Uses of Class
org.biojava.nbio.core.sequence.template.AbstractSequence

Packages that use AbstractSequence

Package	Description
org.biojava.nbio.alignment.io
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.features
org.biojava.nbio.core.sequence.io
org.biojava.nbio.core.sequence.io.template
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.location
org.biojava.nbio.core.sequence.template
org.biojava.nbio.genome.io.fastq	FASTQ and variants sequence format I/O.

Uses of AbstractSequence in org.biojava.nbio.alignment.io

Methods in org.biojava.nbio.alignment.io that return types with arguments of type AbstractSequence

Modifier and Type	Method and Description
List<AbstractSequence<? extends AbstractCompound>>	StockholmStructure.getBioSequences() used to retrieve sequences from the structure
List<AbstractSequence<? extends AbstractCompound>>	StockholmStructure.getBioSequences(boolean ignoreCase) Because some database files have incorrectly small letters (e.g.
List<AbstractSequence<? extends AbstractCompound>>	StockholmStructure.getBioSequences(boolean ignoreCase, String forcedSequenceType) This function tolerates mixed case letters, and allows for forcing the output biosequence type (PFAM/RFAM).

Uses of AbstractSequence in org.biojava.nbio.core.sequence

Subclasses of AbstractSequence in org.biojava.nbio.core.sequence

Modifier and Type	Class and Description
class	BasicSequence<C extends Compound> Bare bones version of the Sequence object to be used sparingly.
class	CDSSequence Represents a exon or coding sequence in a gene.
class	ChromosomeSequence A ChromosomeSequence is a DNASequence but keeps track of geneSequences
class	DNASequence This is class should model the attributes associated with a DNA sequence
class	ExonSequence A gene contains a collection of Exon sequences
class	GeneSequence
class	IntronSequence
class	ProteinSequence The representation of a ProteinSequence
class	RNASequence RNASequence where RNACompoundSet are the allowed values
class	StartCodonSequence Used to map the start codon feature on a gene
class	StopCodonSequence Used to map the stop codon sequence on a gene
class	TranscriptSequence This is the sequence if you want to go from a gene sequence to a protein sequence.

Methods in org.biojava.nbio.core.sequence with parameters of type AbstractSequence

Modifier and Type	Method and Description
int	SequenceComparator.compare(AbstractSequence<?> o1, AbstractSequence<?> o2)
int	SequenceComparator.compare(AbstractSequence<?> o1, AbstractSequence<?> o2)
void	ProteinSequence.setParentDNASequence(AbstractSequence<NucleotideCompound> parentDNASequence, Integer begin, Integer end) A Protein sequence can be stand alone or loaded from a transcript sequence.

Uses of AbstractSequence in org.biojava.nbio.core.sequence.features

Classes in org.biojava.nbio.core.sequence.features with type parameters of type AbstractSequence

Modifier and Type	Class and Description
class	AbstractFeature<S extends AbstractSequence<C>,C extends Compound> A feature is currently any descriptive item that can be associated with a sequence position(s) A feature has a type and a source which is currently a string to allow flexibility for the user Ideally well defined features should have a class to describe attributes of that feature
class	FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound> It is DBReferenceInfo which implements FeatureInterface.
interface	FeatureInterface<S extends AbstractSequence<C>,C extends Compound> Interface class to handle describing arbitrary features.
class	QualityFeature<S extends AbstractSequence<C>,C extends Compound> DNA Sequences produced by modern sequencers usually have quality informaion attached to them.
class	QuantityFeature<S extends AbstractSequence<C>,C extends Compound> It is common to have a numerical value or values associated with a feature.
class	TextFeature<S extends AbstractSequence<C>,C extends Compound> A implmentation of AbstractFeature

Uses of AbstractSequence in org.biojava.nbio.core.sequence.io

Classes in org.biojava.nbio.core.sequence.io with type parameters of type AbstractSequence

Modifier and Type	Class and Description
class	GenbankReader<S extends AbstractSequence<C>,C extends Compound> Use GenbankReaderHelper as an example of how to use this class where GenbankReaderHelper should be the primary class used to read Genbank files
class	GenbankSequenceParser<S extends AbstractSequence<C>,C extends Compound>
class	GenericFastaHeaderFormat<S extends AbstractSequence<?>,C extends Compound> We store the original header if the sequence is parsed from a fasta file and will use that exact sequence if we write out the sequences to a fasta file.
class	GenericFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> The default fasta header parser where some headers are well defined based on the source database which allows us to set the source of the protein sequence and the identifier that can be used in future implementations to load features from external sources If the user has a custom header with local data then they can create their own implementation of a FastaHeaderParserInterface GenBank gi|gi-number|gb|accession|locus ENA Data Library gi|gi-number|emb|accession|locus DDBJ, DNA Database of Japan gi|gi-number|dbj|accession|locus NBRF PIR pir||entry Protein Research Foundation prf||name SWISS-PROT sp|accession|name Brookhaven Protein Data Bank (1) pdb|entry|chain Brookhaven Protein Data Bank (2) entry:chain|PDBID|CHAIN|SEQUENCE PDB EBI PDB:1ECY_A mol:protein length:142 ECOTIN Patents pat|country|number GenInfo Backbone Id bbs|number General database identifier gnl|database|identifier NCBI Reference Sequence ref|accession|locus Local Sequence identifier lcl|identifier
class	GenericGenbankHeaderFormat<S extends AbstractSequence<C>,C extends Compound>
class	GenericGenbankHeaderParser<S extends AbstractSequence<C>,C extends Compound>
class	GenericInsdcHeaderFormat<S extends AbstractSequence<C>,C extends Compound>
class	PlainFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound> The plain fasta header takes everything in the header as a single entity.

Methods in org.biojava.nbio.core.sequence.io that return AbstractSequence

Modifier and Type	Method and Description
AbstractSequence<NucleotideCompound>	ABITrace.getSequence() Returns the original programmatically determined (unedited) sequence as a AbstractSequence.
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(List<AminoAcidCompound> list) Assumes all compounds were uppercase
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(List<AminoAcidCompound> list) Not sure of use case and currently not supported
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	FileProxyDNASequenceCreator.getSequence(List<NucleotideCompound> list) Not sure of use case and currently not supported
AbstractSequence<NucleotideCompound>	FileProxyRNASequenceCreator.getSequence(List<NucleotideCompound> list) Not sure of use case and currently not supported
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index) Should be able to extend the same concept to a remote URL call or database connection.
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	FileProxyDNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index) Should be able to extend the same concept to a remote URL call or database connection.
AbstractSequence<NucleotideCompound>	FileProxyRNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index) Should be able to extend the same concept to a remote URL call or database connection.
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	FileProxyDNASequenceCreator.getSequence(String sequence, long index) Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
AbstractSequence<NucleotideCompound>	FileProxyRNASequenceCreator.getSequence(String sequence, long index) Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(String sequence, long index) Even though we are passing in the sequence we really only care about the length of the sequence and the offset index in the fasta file.

Methods in org.biojava.nbio.core.sequence.io with parameters of type AbstractSequence

Modifier and Type	Method and Description
void	GenbankSequenceParser.parseFeatures(AbstractSequence<C> sequence)

Method parameters in org.biojava.nbio.core.sequence.io with type arguments of type AbstractSequence

Modifier and Type	Method and Description
protected String	GenericInsdcHeaderFormat._write_feature(FeatureInterface<AbstractSequence<C>,C> feature, int record_length) Write a single SeqFeature object to features table.

Uses of AbstractSequence in org.biojava.nbio.core.sequence.io.template

Methods in org.biojava.nbio.core.sequence.io.template that return AbstractSequence

Modifier and Type	Method and Description
AbstractSequence<C>	SequenceCreatorInterface.getSequence(List<C> list)
AbstractSequence<C>	SequenceCreatorInterface.getSequence(ProxySequenceReader<C> proxyLoader, long index)
AbstractSequence<C>	SequenceCreatorInterface.getSequence(String sequence, long index)

Uses of AbstractSequence in org.biojava.nbio.core.sequence.loader

Methods in org.biojava.nbio.core.sequence.loader that return types with arguments of type AbstractSequence

Modifier and Type	Method and Description
GenericGenbankHeaderParser<AbstractSequence<C>,C>	GenbankProxySequenceReader.getHeaderParser()

Uses of AbstractSequence in org.biojava.nbio.core.sequence.location

Classes in org.biojava.nbio.core.sequence.location with type parameters of type AbstractSequence

Modifier and Type	Class and Description
class	InsdcParser<S extends AbstractSequence<C>,C extends Compound> Parser for working with INSDC style locations.
class	SequenceLocation<S extends AbstractSequence<C>,C extends Compound> A location in a sequence that keeps a reference to its parent sequence

Uses of AbstractSequence in org.biojava.nbio.core.sequence.template

Methods in org.biojava.nbio.core.sequence.template that return AbstractSequence

Modifier and Type	Method and Description
AbstractSequence<?>	AbstractSequence.getParentSequence()

Methods in org.biojava.nbio.core.sequence.template that return types with arguments of type AbstractSequence

Modifier and Type	Method and Description
List<FeatureInterface<AbstractSequence<C>,C>>	AbstractSequence.getFeatures()
List<FeatureInterface<AbstractSequence<C>,C>>	AbstractSequence.getFeatures(int bioSequencePosition) Return features at a sequence position
List<FeatureInterface<AbstractSequence<C>,C>>	AbstractSequence.getFeatures(String featureType, int bioSequencePosition) Return features at a sequence position by type
List<FeatureInterface<AbstractSequence<C>,C>>	AbstractSequence.getFeaturesByType(String type)

Methods in org.biojava.nbio.core.sequence.template with parameters of type AbstractSequence

Modifier and Type	Method and Description
void	AbstractSequence.setParentSequence(AbstractSequence<?> parentSequence)

Method parameters in org.biojava.nbio.core.sequence.template with type arguments of type AbstractSequence

Modifier and Type	Method and Description
void	AbstractSequence.addFeature(FeatureInterface<AbstractSequence<C>,C> feature) Add a feature to this sequence.
void	AbstractSequence.addFeature(int bioStart, int bioEnd, FeatureInterface<AbstractSequence<C>,C> feature) Method to help set the proper details for a feature as it relates to a sequence where the feature needs to have a location on the sequence
void	AbstractSequence.removeFeature(FeatureInterface<AbstractSequence<C>,C> feature) Remove a feature from the sequence

Uses of AbstractSequence in org.biojava.nbio.genome.io.fastq

Methods in org.biojava.nbio.genome.io.fastq that return types with arguments of type AbstractSequence

Modifier and Type	Method and Description
static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	FastqTools.createErrorProbabilities(Fastq fastq) Create and return a new QuantityFeature from the error probabilities of the specified FASTQ formatted sequence.
static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>	FastqTools.createQualityScores(Fastq fastq) Create and return a new QualityFeature from the quality scores of the specified FASTQ formatted sequence.