com.biomatters.geneious.publicapi.implementations.sequence

Class CombinedAlignmentAndNucleotideSequenceDocument

java.lang.Object

com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument

com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument

com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndNucleotideSequenceDocument

All Implemented Interfaces:

PluginDocument, EditableSequenceDocument, NucleotideSequenceDocument, PairedReads, SequenceDocument, SequenceDocumentWithEditableAnnotations, XMLSerializable, XMLSerializable.OldVersionCompatible

public class CombinedAlignmentAndNucleotideSequenceDocument
extends CombinedAlignmentAndSequenceDocument
implements NucleotideSequenceDocument

See documentation at CombinedAlignmentAndSequenceDocument

Nested Class Summary

Nested classes/interfaces inherited from class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument

SequenceAlignmentDocument.ReferencedSequence

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument

SequenceDocument.Alphabet, SequenceDocument.Transformer

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument

PluginDocument.ReferencedDocumentsAlwaysLoaded, PluginDocument.ReferencedDocumentsNotLoaded, PluginDocument.SizeRequiredToLoadIntoMemoryProvider

Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable

XMLSerializable.OldVersionCompatible, XMLSerializable.VersionSupportType

Field Summary

Fields inherited from interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument

NICE_NAME

Fields inherited from interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument

GENOME_SEQUENCE_THRESHOLD

Fields inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument

FILE_DATA_ATTRIBUTE_NAME, MAXIMUM_HTML_LENGTH, MODIFIED_DATE_FIELD

Fields inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable

ROOT_ELEMENT_NAME

Constructor Summary

Constructors

Constructor and Description
CombinedAlignmentAndNucleotideSequenceDocument() XML Deserialization constructor.
CombinedAlignmentAndNucleotideSequenceDocument(NucleotideSequenceDocument sequenceDocument, SequenceAlignmentDocument alignmentDocument, boolean obtainSharedPropertiesFromSequence, boolean showSequenceView) Constructs a new combined alignment and sequence document.

Method Summary

Methods inherited from class com.biomatters.geneious.publicapi.implementations.sequence.CombinedAlignmentAndSequenceDocument

addSequence, asJeblAlignment, canAddAndRemoveSequences, canSetAnnotations, canSetAnnotationsOnConsensus, canSetSequenceNames, fromXML, getAlignmentDocument, getAnnotationsOnConsensus, getCharSequence, getContigReferenceSequenceIndex, getCreationDate, getDescription, getDisplayableFields, getFieldValue, getName, getNumberOfSequences, getReferencedDocument, getReferencedSequence, getSequence, getSequenceAnnotations, getSequenceAsJeblSequence, getSequenceDocument, getSequenceLength, getSequences, getSequenceString, getURN, getVersionSupport, isCircular, isContig, isEditable, isFreeEndGapAlignment, isReferencedDocumentReversed, removeSequence, reorderSequences, setAnnotations, setAnnotations, setAnnotationsOnConsensus, setCircular, setReferencedDocument, setReferencedSequence, setSequenceAndAnnotations, setSequenceName, showSequenceView, toHTML, toXML, toXML, updateSequence

Methods inherited from class com.biomatters.geneious.publicapi.documents.sequence.SequenceAlignmentDocument

asJeblAlignmentIfMemoryAllows, canSetFieldValue, getCircularLength, getImmutablePairedReadManager, getMateExpectedDistance, getMateIndex, getRealignedName, getReferencedDocuments, getReferencedSequences, getRefinedName, getSequencesInImmutableList, getSequenceType, isQueryCentricAlignment, setFieldValue, setMates, setReferencedSequence

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument

getCharSequence, getSequenceAnnotations, getSequenceLength, getSequenceString, isCircular

Methods inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument

getCreationDate, getDescription, getDisplayableFields, getFieldValue, getName, getURN, toHTML

Methods inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable

fromXML, toXML

Constructor Detail

CombinedAlignmentAndNucleotideSequenceDocument

public CombinedAlignmentAndNucleotideSequenceDocument(NucleotideSequenceDocument sequenceDocument,
                                              SequenceAlignmentDocument alignmentDocument,
                                              boolean obtainSharedPropertiesFromSequence,
                                              boolean showSequenceView)

Constructs a new combined alignment and sequence document. See CombinedAlignmentAndSequenceDocument for documentation for the parameters to this method.

CombinedAlignmentAndNucleotideSequenceDocument

public CombinedAlignmentAndNucleotideSequenceDocument()

XML Deserialization constructor. See XMLSerializable