# Uses of Class
org.snpeff.interval.GffMarker

Packages that use GffMarker
Package
Description
org.snpeff.fileIterator
org.snpeff.interval
org.snpeff.snpEffect.factory

## Uses of GffMarker in org.snpeff.fileIterator

Methods in org.snpeff.fileIterator that return GffMarker
Modifier and Type
Method
Description
`protected GffMarker`
Gff3FileIterator.`readNext()`

## Uses of GffMarker in org.snpeff.interval

Subclasses of GffMarker in org.snpeff.interval
Modifier and Type
Class
Description
`class`
`Gtf2Marker`
An interval intended as a mark

## Uses of GffMarker in org.snpeff.snpEffect.factory

Methods in org.snpeff.snpEffect.factory with parameters of type GffMarker
Modifier and Type
Method
Description
`protected Exon`
SnpEffPredictorFactoryGff.`addExon(Transcript tr, GffMarker gffMarker, String exonId)`
Create a new exon
`protected List<Exon>`
SnpEffPredictorFactoryGff.`addExons(GffMarker gffMarker)`
Create and add a new exon
`protected Gene`
SnpEffPredictorFactoryGff.`addGene(GffMarker gffMarker)`
`protected Gene`
SnpEffPredictorFactoryGff.`addGene(GffMarker gffMarker, boolean findNextGeneId)`
Create and add a gene based on GffMarker
`protected IntergenicConserved`
SnpEffPredictorFactoryGff.`addIntergenicConserved(GffMarker gffMarker)`
Add an intergenic conserved region
`protected boolean`
SnpEffPredictorFactoryGff.`addInterval(GffMarker gffMarker)`
Add interval based on GffMarker data
`protected IntronConserved`
SnpEffPredictorFactoryGff.`addIntronConserved(GffMarker gffMarker)`
Add an intron conserved region
`protected List<Utr3prime>`
SnpEffPredictorFactoryGff.`addUtr3(GffMarker gffMarker)`
Create new UTR3primes
`protected List<Utr5prime>`
SnpEffPredictorFactoryGff.`addUtr5(GffMarker gffMarker)`
Create UTR5primes
`protected Exon`
SnpEffPredictorFactoryGff.`findOrCreateExon(String parentId, GffMarker gffMarker)`
Find an exon for a given parentId
`protected Gene`
SnpEffPredictorFactoryGff.`findOrCreateGene(GffMarker gffMarker)`
Find or create a gene based on GffMarker
`protected Transcript`
SnpEffPredictorFactoryGff.`findOrCreateTranscript(GffMarker gffMarker)`
Create and add a transcript based on GffMarker