Package | Description |
---|---|
org.biojava.nbio.core.sequence.features | |
org.biojava.nbio.core.sequence.location |
Modifier and Type | Method and Description |
---|---|
AbstractLocation |
AbstractFeature.getLocations()
A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
|
AbstractLocation |
FeatureInterface.getLocations()
The location(s) of this feature where the location should contain a reference to parent and sequence etc.
|
AbstractLocation |
FeatureDbReferenceInfo.getLocations() |
Modifier and Type | Method and Description |
---|---|
void |
AbstractFeature.setLocation(AbstractLocation loc)
A feature could be a single sequence position like a mutation or a post translational modification of an amino acid.
|
void |
FeatureInterface.setLocation(AbstractLocation loc)
The new location for this feature.
|
void |
FeatureDbReferenceInfo.setLocation(AbstractLocation loc) |
Modifier and Type | Class and Description |
---|---|
static class |
InsdcLocations.BondLocation
Used to represent bond locations equivalent to bond(7,8) or bond(7).
|
static class |
InsdcLocations.GroupLocation
Deprecated in INSDC yet still appears; equivalent to the order()
directive except no 5' to 3' ordering is defined.
|
static class |
InsdcLocations.OneOfLocation
Deprecated in INSDC; refers to a set of locations of which one
location could be valid e.g.
|
static class |
InsdcLocations.OrderLocation
Used to describe a 5' to 3' ordering but no firm assurance it is correct
|
class |
SequenceLocation<S extends AbstractSequence<C>,C extends Compound>
A location in a sequence that keeps a reference to its parent sequence
|
class |
SimpleLocation
Very basic implementation of the Location interface which defines a series
of simple constructors.
|
Modifier and Type | Method and Description |
---|---|
List<AbstractLocation> |
InsdcParser.parse(Reader reader)
Reader based version of the parse methods.
|
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