Uses of Class
com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument
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Packages that use SequenceAlignmentDocument Package Description 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.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. -
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Uses of SequenceAlignmentDocument in com.biomatters.geneious.publicapi.documents.sequence
Methods in com.biomatters.geneious.publicapi.documents.sequence that return types with arguments of type SequenceAlignmentDocument Modifier and Type Method Description java.util.List<SequenceAlignmentDocument>
SequenceAlignmentListDocument. getAlignments()
java.util.List<SequenceAlignmentDocument>
SequenceAnnotation. getAlignmentsFromHiddenQualifiers()
All alignments that can be created from hidden qualifiers returned fromSequenceAnnotation.getAlignmentHiddenQualifierName(SequenceDocument.Alphabet, boolean, String, String)
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Uses of SequenceAlignmentDocument in com.biomatters.geneious.publicapi.documents.types
Subclasses of SequenceAlignmentDocument in com.biomatters.geneious.publicapi.documents.types Modifier and Type Class Description class
PhylogenyDocument
A document containing an alignment and one or more trees whose tips are the sequences (i.e.Constructors in com.biomatters.geneious.publicapi.documents.types with parameters of type SequenceAlignmentDocument Constructor Description PhylogenyDocument(SequenceAlignmentDocument alignment)
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Uses of SequenceAlignmentDocument in com.biomatters.geneious.publicapi.implementations
Subclasses of SequenceAlignmentDocument in com.biomatters.geneious.publicapi.implementations Modifier and Type Class Description class
DefaultAlignmentDocument
An implementation of aSequenceAlignmentDocument
.class
DefaultPhylogenyDocument
An implementation of a Phylogeny document.Methods in com.biomatters.geneious.publicapi.implementations that return SequenceAlignmentDocument Modifier and Type Method Description static SequenceAlignmentDocument
SequenceExtractionUtilities. reverseComplement(SequenceAlignmentDocument alignmentToReverse)
Methods in com.biomatters.geneious.publicapi.implementations with parameters of type SequenceAlignmentDocument Modifier and Type Method Description static SequenceAlignmentDocument
SequenceExtractionUtilities. reverseComplement(SequenceAlignmentDocument alignmentToReverse)
static DefaultAlignmentDocument
SequenceExtractionUtilities. reverseComplement(SequenceAlignmentDocument alignmentToReverse, jebl.util.ProgressListener progressListener)
Creates a new alignment that is the reverse complement of the given alignment.static DefaultAlignmentDocument
SequenceExtractionUtilities. withoutAnnotations(SequenceAlignmentDocument alignment, jebl.util.ProgressListener progressListener)
Creates a new alignment that is the same as the given alignment, but without annotations Any documents referenced by the original alignment will not be referenced in the new alignment (because references always preserve annotations)Constructors in com.biomatters.geneious.publicapi.implementations with parameters of type SequenceAlignmentDocument Constructor Description DefaultAlignmentDocument(SequenceAlignmentDocument alignment)
Construct a default alignment as a deep copy of another alignment.EndGapsManager(SequenceAlignmentDocument alignment, int minimumHashSize)
Creates an EndGapsManager for the sequences in the given alignment. -
Uses of SequenceAlignmentDocument in com.biomatters.geneious.publicapi.implementations.sequence
Subclasses of SequenceAlignmentDocument in com.biomatters.geneious.publicapi.implementations.sequence Modifier and Type Class Description class
CombinedAlignmentAndAminoAcidSequenceDocument
See documentation atCombinedAlignmentAndSequenceDocument
class
CombinedAlignmentAndNucleotideGraphSequenceDocument
See documentation atCombinedAlignmentAndSequenceDocument
class
CombinedAlignmentAndNucleotideSequenceDocument
See documentation atCombinedAlignmentAndSequenceDocument
class
CombinedAlignmentAndSequenceDocument
A wrapper to both an alignment and a stand-alone sequence that appears as a single EditableSequenceDocument.Methods in com.biomatters.geneious.publicapi.implementations.sequence that return SequenceAlignmentDocument Modifier and Type Method Description SequenceAlignmentDocument
CombinedAlignmentAndSequenceDocument. getAlignmentDocument()
Get the alignment document contained within this documentMethods in com.biomatters.geneious.publicapi.implementations.sequence with parameters of type SequenceAlignmentDocument Modifier and Type Method Description static java.lang.String
SequenceTrack. getSuggestedTrackNameSuffixForAlignmentWithReferenceSequence(AnnotatedPluginDocument document, SequenceAlignmentDocument alignment)
Returns a suggested track name suffix to use for tracks created on an alignment with a reference sequence.static SequenceTrack.Manager
SequenceTrack. getTrackManager(SequenceAlignmentDocument alignmentDocument)
Equivalent togetTrackManager(sequenceAlignmentDocument, true)
static SequenceTrack.Manager
SequenceTrack. getTrackManager(SequenceAlignmentDocument alignmentDocument, boolean mayReturnNullIfNoTracks)
Gets the track manager (if any) for the consensus sequence of an alignment.Constructors in com.biomatters.geneious.publicapi.implementations.sequence with parameters of type SequenceAlignmentDocument Constructor Description CombinedAlignmentAndAminoAcidSequenceDocument(AminoAcidSequenceDocument sequenceDocument, SequenceAlignmentDocument alignmentDocument, boolean obtainSharedPropertiesFromSequence, boolean showSequenceView)
Constructs a new combined alignment and sequence document.CombinedAlignmentAndNucleotideGraphSequenceDocument(NucleotideGraphSequenceDocument sequenceDocument, SequenceAlignmentDocument alignmentDocument, boolean obtainSharedPropertiesFromSequence, boolean showSequenceView)
Constructs a new combined alignment and sequence document.CombinedAlignmentAndNucleotideSequenceDocument(NucleotideSequenceDocument sequenceDocument, SequenceAlignmentDocument alignmentDocument, boolean obtainSharedPropertiesFromSequence, boolean showSequenceView)
Constructs a new combined alignment and sequence document.CombinedAlignmentAndSequenceDocument(EditableSequenceDocument sequenceDocument, SequenceAlignmentDocument alignmentDocument, boolean obtainSharedPropertiesFromSequence, boolean showSequenceView)
Construct a new CombinedAlignmentAndSequenceDocument. -
Uses of SequenceAlignmentDocument in com.biomatters.geneious.publicapi.plugin
Fields in com.biomatters.geneious.publicapi.plugin with type parameters of type SequenceAlignmentDocument Modifier and Type Field Description static DocumentType<SequenceAlignmentDocument>
DocumentType. ALIGNMENT_TYPE
SequenceAlignmentDocument document typestatic DocumentType<SequenceAlignmentDocument>
DocumentType. CONTIG_TYPE
Contig document typeMethods in com.biomatters.geneious.publicapi.plugin that return SequenceAlignmentDocument 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.SequenceAlignmentDocument
AssemblerInput.Read. getContig()
If this read represents a contig as input to the assembler, returns that contig.Methods in com.biomatters.geneious.publicapi.plugin with parameters of type SequenceAlignmentDocument Modifier and Type Method Description abstract void
Assembler.Callback. addContigDocument(SequenceAlignmentDocument contig, NucleotideSequenceDocument contigConsensus, boolean isThisTheOnlyContigGeneratedByDeNovoAssembly, jebl.util.ProgressListener progressListener)
Adds a contig generated by this assembler.void
Assembler.Callback. addContigOrScaffoldDocument(SequenceAlignmentDocument contig, NucleotideSequenceDocument contigConsensus, boolean isThisTheOnlyContigGeneratedByDeNovoAssembly, boolean isScaffoldRatherThanContig, jebl.util.ProgressListener progressListener)
Adds a contig or scaffold generated by this assembler.static SequenceGraph.SequencePropertyRetriever
SequenceGraph.SequencePropertyRetriever. forAlignment(SequenceAlignmentDocument alignment)
Creates a SequencePropertyRetriever for this alignment.static SequenceViewerExtension.PropertyRetrieverAndEditor
SequenceViewerExtension.PropertyRetrieverAndEditor. forAlignment(SequenceAlignmentDocument alignment)
Creates a SequencePropertyRetriever for an alignment.Constructors in com.biomatters.geneious.publicapi.plugin with parameters of type SequenceAlignmentDocument Constructor Description Read(SequenceAlignmentDocument contig, int indexOfAssemblyReferenceSequenceForContig)
Constructs a new read consisting of a single contig. -
Uses of SequenceAlignmentDocument in com.biomatters.geneious.publicapi.utilities
Methods in com.biomatters.geneious.publicapi.utilities that return SequenceAlignmentDocument Modifier and Type Method Description static SequenceAlignmentDocument
ImportUtilities. importFastaAlignment(java.io.File fastaFile, SequenceDocument.Alphabet alphabet, jebl.util.ProgressListener progressListener)
Imports the given fasta file as a list of aligned sequences, padding the sequences with trailing gaps if necessary.Methods in com.biomatters.geneious.publicapi.utilities with parameters of type SequenceAlignmentDocument Modifier and Type Method Description 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)
static java.lang.String
SequenceUtilities. getBlastAlignmentText(SequenceAlignmentDocument alignment, boolean geneiousFriendly)
Formats the given alignment in BLAST text format
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