org.snpeff.snpEffect.factory.SnpEffPredictorFactory

org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures

Direct Known Subclasses:: SnpEffPredictorFactoryEmbl, SnpEffPredictorFactoryGenBank

public abstract class SnpEffPredictorFactoryFeatures extends SnpEffPredictorFactory

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

Field Summary

Fields

Modifier and Type

Field

Description

static final int

OFFSET

Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
Constructor Summary

Constructors

Constructor

Description

SnpEffPredictorFactoryFeatures(Config config)
Method Summary

Modifier and Type

Method

Description

protected void

addFeatures(Features features)

Add all features

SnpEffectPredictor

create()

protected String

geneId(Feature f, int start, int end)

Try to get geneIDs

protected String

geneName(Feature f, int start, int end)

Get gene name from feature

Map<String,String>

getProteinByTrId()

Methods 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

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

Field Details
- OFFSET
  
  public static final int OFFSET
  See Also:
  
  Constant Field Values
Constructor Details
- SnpEffPredictorFactoryFeatures
  
  public SnpEffPredictorFactoryFeatures(Config config)
Method Details
- addFeatures
  
  protected void addFeatures(Features features)
  
  Add all features
- create
  
  public SnpEffectPredictor create()
  
  Specified by:
  
  create in class SnpEffPredictorFactory
- geneId
  
  protected String geneId(Feature f, int start, int end)
  
  Try to get geneIDs
- geneName
  
  protected String geneName(Feature f, int start, int end)
  
  Get gene name from feature
- getProteinByTrId
  
  public Map<String,String> getProteinByTrId()
  
  Overrides:
  
  getProteinByTrId in class SnpEffPredictorFactory

Class SnpEffPredictorFactoryFeatures

Field Summary

Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory

Constructor Summary

Method Summary

Methods inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory

Methods inherited from class java.lang.Object

Field Details

OFFSET

Constructor Details

SnpEffPredictorFactoryFeatures

Method Details

addFeatures

create

geneId

geneName

getProteinByTrId