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| Uses of Strand in org.biojava3.core.sequence |
|---|
| Methods in org.biojava3.core.sequence that return Strand | |
|---|---|
Strand |
Strand.getReverse()
|
Strand |
TranscriptSequence.getStrand()
|
Strand |
GeneSequence.getStrand()
A gene should have Strand |
Strand |
CDSSequence.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.biojava3.core.sequence with parameters of type Strand | |
|---|---|
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.biojava3.core.sequence with parameters of type Strand | |
|---|---|
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.biojava3.core.sequence.loader |
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| Methods in org.biojava3.core.sequence.loader with parameters of type Strand | |
|---|---|
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)
|
| Uses of Strand in org.biojava3.core.sequence.location |
|---|
| Methods in org.biojava3.core.sequence.location that return Strand | |
|---|---|
static Strand |
LocationHelper.detectStrand(List<Location> subLocations)
Loops through the given list of locations and returns the consensus Strand class. |
| Methods in org.biojava3.core.sequence.location with parameters of type Strand | |
|---|---|
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. |
protected List<Location> |
InsdcParser.parse(Reader reader,
Strand strand)
|
protected Location |
InsdcParser.parseLocation(String location,
Strand strand)
|
protected Location |
InsdcParser.parseRange(Matcher matcher,
Strand strand)
|
protected Location |
InsdcParser.parseSingle(Matcher matcher,
Strand strand)
|
| Constructors in org.biojava3.core.sequence.location with parameters of type Strand | |
|---|---|
InsdcLocations.GroupLocation(int start,
int end,
Strand strand,
List<Location> subLocations)
|
|
InsdcLocations.GroupLocation(int start,
int end,
Strand strand,
Location... subLocations)
|
|
InsdcLocations.GroupLocation(Point start,
Point end,
Strand strand,
boolean circular,
List<Location> subLocations)
|
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InsdcLocations.GroupLocation(Point start,
Point end,
Strand strand,
boolean circular,
Location... subLocations)
|
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InsdcLocations.GroupLocation(Point start,
Point end,
Strand strand,
List<Location> subLocations)
|
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InsdcLocations.GroupLocation(Point start,
Point end,
Strand strand,
Location... subLocations)
|
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InsdcLocations.OrderLocation(int start,
int end,
Strand strand,
List<Location> subLocations)
|
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InsdcLocations.OrderLocation(int start,
int end,
Strand strand,
Location... subLocations)
|
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InsdcLocations.OrderLocation(Point start,
Point end,
Strand strand,
boolean circular,
List<Location> subLocations)
|
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InsdcLocations.OrderLocation(Point start,
Point end,
Strand strand,
boolean circular,
Location... subLocations)
|
|
InsdcLocations.OrderLocation(Point start,
Point end,
Strand strand,
List<Location> subLocations)
|
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InsdcLocations.OrderLocation(Point start,
Point end,
Strand strand,
Location... subLocations)
|
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SimpleLocation(int start,
int end,
Strand strand)
|
|
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)
|
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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,
List<Location> subLocations)
|
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SimpleLocation(Point start,
Point end,
Strand strand,
boolean circular,
List<Location> subLocations)
|
|
SimpleLocation(Point start,
Point end,
Strand strand,
boolean circular,
Location... subLocations)
|
|
SimpleLocation(Point start,
Point end,
Strand strand,
Location... subLocations)
|
|
| Uses of Strand in org.biojava3.core.sequence.location.template |
|---|
| Methods in org.biojava3.core.sequence.location.template that return Strand | |
|---|---|
Strand |
Location.getStrand()
Strand which the location is located on |
Strand |
AbstractLocation.getStrand()
|
| Methods in org.biojava3.core.sequence.location.template with parameters of type Strand | |
|---|---|
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. |
protected void |
AbstractLocation.setStrand(Strand strand)
|
| Constructors in org.biojava3.core.sequence.location.template with parameters of type Strand | |
|---|---|
AbstractLocation(Point start,
Point end,
Strand strand,
boolean circular,
boolean betweenCompounds,
AccessionID accession,
List<Location> subLocations)
Default constructor |
|
AbstractLocation(Point start,
Point end,
Strand strand,
boolean circular,
boolean betweenCompounds,
List<Location> subLocations)
Default constructor |
|
| Uses of Strand in org.biojava3.core.sequence.storage |
|---|
| Methods in org.biojava3.core.sequence.storage with parameters of type Strand | |
|---|---|
String |
ArrayListSequenceReader.getSequenceAsString(Integer begin,
Integer end,
Strand strand)
|
String |
SequenceAsStringHelper.getSequenceAsString(List<C> parsedCompounds,
CompoundSet<C> compoundSet,
Integer bioBegin,
Integer bioEnd,
Strand strand)
|
| Uses of Strand in org.biojava3.core.sequence.template |
|---|
| Methods in org.biojava3.core.sequence.template with parameters of type Strand | |
|---|---|
String |
AbstractSequence.getSequenceAsString(Integer bioStart,
Integer bioEnd,
Strand strand)
|
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