Class DefaultNucleotideSequence
- java.lang.Object
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- com.biomatters.geneious.publicapi.documents.AbstractPluginDocument
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- com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
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- com.biomatters.geneious.publicapi.implementations.sequence.DefaultNucleotideSequence
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- All Implemented Interfaces:
PluginDocument
,Renamable
,EditableSequenceDocument
,NucleotideSequenceDocument
,SequenceDocument
,SequenceDocumentWithEditableAnnotations
,XMLSerializable
,XMLSerializable.OldVersionCompatible
,SequenceTrack.Manager.Provider
,SequenceGapInformation.Provider
- Direct Known Subclasses:
DefaultNucleotideGraphSequence
,OligoSequenceDocument
public class DefaultNucleotideSequence extends DefaultSequenceDocument implements NucleotideSequenceDocument
A plugin document holding one nucleotide sequence.
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Nested Class Summary
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Nested classes/interfaces inherited from class com.biomatters.geneious.publicapi.implementations.sequence.DefaultSequenceDocument
DefaultSequenceDocument.Cache
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Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument
PluginDocument.ReferencedDocumentsAlwaysLoaded, PluginDocument.ReferencedDocumentsNotLoaded, PluginDocument.SizeRequiredToLoadIntoMemoryProvider
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Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument
SequenceDocument.Alphabet, SequenceDocument.Transformer
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Nested classes/interfaces inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable
XMLSerializable.OldVersionCompatible, XMLSerializable.VersionSupportType
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Field Summary
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Fields inherited from interface com.biomatters.geneious.publicapi.documents.sequence.NucleotideSequenceDocument
NICE_NAME
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Fields inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument
FILE_DATA_ATTRIBUTE_NAME, MAXIMUM_HTML_LENGTH, MODIFIED_DATE_FIELD
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Fields inherited from interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument
GENOME_SEQUENCE_THRESHOLD
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Fields inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable
ROOT_ELEMENT_NAME
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Constructor Summary
Constructors Constructor Description DefaultNucleotideSequence()
empty constructor, Plugin document requirement.DefaultNucleotideSequence(NucleotideSequenceDocument sequence, java.util.Date created)
Constructs a DefaultNucleotideSequence as a copy of an existing NucleotideSequenceDocument.DefaultNucleotideSequence(java.lang.String name, java.lang.CharSequence charSequence)
Construct a new nucleotide sequence.DefaultNucleotideSequence(java.lang.String name, java.lang.String description, java.lang.CharSequence charSequence, java.util.Date created)
Construct a new nucelotide sequence.DefaultNucleotideSequence(java.lang.String name, java.lang.String description, java.lang.CharSequence charSequence, java.util.Date created, URN urn)
Construct a new nucelotide sequence.DefaultNucleotideSequence(jebl.evolution.sequences.Sequence jeblSequence)
Construct from a sequence in jebl format.
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Method Summary
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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
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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
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface com.biomatters.geneious.publicapi.documents.PluginDocument
getCreationDate, getDescription, getDisplayableFields, getFieldValue, getName, getURN, toHTML
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Methods inherited from interface com.biomatters.geneious.publicapi.documents.sequence.SequenceDocument
getCharSequence, getSequenceAnnotations, getSequenceLength, getSequenceString, isCircular
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Methods inherited from interface com.biomatters.geneious.publicapi.documents.XMLSerializable
fromXML, toXML
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Constructor Detail
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DefaultNucleotideSequence
public DefaultNucleotideSequence()
empty constructor, Plugin document requirement.
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DefaultNucleotideSequence
public DefaultNucleotideSequence(java.lang.String name, java.lang.CharSequence charSequence)
Construct a new nucleotide sequence.- Parameters:
name
- document name (must not be null)charSequence
- the sequence residues. The length ofcharSequence
and the characters retured fromcharSequence
must not change after calling this method.
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DefaultNucleotideSequence
public DefaultNucleotideSequence(java.lang.String name, java.lang.String description, java.lang.CharSequence charSequence, java.util.Date created)
Construct a new nucelotide sequence.- Parameters:
name
- document name (must not be null)description
- sequence descriptions (may be null or "")charSequence
- the sequence residues. The length ofcharSequence
and the characters retured fromcharSequence
must not change after calling this method.created
- sequence creation date. May be null.
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DefaultNucleotideSequence
public DefaultNucleotideSequence(java.lang.String name, java.lang.String description, java.lang.CharSequence charSequence, java.util.Date created, URN urn)
Construct a new nucelotide sequence.- Parameters:
name
- document name (must not be null)description
- sequence descriptions (may be null or "")charSequence
- the sequence residues. The length ofcharSequence
and the characters retured fromcharSequence
must not change after calling this method.created
- sequence creation date. May be null.
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DefaultNucleotideSequence
public DefaultNucleotideSequence(NucleotideSequenceDocument sequence, java.util.Date created)
Constructs a DefaultNucleotideSequence as a copy of an existing NucleotideSequenceDocument.- Parameters:
sequence
- sequencecreated
- sequence creation time
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DefaultNucleotideSequence
public DefaultNucleotideSequence(jebl.evolution.sequences.Sequence jeblSequence)
Construct from a sequence in jebl format.- Parameters:
jeblSequence
- holds sequence name and sites
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