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

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	StartCodonSequence.parentGeneSequence
DNASequence	StopCodonSequence.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