Inheritance diagram for umms.core.annotation.CompoundInterval:

Collaboration diagram for umms.core.annotation.CompoundInterval:

Public Member Functions
	CompoundInterval ()

	CompoundInterval (int start, int end)

	CompoundInterval (CompoundInterval other)

int	getStart ()

int	getEnd ()

int	numBlocks ()

int	length ()

int	getSpan ()

int	getCoordinateAtPosition (int positionInInterval)

int	getPositionAtCoordinate (int coordinateInReference)

void	setStart (int start)

void	setEnd (int end)

void	addInterval (SingleInterval newInterval)

void	addInterval (int start, int end)

void	shift (int delta)

void	moveToCoordinate (int coordinateInReference)

boolean	containsExactInterval (SingleInterval i)

boolean	containsInterval (SingleInterval i)

boolean	contains (CompoundInterval other)

boolean	overlaps (CompoundInterval other)

boolean	overlaps (CompoundInterval other, int buffer, boolean ignoreBlocks)

boolean	overlaps (CompoundInterval other, boolean ignoreBlocks)

boolean	overlaps (CompoundInterval other, int buffer)

boolean	overlaps (SingleInterval interval)

boolean	overlaps (SingleInterval interval, int buffer)

void	removeInterval (SingleInterval i)

CompoundInterval	intersect (CompoundInterval other)

CompoundInterval	union (CompoundInterval other)

CompoundInterval	complement ()

CompoundInterval	complement (int start, int end)

CompoundInterval	minus (CompoundInterval other)

final SortedSet< SingleInterval >	getBlocks ()

boolean	equals (CompoundInterval other)

int	compareTo (CompoundInterval other)

String	toString ()

Detailed Description

Author: engreitz This class contains multiple non-overlapping intervals on an arbitrary integer coordinate space. Intervals are stored using red-black trees so O(log n) performance is guaranteed.

Constructor & Destructor Documentation

umms.core.annotation.CompoundInterval.CompoundInterval ( )

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umms.core.annotation.CompoundInterval.CompoundInterval	(	int	start,
		int	end
	)

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umms.core.annotation.CompoundInterval.CompoundInterval ( CompoundInterval other )

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Member Function Documentation

void umms.core.annotation.CompoundInterval.addInterval ( SingleInterval newInterval )

Adds an interval, updating the compound interval to reflect the intersection of its previous state and the new interval.

Author: engreitz

Parameters

newInterval

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void umms.core.annotation.CompoundInterval.addInterval	(	int	start,
		int	end
	)

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int umms.core.annotation.CompoundInterval.compareTo ( CompoundInterval other )

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CompoundInterval umms.core.annotation.CompoundInterval.complement ( )

Returns: a new CompoundInterval containing the gaps between the blocks in this interval

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CompoundInterval umms.core.annotation.CompoundInterval.complement	(	int	start,
		int	end
	)

Returns: complement of this CompoundInterval using the provided bounds

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boolean umms.core.annotation.CompoundInterval.contains ( CompoundInterval other )

Parameters

other

Returns: returns true if all blocks in "other" are contained in blocks of this object

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boolean umms.core.annotation.CompoundInterval.containsExactInterval ( SingleInterval i )

Parameters

i

Returns: true if an interval with these exact boundaries is present in the CompoundInterval

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boolean umms.core.annotation.CompoundInterval.containsInterval ( SingleInterval i )

Parameters

i

Returns: true if i is entirely contained within a block (i can be smaller than the block)

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boolean umms.core.annotation.CompoundInterval.equals ( CompoundInterval other )

Parameters

other

Returns: true if all contained intervals are equal

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final SortedSet<SingleInterval> umms.core.annotation.CompoundInterval.getBlocks ( )

Returns: individual SingleIntervals. should not be modified

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int umms.core.annotation.CompoundInterval.getCoordinateAtPosition ( int positionInInterval )

Parameters

positionInInterval 0-based position in the compound interval

Returns: reference coordinate at the given interval position. e.g. for positionInInterval=0, returns getStart()

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int umms.core.annotation.CompoundInterval.getEnd ( )

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int umms.core.annotation.CompoundInterval.getPositionAtCoordinate ( int coordinateInReference )

Parameters

coordinateInReference

Returns: 0-based interval position at given reference coordinate

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int umms.core.annotation.CompoundInterval.getSpan ( )

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int umms.core.annotation.CompoundInterval.getStart ( )

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CompoundInterval umms.core.annotation.CompoundInterval.intersect ( CompoundInterval other )

Parameters

other

Returns: new CompoundInterval containing intersections of the blocks of the two objects

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int umms.core.annotation.CompoundInterval.length ( )

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CompoundInterval umms.core.annotation.CompoundInterval.minus ( CompoundInterval other )

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void umms.core.annotation.CompoundInterval.moveToCoordinate ( int coordinateInReference )

Move an annotation, preserving the relationships between its blocks, to a new coordinate.

Parameters

coordinateInReference

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int umms.core.annotation.CompoundInterval.numBlocks ( )

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boolean umms.core.annotation.CompoundInterval.overlaps ( CompoundInterval other )

Parameters

other

Returns: returns true if any block in "other" overlaps with any block of this object

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boolean umms.core.annotation.CompoundInterval.overlaps	(	CompoundInterval	other,
		int	buffer,
		boolean	ignoreBlocks
	)

Parameters

other
ignoreBlocks	if true, then overlap will consider only the start and end boundaries, ignoring blocks

Returns: true if the two intervals overlap

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boolean umms.core.annotation.CompoundInterval.overlaps	(	CompoundInterval	other,
		boolean	ignoreBlocks
	)

Parameters

other
ignoreBlocks

Returns: true if the boundaries of the intervals overlap

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boolean umms.core.annotation.CompoundInterval.overlaps	(	CompoundInterval	other,
		int	buffer
	)

Parameters

other
buffer

Returns: true if any of the blocks come within the buffer distance of each other

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boolean umms.core.annotation.CompoundInterval.overlaps ( SingleInterval interval )

Parameters

interval

Returns: returns true if "interval" overlaps with any block of this object

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boolean umms.core.annotation.CompoundInterval.overlaps	(	SingleInterval	interval,
		int	buffer
	)

Parameters

interval
buffer

Returns: true if any block comes within the buffer distance from the given interval

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void umms.core.annotation.CompoundInterval.removeInterval ( SingleInterval i )

Remove an interval. Throws exception if the interval does not exist - so check first.

Parameters

i

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void umms.core.annotation.CompoundInterval.setEnd ( int end )

Extends or trims the end coordinate. If trimming, removes blocks that fall after the new end coordinate. If expanding, extends the last block to the new end coordinate.

Parameters

end	new end coordinate

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void umms.core.annotation.CompoundInterval.setStart ( int start )

Extends or trims the start coordinate. If trimming, removes any blocks that fall before the new start position and truncates the block that overlaps the start position, if it exists. If expanding, extends the first block to the new start position.

Parameters

start new start coordinate

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