Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryFeatures
java.lang.Object
org.snpeff.snpEffect.factory.SnpEffPredictorFactory
org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
- Direct Known Subclasses:
SnpEffPredictorFactoryEmbl
,SnpEffPredictorFactoryGenBank
This class creates a SnpEffectPredictor from a 'features' file.
This includes derived formats as GenBank and Embl.
References:
http://www.ebi.ac.uk/embl/Documentation/User_manual/printable.html
http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
- Author:
- pcingola
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Field Summary
FieldsFields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprotected void
addFeatures
(Features features) Add all featurescreate()
protected String
Try to get geneIDsprotected String
Get gene name from featureMethods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
add, add, add, add, add, add, addMarker, addSequences, adjustChromosomes, adjustTranscripts, beforeExonSequences, codingFromCds, collapseZeroLenIntrons, createRandSequences, deleteRedundant, exonsFromCds, exonsFromCds, findGene, findGene, findMarker, findTranscript, findTranscript, getOrCreateChromosome, parsePosition, readExonSequences, replaceTranscript, setCircularCorrectLargeGap, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Field Details
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OFFSET
public static final int OFFSET- See Also:
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Constructor Details
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SnpEffPredictorFactoryFeatures
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Method Details
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addFeatures
Add all features -
create
- Specified by:
create
in classSnpEffPredictorFactory
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geneId
Try to get geneIDs -
geneName
Get gene name from feature -
getProteinByTrId
- Overrides:
getProteinByTrId
in classSnpEffPredictorFactory
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