Uses of Interface
org.biojava.bio.seq.Sequence

Packages that use Sequence
org.biojava.bio.dist Probability distributions over Alphabets. 
org.biojava.bio.dp HMM and Dynamic Programming Algorithms. 
org.biojava.bio.gui.sequence Graphical displays of biological sequences and associated annotations. 
org.biojava.bio.molbio The classes and interfaces in this package cover common molecular biological techniques such as restriction digests and PCR. 
org.biojava.bio.program.das Development client for the Distributed Annotation System. 
org.biojava.bio.program.gff GFF manipulation. 
org.biojava.bio.program.phred Parser for Phred output 
org.biojava.bio.program.ssbind Creation of objects from SAX events using the BioJava BlastLikeDataSetCollection DTD. 
org.biojava.bio.program.unigene Objects for representing Unigene clusters. 
org.biojava.bio.program.xff Event-driven parsing system for the Extensible Feature Format (XFF). 
org.biojava.bio.proteomics Utilities to aid in performing various physical analysis of proteins. 
org.biojava.bio.search Interfaces and classes for representing sequence similarity search results. 
org.biojava.bio.seq Classes and interfaces for defining biological sequences and informatics objects. 
org.biojava.bio.seq.db Collections of biological sequence data. 
org.biojava.bio.seq.db.biofetch Client for the OBDA BioFetch protocol. 
org.biojava.bio.seq.db.biosql General purpose Sequence storage in a relational database. 
org.biojava.bio.seq.db.flat Support for OBDA flatfile databases. 
org.biojava.bio.seq.distributed Sequences and SequenceDBs which are composed from data taken from a number of data sources. 
org.biojava.bio.seq.impl Standard in-memory implementations of Sequence and Feature
org.biojava.bio.seq.io Classes and interfaces for processing and producing flat-file representations of sequences. 
org.biojava.bio.seq.io.agave Classes for converting between AGAVE XML and BioJava objects. 
org.biojava.bio.seq.projection Code for projecting Feature objects into alternate coordinate systems. 
org.biojava.bio.seq.ragbag The Ragbag package is a set of classes for setting up a virtual sequence contig without the need for writing Biojava code. 
 

Uses of Sequence in org.biojava.bio.dist
 

Methods in org.biojava.bio.dist that return Sequence
static Sequence DistributionTools.generateSequence(java.lang.String name, Distribution d, int length)
          Produces a sequence by randomly sampling the Distribution
protected static Sequence DistributionTools.generateOrderNSequence(java.lang.String name, OrderNDistribution d, int length)
           
 

Uses of Sequence in org.biojava.bio.dp
 

Methods in org.biojava.bio.dp that return Sequence
 Sequence WeightMatrixAnnotator.annotate(Sequence seq)
           
 

Methods in org.biojava.bio.dp with parameters of type Sequence
 Sequence WeightMatrixAnnotator.annotate(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.gui.sequence
 

Methods in org.biojava.bio.gui.sequence that return Sequence
 Sequence TranslatedSequencePanel.getSequence()
          getSequence returns the entire Sequence currently being rendered.
 Sequence PairwiseSequencePanel.getSequence()
          getSequence returns the entire Sequence currently being rendered.
 Sequence PairwiseSequencePanel.getSecondarySequence()
          getSecondarySequence returns the entire secondary Sequence currently being rendered.
 Sequence SequencePoster.getSequence()
           
 Sequence SequencePanel.getSequence()
           
 

Methods in org.biojava.bio.gui.sequence with parameters of type Sequence
 void TranslatedSequencePanel.setSequence(Sequence sequence)
          setSequence sets the Sequence to be rendered.
 void PairwiseSequencePanel.setSequence(Sequence sequence)
          setSequence sets the Sequence to be rendered.
 void PairwiseSequencePanel.setSecondarySequence(Sequence sequence)
          setSecondarySequence sets the secondary Sequence to be rendered.
 void SequencePoster.setSequence(Sequence s)
          Set the SymboList to be rendered.
 void SequencePanel.setSequence(Sequence s)
          Set the SymboList to be rendered.
 

Constructors in org.biojava.bio.gui.sequence with parameters of type Sequence
HeadlessRenderContext(Sequence seq, RangeLocation range, int width)
           
 

Uses of Sequence in org.biojava.bio.molbio
 

Methods in org.biojava.bio.molbio that return Sequence
 Sequence RestrictionMapper.annotate(Sequence sequence)
          annotate adds Features which represent restriction sites.
 

Methods in org.biojava.bio.molbio with parameters of type Sequence
 Sequence RestrictionMapper.annotate(Sequence sequence)
          annotate adds Features which represent restriction sites.
 

Uses of Sequence in org.biojava.bio.program.das
 

Methods in org.biojava.bio.program.das that return Sequence
 Sequence DASSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.program.das with parameters of type Sequence
 void DASSequenceDB.addSequence(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.program.gff
 

Methods in org.biojava.bio.program.gff that return Sequence
static Sequence GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents)
          Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
static Sequence GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents, boolean checkSeqName)
          Annotates a sequence with the features from a GFF entry set.
 

Methods in org.biojava.bio.program.gff with parameters of type Sequence
protected  void SequencesAsGFF.doProcessSequence(Sequence seq, GFFDocumentHandler handler, java.lang.String id)
          Internal method to process an individual Sequence.
 void SequencesAsGFF.processSequence(Sequence seq, GFFDocumentHandler handler)
          Process an individual Sequence, informing handler of any suitable features.
static Sequence GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents)
          Annotates a sequence with the features from a GFF entry set with sequence name matching this sequence.
static Sequence GFFTools.annotateSequence(Sequence seq, GFFEntrySet ents, boolean checkSeqName)
          Annotates a sequence with the features from a GFF entry set.
static GFFEntrySet GFFTools.gffFromSequence(Sequence seq)
          Creates a GFFEntrySet containing one entry for each feature on a sequence.
 

Uses of Sequence in org.biojava.bio.program.phred
 

Classes in org.biojava.bio.program.phred that implement Sequence
 class PhredSequence
          PhredSequence is an extension of SimpleSequence that implements Qualitative to hold Phred quality scores.
 

Methods in org.biojava.bio.program.phred with parameters of type Sequence
protected  java.lang.String PhredFormat.describeSequence(Sequence seq)
          Return a suitable description line for a Sequence.
 void PhredFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          This method will print symbols to the line width followed by a new line etc.
 void PhredFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
 

Uses of Sequence in org.biojava.bio.program.ssbind
 

Methods in org.biojava.bio.program.ssbind that return Sequence
 Sequence SimilarityPairBuilder.getAnnotatedQuerySeq(java.lang.String queryID)
           
 Sequence SimilarityPairBuilder.getAnnotatedSubjectSeq(java.lang.String subjectID)
           
protected  Sequence ViewSequenceFactory.makeQueryViewSequence(java.lang.String queryID)
           
protected  Sequence ViewSequenceFactory.makeSubjectViewSequence(java.lang.String subjectID)
           
 

Uses of Sequence in org.biojava.bio.program.unigene
 

Methods in org.biojava.bio.program.unigene that return Sequence
 Sequence UnigeneCluster.getUnique()
          The unique sequence that is used as a representative for this cluster.
 

Uses of Sequence in org.biojava.bio.program.xff
 

Methods in org.biojava.bio.program.xff that return Sequence
static Sequence XFFTools.readXFF(java.io.File xffFile, java.lang.String seqID, FiniteAlphabet alpha)
           
 

Methods in org.biojava.bio.program.xff with parameters of type Sequence
static void XFFTools.annotateXFF(java.io.File xffFile, Sequence sequence)
           
 

Uses of Sequence in org.biojava.bio.proteomics
 

Methods in org.biojava.bio.proteomics that return Sequence
 Sequence Digest.getSequence()
           
 

Methods in org.biojava.bio.proteomics with parameters of type Sequence
 void Digest.setSequence(Sequence sequence)
           
 

Uses of Sequence in org.biojava.bio.search
 

Methods in org.biojava.bio.search that return Sequence
 Sequence SimpleSeqSimilaritySearchResult.getQuerySequence()
           
 Sequence SeqSimilaritySearchResult.getQuerySequence()
          Returns the query sequence which was used to perform the search.
 Sequence SequenceDBSearchResult.getQuerySequence()
          Deprecated.  
 

Constructors in org.biojava.bio.search with parameters of type Sequence
SimpleSeqSimilaritySearchResult(Sequence querySequence, SequenceDB sequenceDB, java.util.Map searchParameters, java.util.List hits, Annotation annotation)
          Creates a new SimpleSeqSimilaritySearchResult.
SequenceDBSearchResult(Sequence querySequence, SequenceDB sequenceDB, java.util.Map searchParameters, java.util.List hits, Annotation annotation)
          Deprecated. Creates a new SequenceDBSearchResult.
 

Uses of Sequence in org.biojava.bio.seq
 

Subinterfaces of Sequence in org.biojava.bio.seq
 interface GappedSequence
          Extension of GappedSymbolList which also projects features into the gapped coordinate system.
 

Classes in org.biojava.bio.seq that implement Sequence
 class CircularView
           A circular view onto another Sequence object.
 class DummySequence
           
 class SimpleAssembly
          A Sequence which is assembled from other sequences contained in a set of ComponentFeature objects.
 class SimpleGappedSequence
          Simple implementation of GappedSequence.
 class SubSequence
          View a sub-section of a given sequence object, including all the features intersecting that region.
 class ViewSequence
          A view onto another Sequence object.
 

Fields in org.biojava.bio.seq declared as Sequence
 Sequence ComponentFeature.Template.componentSequence
           
 

Methods in org.biojava.bio.seq that return Sequence
 Sequence SequenceIterator.nextSequence()
          Returns the next sequence in the iterator.
 Sequence SubSequence.getSequence()
          Return the parent sequence of which this is a partial view
 Sequence ComponentFeature.getComponentSequence()
          Get the sequence object which provides a component of this feature's parent sequence.
static Sequence NucleotideTools.createNucleotideSequence(java.lang.String nucleotide, java.lang.String name)
          Return a new Nucleotide Sequence for nucleotide.
 Sequence SequenceAnnotator.annotate(Sequence seq)
          Return an annotated version of a sequence.
static Sequence RNATools.createRNASequence(java.lang.String rna, java.lang.String name)
          Return a new RNA Sequence for rna.
static Sequence DNATools.createDNASequence(java.lang.String dna, java.lang.String name)
          Return a new DNA Sequence for dna.
 Sequence SequenceFactory.createSequence(SymbolList symList, java.lang.String uri, java.lang.String name, Annotation annotation)
          Creates a sequence using these parameters.
static Sequence SequenceTools.createSequence(SymbolList syms, java.lang.String uri, java.lang.String name, Annotation ann)
           
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end)
           
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end, java.lang.String name)
           
static Sequence SequenceTools.reverseComplement(Sequence seq)
           
static Sequence SequenceTools.view(Sequence seq)
           
static Sequence SequenceTools.view(Sequence seq, java.lang.String name)
           
 Sequence Feature.getSequence()
          Return the Sequence object to which this feature is (ultimately) attached.
static Sequence ProteinTools.createProteinSequence(java.lang.String protein, java.lang.String name)
          Return a new PROTEIN Sequence for protein.
 Sequence ProjectedFeatureHolder.getSequence(Feature f)
           
 

Methods in org.biojava.bio.seq with parameters of type Sequence
 Feature FeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template template)
          Install a feature on the specified sequence.
 Sequence SequenceAnnotator.annotate(Sequence seq)
          Return an annotated version of a sequence.
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end)
           
static Sequence SequenceTools.subSequence(Sequence seq, int start, int end, java.lang.String name)
           
static Sequence SequenceTools.reverseComplement(Sequence seq)
           
static Sequence SequenceTools.view(Sequence seq)
           
static Sequence SequenceTools.view(Sequence seq, java.lang.String name)
           
static void SequenceTools.addAllFeatures(Sequence seq, FeatureHolder fh)
          Add features to a sequence that contain the same information as all those in a feature holder.
 Feature SimpleFeatureRealizer.realizeFeature(Sequence seq, FeatureHolder parent, Feature.Template temp)
           
 

Constructors in org.biojava.bio.seq with parameters of type Sequence
SubSequence(Sequence seq, int start, int end)
          Construct a new SubSequence of the specified sequence.
SubSequence(Sequence seq, int start, int end, java.lang.String name)
          Construct a new SubSequence of the specified sequence.
SubSequence(Sequence seq, int start, int end, FeatureFilter ff, boolean recurse)
          Construct a new SubSequence of the specified sequence.
SubSequence(Sequence seq, int start, int end, FeatureFilter ff, boolean recurse, java.lang.String name)
          Construct a new SubSequence of the specified sequence with a new name.
SimpleGappedSequence(Sequence seq)
           
ViewSequence(Sequence seq, java.lang.String name)
          Construct a view onto an existing sequence and give it a new name.
ViewSequence(Sequence seq)
          Construct a view onto an existing sequence which takes on that sequence's name.
ViewSequence(Sequence seq, FeatureRealizer fr)
          Construct a view onto a sequence, using a specific FeatureRealizer
CircularView(Sequence seq, FeatureRealizer fr)
           
CircularView(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.seq.db
 

Methods in org.biojava.bio.seq.db that return Sequence
 Sequence SwissprotSequenceDB.getSequence(java.lang.String id)
           
 Sequence SequenceDBLite.getSequence(java.lang.String id)
          Retrieve a single sequence by its id.
 Sequence CachingSequenceDB.getSequence(java.lang.String id)
           
 Sequence GenbankSequenceDB.getSequence(java.lang.String id)
           
 Sequence DummySequenceDB.getSequence(java.lang.String id)
           
 Sequence ViewingSequenceDB.getSequence(java.lang.String id)
           
 Sequence AnnotatedSequenceDB.getSequence(java.lang.String id)
           
protected  Sequence AnnotatedSequenceDB.doAnnotation(Sequence seq)
          Apply the annotation to a sequence.
 Sequence HashSequenceDB.getSequence(java.lang.String id)
           
 Sequence WebSequenceDB.getSequence(java.lang.String id)
          Gets a sequence using its unique ID (eg for GenBank this would be the GI number)
 Sequence SubSequenceDB.getSequence(java.lang.String id)
           
 Sequence IndexedSequenceDB.getSequence(java.lang.String id)
           
 Sequence GenpeptSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.seq.db with parameters of type Sequence
 void SequenceDBLite.addSequence(Sequence seq)
          Adds a sequence to the database.
 void AbstractSequenceDB.addSequence(Sequence seq)
           
 void DummySequenceDB.addSequence(Sequence seq)
           
protected  Sequence AnnotatedSequenceDB.doAnnotation(Sequence seq)
          Apply the annotation to a sequence.
 void HashSequenceDB.addSequence(java.lang.String id, Sequence seq)
          Add a sequence under a particular id.
 void HashSequenceDB.addSequence(Sequence seq)
           
 void WebSequenceDB.addSequence(Sequence seq)
          Not supported, You can't add sequences to a WebDB!
 java.lang.String IDMaker.calcID(Sequence seq)
          Calculate the id for a sequence.
 java.lang.String IDMaker.ByURN.calcID(Sequence seq)
           
 java.lang.String IDMaker.ByName.calcID(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.seq.db.biofetch
 

Methods in org.biojava.bio.seq.db.biofetch that return Sequence
 Sequence BioFetchSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.seq.db.biofetch with parameters of type Sequence
 void BioFetchSequenceDB.addSequence(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.seq.db.biosql
 

Methods in org.biojava.bio.seq.db.biosql that return Sequence
 Sequence BioSQLSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.seq.db.biosql with parameters of type Sequence
 void BioSQLSequenceDB.addSequence(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.seq.db.flat
 

Methods in org.biojava.bio.seq.db.flat that return Sequence
 Sequence FlatSequenceDB.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.seq.db.flat with parameters of type Sequence
 void FlatSequenceDB.addSequence(Sequence sequence)
          addSequence always throws a ChangeVetoException as this implementation is immutable.
 

Uses of Sequence in org.biojava.bio.seq.distributed
 

Methods in org.biojava.bio.seq.distributed that return Sequence
 Sequence DistributedSequenceDB.getSequence(java.lang.String id)
           
 Sequence GFFDataSource.getSequence(java.lang.String id)
           
 Sequence DistDataSource.getSequence(java.lang.String id)
          Get a Sequence object for an ID.
 Sequence SequenceDBDataSource.getSequence(java.lang.String id)
           
 

Methods in org.biojava.bio.seq.distributed with parameters of type Sequence
 void DistributedSequenceDB.addSequence(Sequence seq)
           
 

Uses of Sequence in org.biojava.bio.seq.impl
 

Classes in org.biojava.bio.seq.impl that implement Sequence
 class RevCompSequence
          A reverse complement view onto Sequence interface.
 class SimpleSequence
          A basic implementation of the Sequence interface.
 

Fields in org.biojava.bio.seq.impl declared as Sequence
protected  Sequence RevCompSequence.origSeq
           
 

Methods in org.biojava.bio.seq.impl that return Sequence
 Sequence SimpleFeature.getSequence()
           
 Sequence SimpleSequenceFactory.createSequence(SymbolList symList, java.lang.String uri, java.lang.String name, Annotation annotation)
           
 

Constructors in org.biojava.bio.seq.impl with parameters of type Sequence
SimpleFramedFeature(Sequence sourceSeq, FeatureHolder parent, FramedFeature.Template template)
           
SimpleFeature(Sequence sourceSeq, FeatureHolder parent, Feature.Template template)
          Create a SimpleFeature on the given sequence.
SimpleHomologyFeature(Sequence sourceSeq, FeatureHolder parent, HomologyFeature.Template template)
           
SimpleSimilarityPairFeature(Sequence sourceSeq, FeatureHolder parent, SimilarityPairFeature.Template template)
          Creates a new SimpleSimilarityPairFeature.
SimpleRestrictionSite(Sequence sourceSeq, FeatureHolder parent, RestrictionSite.Template template)
          Creates a new SimpleRestrictionSite.
RevCompSequence(Sequence seq)
          URN, Name and Annotation are copied as is from the original Sequence, unless you use the the other contructor that sets these.
RevCompSequence(Sequence seq, java.lang.String urn, java.lang.String name, Annotation annotation)
           
SimpleRemoteFeature(Sequence sourceSeq, FeatureHolder parent, RemoteFeature.Template template)
           
SimpleStrandedFeature(Sequence sourceSeq, FeatureHolder parent, StrandedFeature.Template template)
           
 

Uses of Sequence in org.biojava.bio.seq.io
 

Fields in org.biojava.bio.seq.io declared as Sequence
protected  Sequence SequenceBuilderBase.seq
           
 

Methods in org.biojava.bio.seq.io that return Sequence
 Sequence StreamReader.nextSequence()
          Pull the next sequence out of the stream.
 Sequence SimpleSequenceBuilder.makeSequence()
           
 Sequence SequenceBuilderFilter.makeSequence()
           
 Sequence SequenceBuilder.makeSequence()
          Return the Sequence object which has been constructed by this builder.
 Sequence SmartSequenceBuilder.makeSequence()
           
 Sequence SequenceDBSequenceBuilder.makeSequence()
          create the sequence
 Sequence SequenceBuilderBase.makeSequence()
           
 Sequence SimpleAssemblyBuilder.makeSequence()
           
 

Methods in org.biojava.bio.seq.io with parameters of type Sequence
 void SequenceFormat.writeSequence(Sequence seq, java.io.PrintStream os)
          writeSequence writes a sequence to the specified PrintStream, using the default format.
 void SequenceFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
protected  java.lang.String FastaFormat.describeSequence(Sequence seq)
          Return a suitable description line for a Sequence.
 void FastaFormat.writeSequence(Sequence seq, java.io.PrintStream os)
           
 void FastaFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
 void GAMEFormat.writeSequence(Sequence seq, java.io.PrintStream os)
           
 void GAMEFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
           
 void EmblLikeFormat.writeSequence(Sequence seq, java.io.PrintStream os)
           
 void EmblLikeFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
static void SeqIOTools.writeFasta(java.io.OutputStream os, Sequence seq)
          Writes a single Sequence to an OutputStream in Fasta format.
static void SeqIOTools.writeEmbl(java.io.OutputStream os, Sequence seq)
          Writes a single Sequence to an OutputStream in EMBL format.
static void SeqIOTools.writeSwissprot(java.io.OutputStream os, Sequence seq)
          Writes a single Sequence to an OutputStream in SwissProt format.
static void SeqIOTools.writeGenpept(java.io.OutputStream os, Sequence seq)
          Writes a single Sequence to an OutputStream in Genpept format.
static void SeqIOTools.writeGenbank(java.io.OutputStream os, Sequence seq)
          Writes a single Sequence to an OutputStream in Genbank format.
 void GenbankFormat.writeSequence(Sequence seq, java.io.PrintStream os)
           
 void GenbankFormat.writeSequence(Sequence seq, java.lang.String format, java.io.PrintStream os)
          Deprecated. use writeSequence(Sequence seq, PrintStream os)
 

Uses of Sequence in org.biojava.bio.seq.io.agave
 

Fields in org.biojava.bio.seq.io.agave declared as Sequence
protected  Sequence AGAVEBioSeqHandler.sequence
           
protected  Sequence AGAVEContigHandler.sequence
           
 

Methods in org.biojava.bio.seq.io.agave with parameters of type Sequence
protected  void StAXFeatureHandler.addFeatureToSequence(Sequence seq)
           
 void AGAVEHandler.reportSequence(Sequence sequence)
           
 void AGAVECallbackItf.reportSequence(Sequence sequence)
           
 void AGAVEChromosomeHandler.reportSequence(Sequence sequence)
           
 void AGAVEChromosomeCallbackItf.reportSequence(Sequence sequence)
           
 void AgaveWriter.writeSequence(Sequence seq, java.io.PrintStream os)
          Write sequence into AGAVE XML format.
protected  void AgaveWriter.write(Sequence seq)
          Writing Sequence.
 void AGAVEContigHandler.reportSequence(Sequence sequence)
           
 void AGAVEContigCallbackItf.reportSequence(Sequence sequence)
           
 

Uses of Sequence in org.biojava.bio.seq.projection
 

Methods in org.biojava.bio.seq.projection that return Sequence
 Sequence ProjectionContext.getSequence(Feature f)
          Get the Sequence which defines the coordinate system for the projected feature.
 Sequence ProjectedFeature.getSequence()
           
 

Uses of Sequence in org.biojava.bio.seq.ragbag
 

Classes in org.biojava.bio.seq.ragbag that implement Sequence
(package private)  class org.biojava.bio.seq.ragbag.RagbagAbstractSequence
          object that instantiates a sequence in Ragbag.
 class RagbagAssembly
          object that instantiates a sequence when given a Ragbag directory.
 

Methods in org.biojava.bio.seq.ragbag that return Sequence
 Sequence RagbagIdleSequenceBuilder.makeSequence()