Uses of Class
org.jbei.ice.storage.model.Sequence

Packages that use Sequence

Package	Description
org.jbei.ice.lib.entry.sequence
org.jbei.ice.lib.entry.sequence.composers.formatters	Formatters for various sequence file formats.
org.jbei.ice.lib.entry.sequence.composers.pigeon
org.jbei.ice.storage.hibernate.dao
org.jbei.ice.storage.model	Data models for ice objects.

Uses of Sequence in org.jbei.ice.lib.entry.sequence

Methods in org.jbei.ice.lib.entry.sequence that return Sequence

Modifier and Type	Method and Description
static Sequence	SequenceController.dnaSequenceToSequence(DNASequence dnaSequence) Create a Sequence object from an DNASequence object.
Sequence	SequenceController.save(String userId, Sequence sequence) Save the given Sequence into the database, with the option to rebuild the search index.
protected Sequence	SequenceController.update(String userId, Sequence sequence) Update the Sequence in the database, with the option to rebuild the search index.

Methods in org.jbei.ice.lib.entry.sequence with parameters of type Sequence

Modifier and Type	Method and Description
void	TraceSequences.buildOrRebuildAlignment(TraceSequence traceSequence, Sequence sequence) Calculate sequence alignment between the given TraceSequence and Sequence using bl2seq, and save the result into the database.
void	SequenceAnalysisController.buildOrRebuildAlignment(TraceSequence traceSequence, Sequence sequence) Calculate sequence alignment between the given TraceSequence and Sequence using bl2seq, and save the result into the database.
protected String	SequenceController.compose(Sequence sequence, IFormatter formatter) Generate a formatted text of a given IFormatter from the given Sequence.
Sequence	SequenceController.save(String userId, Sequence sequence) Save the given Sequence into the database, with the option to rebuild the search index.
FeaturedDNASequence	SequenceController.sequenceToDNASequence(Sequence sequence) Generate a FeaturedDNASequence from a given Sequence object.
protected FeaturedDNASequence	PartSequence.sequenceToDNASequence(Sequence sequence)
protected Sequence	SequenceController.update(String userId, Sequence sequence) Update the Sequence in the database, with the option to rebuild the search index.

Uses of Sequence in org.jbei.ice.lib.entry.sequence.composers.formatters

Methods in org.jbei.ice.lib.entry.sequence.composers.formatters with parameters of type Sequence

Modifier and Type	Method and Description
void	GenbankFormatter.format(Sequence sequence, OutputStream outputStream)
void	SBOLFormatter.format(Sequence sequence, OutputStream outputStream)
void	AbstractFormatter.format(Sequence sequence, OutputStream outputStream)
void	IFormatter.format(Sequence sequence, OutputStream outputStream) Interface method to take a Sequence object and output the formatted file to the OutputStream.
void	FastaFormatter.format(Sequence sequence, OutputStream outputStream)
void	SBOL2Formatter.format(Sequence sequence, OutputStream outputStream)
void	SBOLVisitor.visit(Sequence sequence)
void	SBOL2Visitor.visit(Sequence sequence)

Uses of Sequence in org.jbei.ice.lib.entry.sequence.composers.pigeon

Methods in org.jbei.ice.lib.entry.sequence.composers.pigeon with parameters of type Sequence

Modifier and Type	Method and Description
static String	PigeonSBOLv.generatePigeonScript(Sequence sequence)
static URI	PigeonSBOLv.generatePigeonVisual(Sequence sequence)

Uses of Sequence in org.jbei.ice.storage.hibernate.dao

Methods in org.jbei.ice.storage.hibernate.dao that return Sequence

Modifier and Type	Method and Description
Sequence	SequenceDAO.get(long id)
Sequence	SequenceDAO.getByEntry(Entry entry) Retrieve the Sequence object associated with the given Entry object.
Sequence	SequenceDAO.getSequence(int offset) Enables retrieving sequences in the database without loading everything in memory Expected usage is long count = getSequenceCount(); int offset = 0; while( offset < count ) { Sequence sequence = dao.getSequence(offset); // do something with sequence }
Sequence	SequenceDAO.saveSequence(Sequence sequence) Save the given Sequence object in the database.
Sequence	SequenceDAO.updateSequence(Sequence sequence, Set<SequenceFeature> newFeatures) Updates an existing feature with a new set of features

Methods in org.jbei.ice.storage.hibernate.dao with parameters of type Sequence

Modifier and Type	Method and Description
void	SequenceDAO.deleteSequence(Sequence sequence, String pigeonImageFolder) Delete the given Sequence object in the database.
Sequence	SequenceDAO.saveSequence(Sequence sequence) Save the given Sequence object in the database.
Sequence	SequenceDAO.updateSequence(Sequence sequence, Set<SequenceFeature> newFeatures) Updates an existing feature with a new set of features

Uses of Sequence in org.jbei.ice.storage.model

Methods in org.jbei.ice.storage.model that return Sequence

Modifier and Type	Method and Description
Sequence	Entry.getSequence()
Sequence	SequenceFeature.getSequence()

Methods in org.jbei.ice.storage.model with parameters of type Sequence

Modifier and Type	Method and Description
void	Entry.setSequence(Sequence sequence)
void	SequenceFeature.setSequence(Sequence sequence)

Constructors in org.jbei.ice.storage.model with parameters of type Sequence

Constructor and Description
SequenceFeature(Sequence sequence, Feature feature, int strand, String name, String genbankType, SequenceFeature.AnnotationType annotationType)