Package com.biomatters.geneious.publicapi.implementations.sequence

Class DefaultAminoAcidSequence

java.lang.Object

com.biomatters.geneious.publicapi.documents.AbstractPluginDocument

com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument

com.biomatters.geneious.publicapi.implementations.sequence.DefaultAminoAcidSequence

All Implemented Interfaces:

PluginDocument, Renamable, AminoAcidSequenceDocument, EditableSequenceDocument, SequenceDocument, SequenceDocumentWithEditableAnnotations, XMLSerializable, XMLSerializable.OldVersionCompatible, SequenceTrack.Manager.Provider, SequenceGapInformation.Provider

public class DefaultAminoAcidSequence
extends DefaultSequenceDocument
implements AminoAcidSequenceDocument

A plugin document holding one amino acid sequence.

Nested Class Summary

Nested classes/interfaces inherited from class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument

DefaultSequenceDocument.Cache

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.sequence.SequenceDocument

SequenceDocument.Alphabet, SequenceDocument.Transformer

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.AminoAcidSequenceDocument

NICE_NAME

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.sequence.SequenceDocument

GENOME_SEQUENCE_THRESHOLD

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

ROOT_ELEMENT_NAME

Constructor Summary

Constructors

Constructor	Description
DefaultAminoAcidSequence()	empty constructor, Plugin document requirement.
DefaultAminoAcidSequence(AminoAcidSequenceDocument sequence, java.util.Date created)	Creates a new DefaultAminoAcidSequence as a copy of the specified AminoAcidSequenceDocument.
DefaultAminoAcidSequence(java.lang.String name, java.lang.CharSequence charSequence)	Construct a new amino acid sequence.
DefaultAminoAcidSequence(java.lang.String name, java.lang.String description, java.lang.CharSequence charSequence, java.util.Date created)	Construct a new amino acid sequence.
DefaultAminoAcidSequence(java.lang.String name, java.lang.String description, java.lang.CharSequence charSequence, java.util.Date created, URN urn)	Construct a new amino acid sequence.
DefaultAminoAcidSequence(jebl.evolution.sequences.Sequence jeblSequence)	Construct from a sequence in jebl format.

Method Summary

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

addSequenceAnnotation, annotationsFromXML, copySequenceTracksFrom, createCopy, createCopy, fromXML, getAnnotationsRevisionNumber, getCharSequence, getCharSequenceRevisionNumber, getDescription, getDisplayableFields, getFieldValue, getName, getSequenceAnnotations, getSequenceGapInformation, getSequenceGapInformation, getSequenceLength, getSequenceString, getTrackManager, getVersionSupport, isBestSerializedToXmlRatherThanBinaryFormat, isCircular, isStandardImplementation, readObject, readObject, sequenceAnnotationsToXML, sequenceAnnotationsToXML, setAnnotations, setCache, setCircular, setDescription, setFieldValue, setModified, setName, setSequenceAndAnnotations, toHTML, toXML, toXML, writeObject, writeObject, writeObject

Methods inherited from class com.biomatters.geneious.publicapi.documents.AbstractPluginDocument

addDisplayableField, addReferencedDocumentUrn, clearReferencedDocumentUrns, createFromBaseElement, getBaseElement, getBaseElementString, getCreationDate, getFieldValueCodes, getReferencedDocumentUrns, getURN, hasProperties, setBaseElement, setCreated, setFieldValue, setFieldValues, setURN

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.PluginDocument

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

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.XMLSerializable

fromXML, toXML

Constructor Detail

DefaultAminoAcidSequence

public DefaultAminoAcidSequence()

empty constructor, Plugin document requirement.

DefaultAminoAcidSequence

public DefaultAminoAcidSequence(java.lang.String name,
                                java.lang.CharSequence charSequence)

Construct a new amino acid sequence.

Parameters:

name - document name (must not be null)

charSequence - the sequence residues. The length of charSequence and the characters retured from charSequence must not change after calling this method.

DefaultAminoAcidSequence

public DefaultAminoAcidSequence(java.lang.String name,
                                java.lang.String description,
                                java.lang.CharSequence charSequence,
                                java.util.Date created)

Construct a new amino acid sequence.

Parameters:

name - document name (must not be null)

description - sequence descriptions (may be null or "")

charSequence - the sequence residues. The length of charSequence and the characters retured from charSequence must not change after calling this method.

created - sequence creation date. May be null.

DefaultAminoAcidSequence

public DefaultAminoAcidSequence(java.lang.String name,
                                java.lang.String description,
                                java.lang.CharSequence charSequence,
                                java.util.Date created,
                                URN urn)

Construct a new amino acid sequence.

Parameters:

name - document name (must not be null)

description - sequence descriptions (may be null or "")

charSequence - the sequence residues. The length of charSequence and the characters retured from charSequence must not change after calling this method.

created - sequence creation date. May be null.

DefaultAminoAcidSequence

public DefaultAminoAcidSequence(AminoAcidSequenceDocument sequence,
                                java.util.Date created)

Creates a new DefaultAminoAcidSequence as a copy of the specified AminoAcidSequenceDocument.

Parameters:

sequence - sequence as a string

created - sequence creation time

DefaultAminoAcidSequence

public DefaultAminoAcidSequence(jebl.evolution.sequences.Sequence jeblSequence)

Construct from a sequence in jebl format.

Parameters:

jeblSequence - holds sequence name and sites