|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
java.lang.Objectorg.biojava3.core.sequence.location.template.Location.Tools
public static class Location.Tools
Helper methods for use with the Location classes. Taking its inspiration from the RichSequence.Tools class from the old BioJava
Constructor Summary | |
---|---|
Location.Tools()
|
Method Summary | |
---|---|
static Location |
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 int |
completeCircularPasses(int index,
int seqLength)
Works in a similar way to modulateCircularLocation but returns the number of complete passes over a Sequence length a circular location makes i.e. |
static Location |
getMax(List<Location> locations)
Scans through a list of locations to find the Location with the highest end |
static Location |
getMin(List<Location> locations)
Scans through a list of locations to find the Location with the lowest start |
static Location |
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(List<Location> locations,
Integer sequenceLength,
String type)
Used for building a location from a series of sub-locations |
static int |
modulateCircularIndex(int index,
int seqLength)
Takes a point on a circular location and moves it left until it falls at the earliest possible point that represents the same base. |
Methods inherited from class java.lang.Object |
---|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Constructor Detail |
---|
public Location.Tools()
Method Detail |
---|
public static Location location(List<Location> locations, Integer sequenceLength, String type)
public static Location location(int start, int end, Strand strand, int length)
public static Location circularLocation(int start, int end, Strand strand, int length)
location
- The location which currently expresses the outer
bounds of a circular location.length
- The length of the circular genomic unit
public static Location getMin(List<Location> locations)
public static Location getMax(List<Location> locations)
public static int modulateCircularIndex(int index, int seqLength)
index
- Index of the position to work withseqLength
- Length of the Sequence
public static int completeCircularPasses(int index, int seqLength)
|
|||||||||
PREV CLASS NEXT CLASS | FRAMES NO FRAMES | ||||||||
SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |