public final class Chromosome extends Object implements Serializable
TranscriptModel
class to make a list of gene models that will be used to annotate chromosomal variants. We
use an IntervalArray
to store all of the TranscriptModel
objects that belong to this Chromosome and
to search for all transcripts that overlap with any given variant. Note that the IntervalTree class has functionality
also to find the neighbors (5' and 3') of the closest gene in order to find the right and left genes of intergenic
variants and to find the correct gene in the cases of complex regions of the chromosome with one gene located in the
intron of the next or with overlapping genes.
Note that the GenomeInterval
objects in the interval tree are defined by the transcription start and stop
sites of the isoform.Constructor and Description |
---|
Chromosome(ReferenceDictionary refDict,
int chrID,
IntervalArray<TranscriptModel> tmIntervalTree)
Initialize object.
|
Modifier and Type | Method and Description |
---|---|
int |
getChrID() |
String |
getChromosomeName() |
int |
getNumberOfGenes() |
ReferenceDictionary |
getRefDict() |
IntervalArray<TranscriptModel> |
getTMIntervalTree() |
public Chromosome(ReferenceDictionary refDict, int chrID, IntervalArray<TranscriptModel> tmIntervalTree)
refDict
- the ReferenceDictionary
to usechrID
- the chromosometmIntervalTree
- An interval tree with all transcripts on this chromosome.public ReferenceDictionary getRefDict()
public int getChrID()
public String getChromosomeName()
"chr2"
public int getNumberOfGenes()
public IntervalArray<TranscriptModel> getTMIntervalTree()
IntervalArray
of the chromosome.Copyright © 2016. All rights reserved.