Uses of Class
org.biojava.nbio.core.sequence.Strand
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Uses of Strand in org.biojava.nbio.core.sequence
Methods in org.biojava.nbio.core.sequence that return Strand Modifier and Type Method Description Strand
Strand. getReverse()
Strand
CDSSequence. getStrand()
Strand
GeneSequence. getStrand()
A gene should have StrandStrand
TranscriptSequence. getStrand()
static Strand
Strand. valueOf(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 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 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 Description String
SequenceFileProxyLoader. getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand)
String
StringProxySequenceReader. getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand)
String
UniprotProxySequenceReader. getSequenceAsString(Integer bioBegin, Integer bioEnd, Strand strand)
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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 Description static Strand
LocationHelper. detectStrand(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 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 Description GroupLocation(int start, int end, Strand strand, List<Location> subLocations)
GroupLocation(int start, int end, Strand strand, Location... subLocations)
GroupLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)
GroupLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)
GroupLocation(Point start, Point end, Strand strand, List<Location> subLocations)
GroupLocation(Point start, Point end, Strand strand, Location... subLocations)
OrderLocation(int start, int end, Strand strand, List<Location> subLocations)
OrderLocation(int start, int end, Strand strand, Location... subLocations)
OrderLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)
OrderLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)
OrderLocation(Point start, Point end, Strand strand, 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, 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, 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, boolean circular, boolean betweenBases)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenBases, List<Location> subLocations)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, List<Location> subLocations)
SimpleLocation(Point start, Point end, Strand strand, boolean betweenCompounds, AccessionID accession)
SimpleLocation(Point start, Point end, Strand strand, boolean circular, Location... subLocations)
SimpleLocation(Point start, Point end, Strand strand, List<Location> subLocations)
SimpleLocation(Point start, Point end, Strand strand, AccessionID accession)
SimpleLocation(Point start, Point end, Strand strand, Location... subLocations)
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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 Description Strand
AbstractLocation. getStrand()
Strand
Location. getStrand()
Strand which the location is located onMethods in org.biojava.nbio.core.sequence.location.template with parameters of type Strand Modifier and Type Method 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 Description AbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, List<Location> subLocations)
Default constructorAbstractLocation(Point start, Point end, Strand strand, boolean circular, boolean betweenCompounds, AccessionID accession, 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 Description String
ArrayListSequenceReader. getSequenceAsString(Integer begin, Integer end, Strand strand)
String
SequenceAsStringHelper. getSequenceAsString(List<C> parsedCompounds, CompoundSet<C> compoundSet, Integer bioBegin, Integer bioEnd, Strand strand)
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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 Description String
AbstractSequence. getSequenceAsString(Integer bioStart, Integer bioEnd, Strand strand)
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