Package org.snpeff.snpEffect.factory
Class SnpEffPredictorFactoryFeatures
- java.lang.Object
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactory
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- org.snpeff.snpEffect.factory.SnpEffPredictorFactoryFeatures
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- 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
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Field Summary
Fields Modifier and Type Field Description static int
OFFSET
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Fields inherited from class org.snpeff.snpEffect.factory.SnpEffPredictorFactory
MARK, MIN_TOTAL_FRAME_COUNT
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Constructor Summary
Constructors Constructor Description SnpEffPredictorFactoryFeatures(Config config)
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected void
addFeatures(Features features)
Add all featuresSnpEffectPredictor
create()
protected java.lang.String
geneId(Feature f, int start, int end)
Try to get geneIDsprotected java.lang.String
geneName(Feature f, int start, int end)
Get gene name from featurejava.util.Map<java.lang.String,java.lang.String>
getProteinByTrId()
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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, setCreateRandSequences, setDebug, setFastaFile, setFileName, setRandom, setReadSequences, setStoreSequences, setVerbose, showChromoNamesDifferences
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Field Detail
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OFFSET
public static final int OFFSET
- See Also:
- Constant Field Values
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Constructor Detail
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SnpEffPredictorFactoryFeatures
public SnpEffPredictorFactoryFeatures(Config config)
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Method Detail
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addFeatures
protected void addFeatures(Features features)
Add all features
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create
public SnpEffectPredictor create()
- Specified by:
create
in classSnpEffPredictorFactory
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geneId
protected java.lang.String geneId(Feature f, int start, int end)
Try to get geneIDs
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geneName
protected java.lang.String geneName(Feature f, int start, int end)
Get gene name from feature
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getProteinByTrId
public java.util.Map<java.lang.String,java.lang.String> getProteinByTrId()
- Overrides:
getProteinByTrId
in classSnpEffPredictorFactory
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