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

Packages that use DNASequence

Package	Description
bacnet.datamodel.sequence
bacnet.datamodel.sequenceNCBI
org.biojava3.core.sequence
org.biojava3.core.sequence.io
org.biojava3.genome
org.biojava3.genome.parsers.geneid
org.biojava3.genome.parsers.gff

Uses of DNASequence in bacnet.datamodel.sequence

Subclasses of DNASequence 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

Methods in bacnet.datamodel.sequence that return DNASequence

Modifier and Type	Method	Description
DNASequence	ChromosomeBacteriaSequence.getCodingRegion(String accession)	Get the gene based on accession.
DNASequence	ChromosomeBacteriaSequence.getNonCodingRegion(String accession)	Get the gene based on accession.

Methods in bacnet.datamodel.sequence that return types with arguments of type DNASequence

Modifier and Type	Method	Description
LinkedHashMap<String,DNASequence>	ChromosomeBacteriaSequence.getCodingSequenceHashMap()
LinkedHashMap<String,DNASequence>	ChromosomeBacteriaSequence.getNoncodingSequenceHashMap()

Method parameters in bacnet.datamodel.sequence with type arguments of type DNASequence

Modifier and Type	Method	Description
static LinkedHashMap<String,Chromosome>	Chromosome.getChromosomeFromDNASequence(LinkedHashMap<String,DNASequence> dnaSequenceList, Genome genome, int k, String fileName)
void	ChromosomeBacteriaSequence.setCodingSequenceHashMap(LinkedHashMap<String,DNASequence> codingSequenceHashMap)
void	ChromosomeBacteriaSequence.setNoncodingSequenceHashMap(LinkedHashMap<String,DNASequence> noncodingSequenceHashMap)

Uses of DNASequence in bacnet.datamodel.sequenceNCBI

Methods in bacnet.datamodel.sequenceNCBI that return DNASequence

Modifier and Type	Method	Description
static DNASequence	GeneNCBITools.convert(Srna sRNA)	Convert an Srna into a DNASequence
DNASequence	GenomeNCBI.getGeneFromName(String name)	Go through codingSequence and nonCodingSequence searching for corresponding accession or locus
static DNASequence	GenomeNCBITools.loadCorrespondingChromosome(String accession)	load and return the chromosome corresponding to an accession

Methods in bacnet.datamodel.sequenceNCBI that return types with arguments of type DNASequence

Modifier and Type	Method	Description
ArrayList<DNASequence>	GenomeNCBI.getCodingSequencesList(boolean allChromosomes)	Put in a list all the CodingSequence found
ArrayList<DNASequence>	GenomeNCBI.getNonCodingSequencesList(boolean allChromosomes)	Put in a list all the NonCodingSequence found
ArrayList<DNASequence>	GenomeNCBI.getSubCodingSequencesList(ArrayList<String> locusTag, boolean allChromosomes)	Put in a sublist all the CodingSequence found in locuTag list

Methods in bacnet.datamodel.sequenceNCBI with parameters of type DNASequence

Modifier and Type	Method	Description
static Gene	GenomeConversionElement.convertDNASequenceGene(DNASequence dnaSeq)	From a DNASequence make a Gene object
static Sequence	GenomeConversionElement.convertDNASequenceGeneral(DNASequence dnaSeq)	From a DNASequence object, create Sequence Mainly used in GenomeConversion methods
static NcRNA	GenomeConversionElement.convertDNASequenceNcRNA(DNASequence dnaSeq)	From a DNASequence make a Gene object
static double	GeneNCBITools.diffBeginPosition(DNASequence gene1, DNASequence gene2)	Calculate difference in begin position
static double	GeneNCBITools.diffCenter(DNASequence gene1, DNASequence gene2)	Calculate the distance between the two center of gene1 and gene2
static double	GeneNCBITools.diffEndPosition(DNASequence gene1, DNASequence gene2)	Calculate difference in end position
static String	GeneNCBITools.getCodonUsage(DNASequence seq)
static String	GeneNCBITools.getCOG(DNASequence seq)
static String	GeneNCBITools.getDbxref(DNASequence seq)
static String	GeneNCBITools.getGene(DNASequence seq)
static String	GeneNCBITools.getGlaserFC(DNASequence seq)
static String	GeneNCBITools.getIsoelectricPoint(DNASequence seq)
static String	GeneNCBITools.getLength(DNASequence seq)
static String	GeneNCBITools.getLengthProt(DNASequence seq)
static String	GeneNCBITools.getMolMass(DNASequence seq)
static String	GeneNCBITools.getNote(DNASequence seq)
static String	GeneNCBITools.getOldLocusTag(DNASequence seq)
static String	GeneNCBITools.getOperon(DNASequence seq)
static String	GeneNCBITools.getProduct(DNASequence seq)
static String	GeneNCBITools.getProteinID(DNASequence seq)	Search for protein-id in the Note section of Gene Search first : protein_id attribute Search then : protein_Id attribute Finally in CDS section of Note search for: "Dbxref :" and "Genbank:" protein id
static String	GeneNCBITools.getRASTinfo(DNASequence seq)
static String	GeneNCBITools.getStrand(DNASequence seq)
static String	GeneNCBITools.getTranstable(DNASequence seq)
static String	GeneNCBITools.getType(DNASequence seq)
static boolean	GeneNCBITools.isEqual(DNASequence gene1, DNASequence gene2, int scale)	Calculates the distance between the two center fo gene1 and gene2 If this distance is under scale, in absolute value, and both gene are on the same strand, True is return
static boolean	GeneNCBITools.isOverlap(DNASequence gene1, DNASequence gene2)	Decide if two genes are overlapping First, calculate the overlapping size of two genes, finding the gene upstream to the other If overlap is negative it will mean that we have no overlap (gene1.end < gene2.begin)
static int	GeneNCBITools.overlap(DNASequence gene1, DNASequence gene2)	Calculate the overlapping size of two genes First, find the gene upstream to the other Then, as we got gene1.begin < gene2.begin, overlap = gene1.end - gene2.begin overlap can be negative, it will mean that we have no overlap (gene1.end < gene2.begin) or overlap can be higher than gene2.length, in that case overlap = gene2.length
static boolean	GeneNCBITools.sameEnd(DNASequence gene1, DNASequence gene2, int scale)	Determine that to gene have the same end if their ending piosition are the same +- scale bp
static String	GeneNCBITools.searchElement(DNASequence seq, String attribute)	Search an element in the Note part of a DNASequence
static String	GeneNCBITools.searchElement(DNASequence seq, String attribute, String section)	Search an element in the Note part of a DNASequence in a sectio of the note : Section = gene, CDS, etc...
static String	GeneNCBITools.toStringCodingInfo(DNASequence coding)	Display the info contain in a coding DNASequence
static String	GeneNCBITools.toStringNonCodingInfo(DNASequence coding)	Display info contain in a non coding DNASequence

Uses of DNASequence in org.biojava3.core.sequence

Subclasses of DNASequence in org.biojava3.core.sequence

Modifier and Type	Class	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.biojava3.core.sequence declared as DNASequence

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

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

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

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

Modifier and Type	Method	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

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

Modifier and Type	Method	Description
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

Uses of DNASequence in org.biojava3.genome

Method parameters in org.biojava3.genome with type arguments of type DNASequence

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

Uses of DNASequence in org.biojava3.genome.parsers.geneid

Methods in org.biojava3.genome.parsers.geneid that return types with arguments of type DNASequence

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

Uses of DNASequence in org.biojava3.genome.parsers.gff

Methods in org.biojava3.genome.parsers.gff with parameters of type DNASequence

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

Method parameters in org.biojava3.genome.parsers.gff with type arguments of type DNASequence

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