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 Description List<AbstractSequence<? extends AbstractCompound>>
StockholmStructure. getBioSequences()
used to retrieve sequences from the structureList<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 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 geneSequencesclass
DNASequence
This is class should model the attributes associated with a DNA sequenceclass
ExonSequence
A gene contains a collection of Exon sequencesclass
GeneSequence
class
IntronSequence
class
ProteinSequence
The representation of a ProteinSequenceclass
RNASequence
RNASequence where RNACompoundSet are the allowed valuesclass
StartCodonSequence
Used to map the start codon feature on a geneclass
StopCodonSequence
Used to map the stop codon sequence on a geneclass
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 Description 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 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 featureclass
FeatureDbReferenceInfo<S extends AbstractSequence<C>,C extends Compound>
It isDBReferenceInfo
which implementsFeatureInterface
.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 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 filesclass
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 FastaHeaderParserInterfaceclass
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 Description AbstractSequence<NucleotideCompound>
ABITrace. getSequence()
Returns the original programmatically determined (unedited) sequence as aAbstractSequence
.AbstractSequence<AminoAcidCompound>
CasePreservingProteinSequenceCreator. getSequence(String sequence, long index)
AbstractSequence<AminoAcidCompound>
CasePreservingProteinSequenceCreator. getSequence(List<AminoAcidCompound> list)
Assumes all compounds were uppercaseAbstractSequence<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 supportedAbstractSequence<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 supportedAbstractSequence<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>
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<NucleotideCompound>
FileProxyRNASequenceCreator. getSequence(List<NucleotideCompound> list)
Not sure of use case and currently not supportedAbstractSequence<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>
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)
Methods in org.biojava.nbio.core.sequence.io with parameters of type AbstractSequence Modifier and Type Method 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 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 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.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 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 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 Description AbstractSequence<?>
AbstractSequence. getParentSequence()
Methods in org.biojava.nbio.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 positionList<FeatureInterface<AbstractSequence<C>,C>>
AbstractSequence. getFeatures(String featureType, int bioSequencePosition)
Return features at a sequence position by typeList<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 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 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 sequencevoid
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 -
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 Description static QuantityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>
FastqTools. createErrorProbabilities(Fastq fastq)
Create and return a newQuantityFeature
from the error probabilities of the specified FASTQ formatted sequence.static QualityFeature<AbstractSequence<NucleotideCompound>,NucleotideCompound>
FastqTools. createQualityScores(Fastq fastq)
Create and return a newQualityFeature
from the quality scores of the specified FASTQ formatted sequence.
-