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

Packages that use Strand

Package	Description
org.biojava.nbio.core.sequence
org.biojava.nbio.core.sequence.loader
org.biojava.nbio.core.sequence.location
org.biojava.nbio.core.sequence.location.template
org.biojava.nbio.core.sequence.storage
org.biojava.nbio.core.sequence.template

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

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

Modifier and Type	Method and Description
Strand	Strand.getReverse()
Strand	TranscriptSequence.getStrand()
Strand	CDSSequence.getStrand()
Strand	GeneSequence.getStrand() A gene should have Strand
static Strand	Strand.valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static Strand[]	Strand.values() Returns an array containing the constants of this enum type, in the order they are declared.

Methods in org.biojava.nbio.core.sequence with parameters of type Strand

Modifier and Type	Method and Description
GeneSequence	ChromosomeSequence.addGene(AccessionID accession, int bioBegin, int bioEnd, Strand strand) Add a gene to the chromosome sequence using bioIndexing starts at 1 instead of 0.
void	GeneSequence.setStrand(Strand strand)

Constructors in org.biojava.nbio.core.sequence with parameters of type Strand

Constructor and Description
GeneSequence(ChromosomeSequence parentSequence, int begin, int end, Strand strand) A class that keeps track of the details of a GeneSequence which is difficult to properly model.

Uses of Strand in org.biojava.nbio.core.sequence.loader

Methods in org.biojava.nbio.core.sequence.loader with parameters of type Strand

Modifier and Type	Method and Description
java.lang.String	UniprotProxySequenceReader.getSequenceAsString(java.lang.Integer bioBegin, java.lang.Integer bioEnd, Strand strand)
java.lang.String	StringProxySequenceReader.getSequenceAsString(java.lang.Integer bioBegin, java.lang.Integer bioEnd, Strand strand)
java.lang.String	SequenceFileProxyLoader.getSequenceAsString(java.lang.Integer bioBegin, java.lang.Integer bioEnd, Strand strand)

Uses of Strand in org.biojava.nbio.core.sequence.location

Methods in org.biojava.nbio.core.sequence.location that return Strand

Modifier and Type	Method and Description
static Strand	LocationHelper.detectStrand(java.util.List<Location> subLocations) Loops through the given list of locations and returns the consensus Strand class.

Methods in org.biojava.nbio.core.sequence.location with parameters of type Strand

Modifier and Type	Method and Description
static Location	LocationHelper.circularLocation(int start, int end, Strand strand, int length) Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
static Location	LocationHelper.location(int start, int end, Strand strand, int length) Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.

Constructors in org.biojava.nbio.core.sequence.location with parameters of type Strand

Constructor and Description
GroupLocation(int start, int end, Strand strand, java.util.List<Location> subLocations)
GroupLocation(int start, int end, Strand strand, Location... subLocations)
GroupLocation(Point start, Point end, Strand strand, boolean circular, java.util.List<Location> subLocations)
GroupLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)
GroupLocation(Point start, Point end, Strand strand, java.util.List<Location> subLocations)
GroupLocation(Point start, Point end, Strand strand, Location... subLocations)
OrderLocation(int start, int end, Strand strand, java.util.List<Location> subLocations)
OrderLocation(int start, int end, Strand strand, Location... subLocations)
OrderLocation(Point start, Point end, Strand strand, boolean circular, java.util.List<Location> subLocations)
OrderLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)
OrderLocation(Point start, Point end, Strand strand, java.util.List<Location> subLocations)
OrderLocation(Point start, Point end, Strand strand, Location... subLocations)
SequenceLocation(int start, int end, S sequence, Strand strand)
SequenceLocation(int start, int end, S sequence, Strand strand, boolean circular, java.util.List<Location> subLocations)
SequenceLocation(Point start, Point end, S sequence, Strand strand)
SimpleLocation(int start, int end, Strand strand)
SimpleLocation(int start, int end, Strand strand, java.util.List<Location> subLocations)
SimpleLocation(int start, int end, Strand strand, Location... subLocations)
SimpleLocation(Point start, Point end, Strand strand)
SimpleLocation(Point start, Point end, Strand strand, AccessionID accession)
SimpleLocation(Point start, Point end, Strand strand, boolean betweenCompounds, AccessionID accession)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenBases)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenBases, java.util.List<Location> subLocations)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, java.util.List<Location> subLocations)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)
SimpleLocation(Point start, Point end, Strand strand, java.util.List<Location> subLocations)
SimpleLocation(Point start, Point end, Strand strand, Location... subLocations)

Uses of Strand in org.biojava.nbio.core.sequence.location.template

Methods in org.biojava.nbio.core.sequence.location.template that return Strand

Modifier and Type	Method and Description
Strand	AbstractLocation.getStrand()
Strand	Location.getStrand() Strand which the location is located on

Methods in org.biojava.nbio.core.sequence.location.template with parameters of type Strand

Modifier and Type	Method and Description
static Location	Location.Tools.circularLocation(int start, int end, Strand strand, int length) Converts a location which defines the outer bounds of a circular location and splits it into the required portions.
static Location	Location.Tools.location(int start, int end, Strand strand, int length) Returns a location object which unlike the location constructors allows you to input reverse coordinates and will convert these into the right location on the positive strand.
void	AbstractLocation.setStrand(Strand strand)

Constructors in org.biojava.nbio.core.sequence.location.template with parameters of type Strand

Constructor and Description
AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, java.util.List<Location> subLocations) Default constructor
AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, java.util.List<Location> subLocations) Default constructor

Uses of Strand in org.biojava.nbio.core.sequence.storage

Methods in org.biojava.nbio.core.sequence.storage with parameters of type Strand

Modifier and Type	Method and Description
java.lang.String	ArrayListSequenceReader.getSequenceAsString(java.lang.Integer begin, java.lang.Integer end, Strand strand)
java.lang.String	SequenceAsStringHelper.getSequenceAsString(java.util.List<C> parsedCompounds, CompoundSet<C> compoundSet, java.lang.Integer bioBegin, java.lang.Integer bioEnd, Strand strand)

Uses of Strand in org.biojava.nbio.core.sequence.template

Methods in org.biojava.nbio.core.sequence.template with parameters of type Strand

Modifier and Type	Method and Description
java.lang.String	AbstractSequence.getSequenceAsString(java.lang.Integer bioStart, java.lang.Integer bioEnd, Strand strand)