| Package | Description |
|---|---|
| org.biojava.nbio.core.sequence.location | |
| org.biojava.nbio.core.sequence.location.template |
| 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 |
|---|---|
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.getMax(List<Location> locations)
Scans through a list of locations to find the Location with the
highest end
|
static Location |
LocationHelper.getMin(List<Location> locations)
Scans through a list of locations to find the Location with the
lowest start
|
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.
|
static Location |
LocationHelper.location(List<Location> subLocations)
Used as a thin wrapper to the
LocationHelper.location(java.util.List, java.lang.String)
method to bring the given location list together as a join (the default
type) |
static Location |
LocationHelper.location(List<Location> subLocations,
String type)
Builds a location from a List of locations; this can be circular or
linear joins.
|
Location |
InsdcParser.parse(String locationString)
Main method for parsing a location from a String instance
|
| Modifier and Type | Method and Description |
|---|---|
static boolean |
LocationHelper.consistentAccessions(List<Location> subLocations)
Scans a list of locations and returns true if all the given locations
are linked to the same sequence.
|
static boolean |
LocationHelper.detectCicular(List<Location> subLocations)
Loops through the given list of locations and returns true if it looks
like they represent a circular location.
|
static Point |
LocationHelper.detectEnd(List<Location> subLocations,
boolean isCircular)
This will attempt to find what the last point is and returns that
position.
|
static Point |
LocationHelper.detectStart(List<Location> subLocations)
Assumes that the first element is the start & clones it
|
static Strand |
LocationHelper.detectStrand(List<Location> subLocations)
Loops through the given list of locations and returns the consensus
Strand class.
|
static Location |
LocationHelper.getMax(List<Location> locations)
Scans through a list of locations to find the Location with the
highest end
|
static Location |
LocationHelper.getMin(List<Location> locations)
Scans through a list of locations to find the Location with the
lowest start
|
static Location |
LocationHelper.location(List<Location> subLocations)
Used as a thin wrapper to the
LocationHelper.location(java.util.List, java.lang.String)
method to bring the given location list together as a join (the default
type) |
static Location |
LocationHelper.location(List<Location> subLocations,
String type)
Builds a location from a List of locations; this can be circular or
linear joins.
|
| Constructor and Description |
|---|
InsdcLocations.BondLocation(Location... subLocations) |
InsdcLocations.GroupLocation(int start,
int end,
Strand strand,
Location... subLocations) |
InsdcLocations.GroupLocation(Location... subLocations) |
InsdcLocations.GroupLocation(Point start,
Point end,
Strand strand,
boolean circular,
Location... subLocations) |
InsdcLocations.GroupLocation(Point start,
Point end,
Strand strand,
Location... subLocations) |
InsdcLocations.OneOfLocation(Location... locations) |
InsdcLocations.OrderLocation(int start,
int end,
Strand strand,
Location... subLocations) |
InsdcLocations.OrderLocation(Location... subLocations) |
InsdcLocations.OrderLocation(Point start,
Point end,
Strand strand,
boolean circular,
Location... subLocations) |
InsdcLocations.OrderLocation(Point start,
Point end,
Strand strand,
Location... subLocations) |
SimpleLocation(int start,
int end,
Strand strand,
Location... subLocations) |
SimpleLocation(Point start,
Point end,
Strand strand,
boolean circular,
Location... subLocations) |
SimpleLocation(Point start,
Point end,
Strand strand,
Location... subLocations) |
| Constructor and Description |
|---|
InsdcLocations.BondLocation(List<Location> subLocations) |
InsdcLocations.GroupLocation(int start,
int end,
Strand strand,
List<Location> subLocations) |
InsdcLocations.GroupLocation(Point start,
Point end,
Strand strand,
boolean circular,
List<Location> subLocations) |
InsdcLocations.GroupLocation(Point start,
Point end,
Strand strand,
List<Location> subLocations) |
InsdcLocations.OneOfLocation(List<Location> locations) |
InsdcLocations.OrderLocation(int start,
int end,
Strand strand,
List<Location> subLocations) |
InsdcLocations.OrderLocation(Point start,
Point end,
Strand strand,
boolean circular,
List<Location> subLocations) |
InsdcLocations.OrderLocation(Point start,
Point end,
Strand strand,
List<Location> subLocations) |
SequenceLocation(int start,
int end,
S sequence,
Strand strand,
boolean circular,
List<Location> subLocations) |
SimpleLocation(int start,
int end,
Strand strand,
List<Location> subLocations) |
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,
List<Location> subLocations) |
| Modifier and Type | Interface and Description |
|---|---|
interface |
AccesionedLocation
A location which is bound to an AccessionID.
|
| Modifier and Type | Class and Description |
|---|---|
class |
AbstractLocation
Base abstraction of a location which encodes for the majority of important
features about a location such as the start, end and strand
|
| Modifier and Type | Field and Description |
|---|---|
static Location |
Location.EMPTY
Basic location which is set to the minimum and maximum bounds of
Integer. |
| 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.getMax(List<Location> locations)
Scans through a list of locations to find the Location with the
highest end
|
static Location |
Location.Tools.getMin(List<Location> locations)
Scans through a list of locations to find the Location with the
lowest start
|
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.
|
static Location |
Location.Tools.location(List<Location> locations,
Integer sequenceLength,
String type)
Used for building a location from a series of sub-locations
|
| Modifier and Type | Method and Description |
|---|---|
List<Location> |
AbstractLocation.getRelevantSubLocations()
Returns the normalised list of sub locations i.e.
|
List<Location> |
Location.getRelevantSubLocations()
An extension to
getSubLocations() which returns sub-locations
of sub-locations; this will continue until it runs out of those locations. |
List<Location> |
AbstractLocation.getSubLocations() |
List<Location> |
Location.getSubLocations()
Gives access to the sub locations for this location.
|
Iterator<Location> |
AbstractLocation.iterator()
Iterates through all known sub-locations for this location but does
not descend
|
| Modifier and Type | Method and Description |
|---|---|
static Location |
Location.Tools.getMax(List<Location> locations)
Scans through a list of locations to find the Location with the
highest end
|
static Location |
Location.Tools.getMin(List<Location> locations)
Scans through a list of locations to find the Location with the
lowest start
|
static Location |
Location.Tools.location(List<Location> locations,
Integer sequenceLength,
String type)
Used for building a location from a series of sub-locations
|
void |
AbstractLocation.setSubLocations(List<Location> subLocations) |
| Constructor and Description |
|---|
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
|
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