Uses of Class
org.biojava3.core.sequence.template.AbstractSequence

Packages that use AbstractSequence

Package	Description
bacnet.datamodel.sequence
bacnet.reader
org.biojava3.core.sequence
org.biojava3.core.sequence.features
org.biojava3.core.sequence.io
org.biojava3.core.sequence.io.template
org.biojava3.core.sequence.location
org.biojava3.core.sequence.template

Uses of AbstractSequence in bacnet.datamodel.sequence

Subclasses of AbstractSequence in bacnet.datamodel.sequence

Modifier and Type	Class	Description
class	Chromosome	A ChromosomeSequence is a DNASequence but keeps track of geneSequences
class	ChromosomeBacteriaSequence	A ChromosomeSequence is a DNASequence but keeps track of geneSequences

Uses of AbstractSequence in bacnet.reader

Classes in bacnet.reader with type parameters of type AbstractSequence

Modifier and Type	Class	Description
class	NCBIFastaHeaderParser<S extends AbstractSequence<C>,C extends Compound>	My own implementation of a FastaHeaderParserInterface to parse Fasta files from NCBI ftp NCBI fna (genome and plasmids) gi|gi-number|ref|accession|name gi|16802048|ref|NC_003210.1| Listeria monocytogenes EGD-e, complete genome NCBI ffn (coding) ref|refGenome gi-number|:start-end name ref|NC_003210.1|:318-1673 chromosomal replication initiation protein [Listeria monocytogenes EGD-e] NCBI frn (non-coding) ref|refGenome gi-number|:start-end| name| [locus-tag] ref|NC_003210|:82705-82777|Lys tRNA| [locus_tag=lmot01] NCBI faa (proteins) gi|gi-number|ref|accession|name gi|16802049|ref|NP_463534.1| chromosomal replication initiation protein [Listeria monocytogenes EGD-e]

Uses of AbstractSequence in org.biojava3.core.sequence

Subclasses of AbstractSequence in org.biojava3.core.sequence

Modifier and Type	Class	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.biojava3.core.sequence with parameters of type AbstractSequence

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

Uses of AbstractSequence in org.biojava3.core.sequence.features

Classes in org.biojava3.core.sequence.features with type parameters of type AbstractSequence

Modifier and Type	Class	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
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.biojava3.core.sequence.io

Classes in org.biojava3.core.sequence.io with type parameters of type AbstractSequence

Modifier and Type	Class	Description
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

Methods in org.biojava3.core.sequence.io that return AbstractSequence

Modifier and Type	Method	Description
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)	Assumes all compounds were uppercase
AbstractSequence<AminoAcidCompound>	CasePreservingProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	DNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, 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>	FileProxyDNASequenceCreator.getSequence(List<NucleotideCompound> list)	Not sure of use case and currently not supported
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<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.
AbstractSequence<AminoAcidCompound>	FileProxyProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)	Not sure of use case and currently not supported
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<AminoAcidCompound>	ProteinSequenceCreator.getSequence(String sequence, long index)
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(List<AminoAcidCompound> list)
AbstractSequence<AminoAcidCompound>	ProteinSequenceCreator.getSequence(ProxySequenceReader<AminoAcidCompound> proxyLoader, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(String sequence, long index)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(List<NucleotideCompound> list)
AbstractSequence<NucleotideCompound>	RNASequenceCreator.getSequence(ProxySequenceReader<NucleotideCompound> proxyLoader, long index)

Uses of AbstractSequence in org.biojava3.core.sequence.io.template

Methods in org.biojava3.core.sequence.io.template that return AbstractSequence

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

Uses of AbstractSequence in org.biojava3.core.sequence.location

Classes in org.biojava3.core.sequence.location with type parameters of type AbstractSequence

Modifier and Type	Class	Description
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.biojava3.core.sequence.template

Methods in org.biojava3.core.sequence.template that return AbstractSequence

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

Methods in org.biojava3.core.sequence.template that return types with arguments of type AbstractSequence

Modifier and Type	Method	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.biojava3.core.sequence.template with parameters of type AbstractSequence

Modifier and Type	Method	Description
void	AbstractSequence.setParentSequence(AbstractSequence<C> abstractSequence)

Method parameters in org.biojava3.core.sequence.template with type arguments of type AbstractSequence

Modifier and Type	Method	Description
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.addFeature(FeatureInterface<AbstractSequence<C>,C> feature)	Add a feature to this sequence.
void	AbstractSequence.removeFeature(FeatureInterface<AbstractSequence<C>,C> feature)	Remove a feature from the sequence