# Uses of Class
org.snpeff.snpEffect.factory.SnpEffPredictorFactory

Packages that use SnpEffPredictorFactory
Package
Description
org.snpeff.snpEffect.factory

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

Subclasses of SnpEffPredictorFactory in org.snpeff.snpEffect.factory
Modifier and Type
Class
Description
`class`
`SnpEffPredictorFactoryEmbl`
This class creates a SnpEffectPredictor from an Embl file.
`class`
`SnpEffPredictorFactoryFeatures`
This class creates a SnpEffectPredictor from a 'features' file.
`class`
`SnpEffPredictorFactoryGenBank`
This class creates a SnpEffectPredictor from a GenBank file.
`class`
`SnpEffPredictorFactoryGenesFile`
This class creates a SnpEffectPredictor from a file (or a set of files) and a configuration The files used are: - genes.txt : Biomart query from Ensembl (see scripts/genes_dataset.xml) - Fasta files: One per chromosome (as described in the config file)
`class`
`SnpEffPredictorFactoryGff`
This class creates a SnpEffectPredictor from a GFF file.
`class`
`SnpEffPredictorFactoryGff2`
This class creates a SnpEffectPredictor from a GFF2 file.
`class`
`SnpEffPredictorFactoryGff3`
This class creates a SnpEffectPredictor from a GFF3 file References: - http://www.sequenceontology.org/gff3.shtml - http://gmod.org/wiki/GFF3 - http://www.eu-sol.net/science/bioinformatics/standards-documents/gff3-format-description
`class`
`SnpEffPredictorFactoryGtf22`
This class creates a SnpEffectPredictor from a GTF 2.2 file References: http://mblab.wustl.edu/GTF22.html
`class`
`SnpEffPredictorFactoryKnownGene`
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser Fields in this table Field Example SQL type Info Description ----- ------- -------- ---- ----------- name uc001aaa.3 varchar(255) values Name of gene chrom chr1 varchar(255) values Reference sequence chromosome or scaffold strand + char(1) values + or - for strand txStart 11873 int(10) unsigned range Transcription start position txEnd 14409 int(10) unsigned range Transcription end position cdsStart 11873 int(10) unsigned range Coding region start cdsEnd 11873 int(10) unsigned range Coding region end exonCount 3 int(10) unsigned range Number of exons exonStarts 11873,12612,13220, longblob Exon start positions exonEnds 12227,12721,14409, longblob Exon end positions proteinID varchar(40) values UniProt display ID for Known Genes, UniProt accession or RefSeq protein ID for UCSC Genes alignID uc001aaa.3 varchar(255) values Unique identifier for each (known gene, alignment position) pair
`class`
`SnpEffPredictorFactoryRand`
This class creates a random set of chromosomes, genes, transcripts and exons
`class`
`SnpEffPredictorFactoryRefSeq`
This class creates a SnpEffectPredictor from a TXT file dumped using UCSC table browser RefSeq table schema: http://genome.ucsc.edu/cgi-bin/hgTables field example SQL type info description bin 585 smallint(5) range Indexing field to speed chromosome range queries.