uk.ac.roslin.ensembl.model

Class CoordinateSet

java.lang.Object

java.util.AbstractCollection<E>

java.util.AbstractSet<E>

java.util.TreeSet<Coordinate>

uk.ac.roslin.ensembl.model.CoordinateSet

All Implemented Interfaces:

Serializable, Cloneable, Iterable<Coordinate>, Collection<Coordinate>, NavigableSet<Coordinate>, Set<Coordinate>, SortedSet<Coordinate>

public class CoordinateSet
extends TreeSet<Coordinate>
implements Serializable

Extension of a TreeSet for holding COordinates ordered using their Comparator which orders Coordinate objects by the plus strand start, or the plus strand end if the starts are identical. Utility methods for this set take account of the DNA coordinate dogma that there is no base 0 (ZERO) (i.e. ... -3,-2,-1,+1,+2,+3...).

See Also:

Serialized Form

Constructor Summary

Constructors

Constructor and Description
CoordinateSet() Public Constructor for a new Empty instance.

Method Summary

Methods

Modifier and Type	Method and Description
Boolean	containsCoordinateWithoutGaps(Coordinate test) Returns whether a test Coordinate is contained in this CoordinateSet range WITHOUT any gaps.
Integer	getEnd() Returns the very last position of the last Coordinate in this CoordinateSet.
CoordinateSet	getGaps() Returns a CoordinateSet containing Coordinates for all of the gaps in this CoordinateSet.
Integer	getLength() Returns the length of the extent/range of this CoordinateSet (accounting for any span of the absent ZERO).
Coordinate	getRange() Returns a Coordinate representing the extent or range of this CoordinateSet
Integer	getStart() Returns the very first position of the first Coordinate in this CoordinateSet.
CoordinateSet	getUncoveredRegions(Coordinate test) Returns the CoordinateSet (ordered set of Coordinates) that define regions of the test Coordinate not represented (covered) in this CoordinateSet.

Methods inherited from class java.util.TreeSet

add, addAll, ceiling, clear, clone, comparator, contains, descendingIterator, descendingSet, first, floor, headSet, headSet, higher, isEmpty, iterator, last, lower, pollFirst, pollLast, remove, size, subSet, subSet, tailSet, tailSet

Methods inherited from class java.util.AbstractSet

equals, hashCode, removeAll

Methods inherited from class java.util.AbstractCollection

containsAll, retainAll, toArray, toArray, toString

Methods inherited from class java.lang.Object

finalize, getClass, notify, notifyAll, wait, wait, wait

Methods inherited from interface java.util.Set

containsAll, equals, hashCode, removeAll, retainAll, toArray, toArray

Constructor Detail

CoordinateSet

public CoordinateSet()

Public Constructor for a new Empty instance.

Method Detail

getStart

public Integer getStart()

Returns the very first position of the first Coordinate in this CoordinateSet.

Returns:

Integer

getEnd

public Integer getEnd()

Returns the very last position of the last Coordinate in this CoordinateSet.

Returns:

Integer

getRange

public Coordinate getRange()

Returns a Coordinate representing the extent or range of this CoordinateSet

Returns:

Coordinate extent

getLength

public Integer getLength()

Returns the length of the extent/range of this CoordinateSet (accounting for any span of the absent ZERO).

Returns:

Integer length

getGaps

public CoordinateSet getGaps()

Returns a CoordinateSet containing Coordinates for all of the gaps in this CoordinateSet.

Returns:

CoordinateSet of gap Coordinates

containsCoordinateWithoutGaps

public Boolean containsCoordinateWithoutGaps(Coordinate test)

Returns whether a test Coordinate is contained in this CoordinateSet range WITHOUT any gaps.

Parameters:

test -

Returns:

Boolean

getUncoveredRegions

public CoordinateSet getUncoveredRegions(Coordinate test)

Returns the CoordinateSet (ordered set of Coordinates) that define regions of the test Coordinate not represented (covered) in this CoordinateSet. Hopefully this handles the horror of test ranges spanning the non-existent zero point!

Parameters:

test -

Returns:

CoordinateSet