentDocument alignment, jebl.util.ProgressListener progressListener)	Generates a consensus sequence for an alignment using default consensus settings.
static SequenceDocument	SequenceUtilities.generateConsensusSequence(SequenceAlignmentDocument alignment, jebl.util.ProgressListener progressListener)	Deprecated. use SequenceUtilities.generateConsensus(com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument, jebl.util.ProgressListener) instead
static SequenceDocument	DataInputOutputUtilities.readSequence(java.io.DataInput input)	Reads a sequence from this input stream that was previously written using DataInputOutputUtilities.writeSequence(java.io.DataOutput, com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument ,jebl.util.ProgressListener)

Methods in com.biomatters.geneious.publicapi.utilities that return types with arguments of type SequenceDocument

Modifier and Type	Method	Description
static java.util.List<? extends SequenceDocument>	SequenceUtilities.getSequences(AnnotatedPluginDocument[] documents, SequenceDocument.Alphabet alphabet, jebl.util.ProgressListener progressListener)	get all the sequences out of a set of AnnotatedPluginDocuments that may wrap SequenceDocuments, SequenceListDocuments or SequenceAlignmentDocuments.
static java.util.List<? extends SequenceDocument>	SequenceUtilities.getSequences(java.util.List<AnnotatedPluginDocument> documents, SequenceDocument.Alphabet alphabet, jebl.util.ProgressListener progressListener)	get all the sequences out of a set of AnnotatedPluginDocuments that may wrap SequenceDocuments, SequenceListDocuments or SequenceAlignmentDocuments.
static java.util.Collection<? extends SequenceDocument>	SequenceUtilities.getSequencesWithoutImmediateLoading(AnnotatedPluginDocument[] documents, SequenceDocument.Alphabet alphabet)	Like SequenceUtilities.getSequences(com.biomatters.geneious.publicapi.documents.AnnotatedPluginDocument[], com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument.Alphabet, jebl.util.ProgressListener) but doesn't require each plugin document to be in memory as long as this Collection is around.
static java.util.List<SequenceDocument>	ImportUtilities.importFastaSequences(java.io.File fastaFile, SequenceDocument.Alphabet alphabet, jebl.util.ProgressListener progressListener)	Imports the given fasta file as a list of unaligned sequences.

Methods in com.biomatters.geneious.publicapi.utilities with parameters of type SequenceDocument

Modifier and Type	Method	Description
static jebl.evolution.sequences.Sequence	SequenceUtilities.asJeblSequence(AnnotatedPluginDocument referenceDocument, SequenceDocument sequence)	Deprecated. use SequenceUtilities.asJeblSequence(SequenceAlignmentDocument.ReferencedSequence, SequenceDocument)
static jebl.evolution.sequences.Sequence	SequenceUtilities.asJeblSequence(SequenceAlignmentDocument.ReferencedSequence referencedSequence, SequenceDocument sequence)	Convert from a Geneious sequence to a jebl sequence.
static jebl.evolution.sequences.Sequence	SequenceUtilities.asJeblSequence(SequenceDocument sequence)	Convert from a Geneious sequence to a jebl sequence.
static java.util.List<jebl.evolution.sequences.Sequence>	SequenceUtilities.asJeblSequences(SequenceDocument... sequences)	Convert a set of Geneious sequences to jebl sequences.
static java.lang.String	SequenceUtilities.containsInvalidResidues(SequenceDocument sequenceDocument, boolean allowGaps, boolean fastIncompleteCheck)	Checks if a sequence contain invalid sequence residues.
static SequenceDocument	SequenceUtilities.createSequenceCopy(SequenceDocument original)	Creates a copy of the original sequence if necessary.
static SequenceDocument	SequenceUtilities.createSequenceCopyAdjustedForGapInsertion(SequenceDocument sequenceDocument, java.lang.CharSequence gappedSequenceCharacters)	Creates a copy of the given sequence with annotations, sequence residues, and chromatogram values adjusted to account for gap insertion.
static SequenceDocument	SequenceUtilities.createSequenceCopyAdjustedForGapInsertion(SequenceDocument sequenceDocument, java.lang.CharSequence gappedSequenceCharacters, boolean includeTracks)	Creates a copy of the given sequence with annotations, sequence residues, and chromatogram values adjusted to account for gap insertion.
static DefaultSequenceDocument	SequenceUtilities.createSequenceCopyEditable(SequenceDocument original)	Creates a copy of the original sequence that is editable.
static SequenceDocument.Alphabet	SequenceUtilities.getAlphabet(SequenceDocument sequence)	Get the Alphabet of a sequence.
static java.util.List<SequenceAnnotation>	SequenceUtilities.getAnnotationsOfType(SequenceDocument document, java.lang.String type)	Deprecated. use SequenceUtilities.getAnnotationsOfType(com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument, String, boolean) instead.
static java.util.List<SequenceAnnotation>	SequenceUtilities.getAnnotationsOfType(SequenceDocument document, java.lang.String type, boolean returnAnnotationsInTracks)	Get all annotations in document matching the given type.
static java.lang.Integer	SequenceUtilities.getIndexBasedOnExtractionAnnotation(SequenceDocument sequenceDocument, int index, boolean mapToOriginal)	Gets the extraction annotations from the sequence document and maps a residue index to a residue index on either the original sequence or the result sequence, depending on the value of mapToOriginal
static SequenceAnnotationInterval	SequenceUtilities.getIntervalBasedOnExtractionAnnotation(SequenceDocument sequenceDocument, SequenceAnnotationInterval interval, boolean mapToOriginal)	Gets the extraction annotations from the sequence document and maps the interval to either the original sequence or the result sequence, depending on the value of mapToOriginal
static int	SequenceUtilities.getOriginalIndex(SequenceDocument sequence, int index)	Gets the original numbering of the given index if it is covered by a SequenceAnnotation.TYPE_EXTRACTED_REGION annotation.
static java.lang.Iterable<SequenceAnnotation>	SequenceUtilities.getSequenceAndTrackAnnotations(SequenceDocument sequence)	A convenience method to get all annotations on the sequence and all annotations on all SequenceTracks on this sequence.
static java.util.List<SequenceAnnotation>	SequenceUtilities.getSequenceAnnotationsIncludingImmutableSequencesTrims(SequenceDocument sequence)	Gets all the annotations on the given sequence.
static java.lang.String	SequenceUtilities.getSequenceHash(SequenceDocument sequence)
static java.lang.String	SequenceUtilities.getSequenceHash(SequenceDocument sequence, java.util.List<Interval> intervals)
static jebl.evolution.sequences.SequenceType	SequenceUtilities.getSequenceType(SequenceDocument sequence)	Get the (jebl) sequence type.
static java.lang.CharSequence	SequenceUtilities.getValidSequence(SequenceDocument sequenceDocument, boolean allowGaps)	Replace any invalid bases/residues in the given sequence document with ambiguity symbols.
static java.lang.CharSequence	SequenceUtilities.getValidSequence(SequenceDocument sequenceDocument, boolean allowGaps, boolean replaceWithGaps)	Replace any invalid bases/residues in the given sequence document with ambiguity symbols or gaps.
static java.lang.String	SequenceUtilities.toHTMLFragment(SequenceDocument sequence, java.lang.String additionalContent)	Generate a HTML fragment that summarises a sequence, including the sequence string.
static void	DataInputOutputUtilities.writeSequence(Geneious.MajorVersion version, java.io.DataOutput out, SequenceDocument sequence, jebl.util.ProgressListener progressListener)	Writes a sequence to a DataOutput which can be read back using DataInputOutputUtilities.readSequence(java.io.DataInput)
static void	DataInputOutputUtilities.writeSequence(java.io.DataOutput out, SequenceDocument sequence, jebl.util.ProgressListener progressListener)	Writes a sequence to a DataOutput which can be read back using DataInputOutputUtilities.readSequence(java.io.DataInput)

Method parameters in com.biomatters.geneious.publicapi.utilities with type arguments of type SequenceDocument

Modifier and Type	Method	Description
static jebl.evolution.alignments.Alignment	SequenceUtilities.asJeblAlignment(java.util.List<SequenceDocument> sequences)	Convert a list of (aligned) Geneious sequences to a jebl alignmnent
static java.util.List<jebl.evolution.sequences.Sequence>	SequenceUtilities.asJeblSequences(java.util.List<SequenceDocument> sequences)	Convert a set of Geneious sequences to jebl sequences.
static SequenceDocument	SequenceUtilities.concatenateSequences(java.util.List<? extends SequenceDocument> sequences, boolean circular, int indexOfDocumentToUseForOrigin, jebl.util.ProgressListener progressListener)	Concatenate a list of sequence documents.