Returns a merged Region representing this plus an additional Block.

The new Block is merged into this Region as in the Region.union method.

If this and the new Block have incompatible Orientations or are on different chromosomes, an exception is thrown.

Returns a list of the Blocks of this Region.

Regardless of Orientation, the returned list is in sorted order by chromosome coordinates.

Returns the position in chromosome coordinates corresponding to a relative position along this Region.

The requested relative position counts with respect to the "beginning" or "5-prime end" of this Region. It counts along the Blocks only, ignoring intervening areas ("introns").

For example, if this Region has Orientation Plus, the relative position zero would map to the start position in chromosome coordinates by this method, and the relative position Region.size minus one would map to the last position (the end position minus one) in chromosome coordinates. If this Region has Orientation Minus, position zero would map to the last position of the Region (the end position minus one) by this method, and Region.size minus one would map to the start position.

This Region must have Orientation Plus or Minus. The requested relative position must be between zero (inclusive) and Region.size (exclusive). Otherwise, an exception is thrown.

Returns a boolean value representing whether this Region contains another Region.

In order to contain the other, the two Regions must be on the same chromosome, have compatible Orientations, and every block of the other Region must be fully contained in the span of a block of this Region.

Returns the zero-based end position of this region.

Regardless of Orientation, this one plus the largest (rightmost) position included in the region span in chromosome coordinates. That is to say, the end position is exclusive. (All coordinate intervals are half-open. All genomic positions are zero-based.)

Returns a Region representing the intersection of this with another Region.

If the two Regions overlap (Region.overlaps), a Region is returned whose blocks are the disjoint sections of overlap between the blocks of the two original Regions, and whose Orientation is the consensus (Orientation.consensus) of those of the two original Regions. If the two Regions do not overlap, Empty is returned.

Returns a boolean value representing whether this Region is empty.

The only possible way for a region to be empty (have no blocks) is for it to be equal to Empty.

Returns a Region representing this minus the overlap with another Region.

If the two Regions overlap (Region.overlaps), a Region is returned whose blocks are the sections of this Region's blocks that are not part of the overlap. Otherwise, this is returned. In either case, the returned Region has the same Orientation as this Region.

Returns the number of Blocks in this Region.

Empty has zero Blocks.

Returns a boolean value representing whether this Region overlaps another Region.

In order to overlap, the two Regions must be on the same chromosome, have compatible Orientations, and have some pair of respective Blocks with overlapping spans.

Returns a boolean value representing whether this Region overlaps another Region and their introns are compatible.

That is, no INTERNAL block boundary for one of the Regions can fall strictly within a Block of the other Region.

Returns the position relative to this Region accounting for splicing and Orientation.

The returned position counts with respect to the "beginning" or "5-prime end" of this Region. It counts along the Blocks only, ignoring intervening areas ("introns").

For example, if this Region has Orientation Plus, the start position would map to position zero by this method, and the last position (the end position minus one) would map to position Region.size minus one. If this Region has Orientation Minus, the last position of the Region (the end position minus one) would map to position zero by this method, and the start position would map to position Region.size minus one.

This Region must have Orientation Plus or Minus. Otherwise an exception is thrown.

If the requested chromosome position does not lie within one of the Blocks of this Region, None is returned.

Returns the zero-based start position of this region.

Regardless of Orientation, this is the smallest (leftmost) position of the region in chromosome coordinates. The start position is inclusive. (All coordinate intervals are half open. All genomic positions are zero-based.)

Returns a Region representing the union of this with another Region.

If the two Regions are on the same chromosome and have compatible Orientations, the blocks will be merged and assigned the consensus Orientation (Orientation.consensus) for the final returned Region.

If this or the other Region is Empty, the non-empty Region will be returned, or if both are Empty, Empty will be returned.

Otherwise, an exception is thrown.

Returns a boolean value representing whether this Region contains another Region and their introns are compatible.

That is, no INTERNAL block boundary for one of the Regions can fall strictly within a Block of the other Region.

Returns a list of Blocks representing the introns of this Region.

The returned list is in order from left to right. Each Block in the returned list is the span of a gap between two Blocks of this Region. The returned Blocks have the same Orientation as this Region. The start position of each returned Block is equal to the end position (exclusive) of the previous adjacent Block in this Region. The end position of each returned Block (exclusive) is equal to the start position of the following adjacent Block in this Region.

If this Region is empty or has only one Block, Nil is returned.

Returns a boolean value representing whether the span of this Region overlaps the span of another Region. That is, intron/exon structure is ignored and only the full span (from start to end) of the Regions are considered. Orientations must be compatible.

Returns the sum of the lengths of the Blocks of this Region.

Block length is the end position minus the start position, where, as always, start position is inclusive and end position is exclusive. Therefore, size is the number of individual genomic positions included in the Region.

The size of Empty is zero.

Returns a Region resulting from trimming back the start and end positions of this Region.

This Region is truncated to the new start and end positions in chromosome coordinates. This may mean some Blocks are removed altogether, some are shortened, and some are left intact. If the new start or end position is outside the span of this Region, that parameter will not affect the returned Region.

As always, start positions are inclusive and end positions are exclusive.