Uses of Class
org.biojava3.core.sequence.DNASequence

Packages that use DNASequence

org.biojava3.core.sequence
org.biojava3.core.sequence.io

Uses of DNASequence in org.biojava3.core.sequence

Subclasses of DNASequence in org.biojava3.core.sequence

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.biojava3.core.sequence declared as DNASequence

DNASequence	StopCodonSequence.parentGeneSequence
DNASequence	StartCodonSequence.parentGeneSequence

Methods in org.biojava3.core.sequence that return DNASequence

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.biojava3.core.sequence.io

Methods in org.biojava3.core.sequence.io that return types with arguments of type DNASequence

static LinkedHashMap<String,DNASequence>	FastaReaderHelper.readFastaDNASequence(File file)
static LinkedHashMap<String,DNASequence>	FastaReaderHelper.readFastaDNASequence(InputStream inStream) Read a fasta DNA sequence

Method parameters in org.biojava3.core.sequence.io with type arguments of type DNASequence

static void	FastaWriterHelper.writeNucleotideSequence(File file, 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