Uses of Class
org.biojava.nbio.core.sequence.DNASequence

Packages that use DNASequence

Package	Description
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.io
org.biojava.nbio.genome
org.biojava.nbio.genome.io.fastq	FASTQ and variants sequence format I/O.
org.biojava.nbio.genome.parsers.geneid
org.biojava.nbio.genome.parsers.gff
org.biojava.nbio.genome.util

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

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

Modifier and Type	Class and Description
class	CDSSequence Represents a exon or coding sequence in a gene.
class	ChromosomeSequence A ChromosomeSequence is a DNASequence but keeps track of geneSequences
class	ExonSequence A gene contains a collection of Exon sequences
class	GeneSequence
class	IntronSequence
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.

Fields in org.biojava.nbio.core.sequence declared as DNASequence

Modifier and Type	Field and Description
DNASequence	StopCodonSequence.parentGeneSequence
DNASequence	StartCodonSequence.parentGeneSequence

Methods in org.biojava.nbio.core.sequence that return DNASequence

Modifier and Type	Method and Description
DNASequence	TranscriptSequence.getDNACodingSequence() Get the stitched together CDS sequences then maps to the cDNA
DNASequence	GeneSequence.getSequence5PrimeTo3Prime() Try to give method clarity where you want a DNASequence coding in the 5' to 3' direction Returns the DNASequence representative of the 5' and 3' reading based on strand

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

Methods in org.biojava.nbio.core.sequence.io that return types with arguments of type DNASequence

Modifier and Type	Method and Description
static LinkedHashMap<String,DNASequence>	FastaReaderHelper.readFastaDNASequence(File file)
static LinkedHashMap<String,DNASequence>	FastaReaderHelper.readFastaDNASequence(File file, boolean lazySequenceLoad) Selecting lazySequenceLoad=true will parse the FASTA file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
static LinkedHashMap<String,DNASequence>	FastaReaderHelper.readFastaDNASequence(InputStream inStream) Read a fasta DNA sequence
static LinkedHashMap<String,DNASequence>	GenbankReaderHelper.readGenbankDNASequence(File file)
static LinkedHashMap<String,DNASequence>	GenbankReaderHelper.readGenbankDNASequence(File file, boolean lazySequenceLoad) Selecting lazySequenceLoad=true will parse the Genbank file and figure out the accessionid and offsets and return sequence objects that can in the future read the sequence from the disk.
static LinkedHashMap<String,DNASequence>	GenbankReaderHelper.readGenbankDNASequence(InputStream inStream) Read a Genbank DNA sequence

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

Modifier and Type	Method and Description
static void	GenbankWriterHelper.writeNucleotideSequence(File file, Collection<DNASequence> dnaSequences) Write a collection of NucleotideSequences to a file
static void	FastaWriterHelper.writeNucleotideSequence(File file, Collection<DNASequence> dnaSequences) Write a collection of NucleotideSequences to a file
static void	GenbankWriterHelper.writeNucleotideSequence(OutputStream outputStream, Collection<DNASequence> dnaSequences) Write a collection of NucleotideSequences to a file
static void	FastaWriterHelper.writeNucleotideSequence(OutputStream outputStream, Collection<DNASequence> dnaSequences) Write a collection of NucleotideSequences to a file
static void	GenbankWriterHelper.writeNucleotideSequence(OutputStream outputStream, Collection<DNASequence> dnaSequences, String seqType) Write a collection of NucleotideSequences to a file

Uses of DNASequence in org.biojava.nbio.genome

Method parameters in org.biojava.nbio.genome with type arguments of type DNASequence

Modifier and Type	Method and Description
static LinkedHashMap<String,ChromosomeSequence>	GeneFeatureHelper.getChromosomeSequenceFromDNASequence(LinkedHashMap<String,DNASequence> dnaSequenceList)

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

Methods in org.biojava.nbio.genome.io.fastq that return DNASequence

Modifier and Type	Method and Description
static DNASequence	FastqTools.createDNASequence(Fastq fastq) Create and return a new DNASequence from the specified FASTQ formatted sequence.
static DNASequence	FastqTools.createDNASequenceWithErrorProbabilities(Fastq fastq) Create and return a new DNASequence with error probabilities from the specified FASTQ formatted sequence.
static DNASequence	FastqTools.createDNASequenceWithQualityScores(Fastq fastq) Create and return a new DNASequence with quality scores from the specified FASTQ formatted sequence.
static DNASequence	FastqTools.createDNASequenceWithQualityScoresAndErrorProbabilities(Fastq fastq) Create and return a new DNASequence with quality scores and error probabilities from the specified FASTQ formatted sequence.

Uses of DNASequence in org.biojava.nbio.genome.parsers.geneid

Methods in org.biojava.nbio.genome.parsers.geneid that return types with arguments of type DNASequence

Modifier and Type	Method and Description
LinkedHashMap<String,DNASequence>	GeneIDXMLReader.getDNACodingSequences()

Uses of DNASequence in org.biojava.nbio.genome.parsers.gff

Methods in org.biojava.nbio.genome.parsers.gff with parameters of type DNASequence

Modifier and Type	Method and Description
String	FeatureList.splice(DNASequence sequence) Concatenate successive portions of the specified sequence using the feature locations in the list.

Method parameters in org.biojava.nbio.genome.parsers.gff with type arguments of type DNASequence

Modifier and Type	Method and Description
static double	GCStats.getGCStats(Collection<DNASequence> sequences)

Uses of DNASequence in org.biojava.nbio.genome.util

Methods in org.biojava.nbio.genome.util that return DNASequence

Modifier and Type	Method and Description
static DNASequence	ChromosomeMappingTools.getTranscriptDNASequence(TwoBitFacade twoBitFacade, GeneChromosomePosition gcp) Extracts the DNA sequence transcribed from the input genetic coordinates.
static DNASequence	ChromosomeMappingTools.getTranscriptDNASequence(TwoBitFacade twoBitFacade, String chromosome, List<Integer> exonStarts, List<Integer> exonEnds, int cdsStart, int cdsEnd, Character orientation) Extracts the DNA sequence transcribed from the input genetic coordinates.

Methods in org.biojava.nbio.genome.util with parameters of type DNASequence

Modifier and Type	Method and Description
static ProteinSequence	ProteinMappingTools.convertDNAtoProteinSequence(DNASequence dnaSequence) Converts the DNA sequence to protein sequence.