SnpEffPredictorFactoryGenBank (SnpEff 5.4 API)

java.lang.Object

org.snpeff.snpEffect.factory.SnpEffPredictorFactory

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGenBank

public class SnpEffPredictorFactoryGenBank extends SnpEffPredictorFactoryFeatures

This class creates a SnpEffectPredictor from a GenBank file.

Author:: pcingola

Field Summary

Fields

Modifier and Type

Field

Description

static final String

EXTENSION_GENBANK

Fields inherited from class SnpEffPredictorFactoryFeatures
OFFSET

Fields inherited from class SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
Constructor Summary

Constructors

Constructor

Description

SnpEffPredictorFactoryGenBank(Config config)

SnpEffPredictorFactoryGenBank(Config config, String fileName)
Method Summary

Methods inherited from class SnpEffPredictorFactoryFeatures
addFeatures, create, geneId, geneName, getProteinByTrId

Methods inherited from class 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

Methods inherited from class Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Details
- EXTENSION_GENBANK
  public static final String EXTENSION_GENBANK
  
  See Also:
  
  Constant Field Values
Constructor Details
- SnpEffPredictorFactoryGenBank
  
  public SnpEffPredictorFactoryGenBank(Config config)
- SnpEffPredictorFactoryGenBank
  
  public SnpEffPredictorFactoryGenBank(Config config, String fileName)