Class: CGRange

CGRange

A CGRange contains a start and stop position (in base pair) on a sequence contig. Ranges are always in a clockise direction. The start is always less than the stop position with following exception. Since the genomes are circular, if the genome contains a single contig (i.e., Sequence.hasMultipleContigs is false) it's possibe for the range to loop around (i.e., that stop can be less than the start).

Ranges and Map Coordinates

Range start and stop positions are in relation to the contig the range is on. To get the positions in relation to the entire map, use mapStart and mapStop.

new CGRange(contig, start, stop)

CGRange.js, line 31

Create a CGRange

Name Type Description
contig Sequence

The contig that contains the range. The contig provides the contig length
start Number

The start position.
stop Number

The stop position.

Members

contigSequence

Get the sequence.

lengthNumber

Get the length of the range.

mapStartNumber

Get or set the range start using the entire map coordinates.

mapStopNumber

Get or set the range stop using the entire map coordinates.

middleNumber

Get the middle of the range.

sequenceSequence

Get the sequence.

startNumber

Get or set the range start. Start must be less than Stop unless the contig represents the entire map, in which case, wrapping is allowed. The value will be constrained between the 1 and the contig length.

stopNumber

Get or set the range stop. Stop must be greater than Start unless the contig represents the entire map, in which case, wrapping is allowed. The value will be constrained between the 1 and the contig length.

Methods

containsMapBp(position){Boolean}

CGRange.js, line 235

Return true if the position in inside the range using map coordinates.

Name Type Description
position Number

The position to check if it's in the range.
Returns:
Type Description
Boolean

copy(){Range}

CGRange.js, line 249

Returns a copy of the Range.

Returns:
Type Description
Range

getStartPlus(value){Number}

CGRange.js, line 190

Return the start of the range plus the value.

Name Type Description
value Number

Number to add.
Returns:
Type Description
Number

getStopPlus(value){Number}

CGRange.js, line 199

Return the stop of the range plus the value.

Name Type Description
value Number

Number to add.
Returns:
Type Description
Number

isMapLength(){Boolean}

CGRange.js, line 207

Return true if the range length is the same as the map sequence length

Returns:
Type Description
Boolean

isWrapped(){Boolean}

CGRange.js, line 226

Return true if the range wraps around the end of the contig (ie. the stop is less than the start position)

Returns:
Type Description
Boolean

mergeWithRange(range2){Range}

CGRange.js, line 273

Merge with the supplied range to give the biggest possible range. This may produce unexpected results of the ranges do not overlap. Both ranges must be on the same contig. If not, the CGRange calling this method will be returned.

Name Type Description
range2 Range

The range to merge with.
Returns:
Type Description
Range

normalize(value){Number}

CGRange.js, line 166

Convert the value to be between the 1 and the contig length. Values will be constrained to the contig unless the Map Sequence only contains a single contig, in which case, values bigger or smaller than the sequence length will be wrappeed around. For example, if sequence length is 1000 and value is 1200, a value of 200 will be returned.

Name Type Description
value Number

The number to normalize.
Returns:
Type Description
Number

overHalfMapLength(){Boolean}

CGRange.js, line 153

Return true if the range length is over half the length of the sequence length

Returns:
Type Description
Boolean

overlapsMapRange(range2){Boolwan}

CGRange.js, line 258

Returns true if the range overlaps with range2.

Name Type Description
range2 Range

The range with which to test overlap.
Returns:
Type Description
Boolwan