Package org.snpeff.genBank
Class GenBank
java.lang.Object
org.snpeff.genBank.Features
org.snpeff.genBank.GenBank
A class representing the same data as a GenBank file (a 'GB' file)
References:
http://www.insdc.org/documents/feature-table
http://www.ncbi.nlm.nih.gov/Sitemap/samplerecord
- Author:
- pablocingolani
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Field Summary
FieldsFields inherited from class org.snpeff.genBank.Features
COMPLEMENT, debug, JOIN, MAX_LEN_TO_SHOW, ORDER
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Constructor Summary
ConstructorsConstructorDescriptionCreate a Genbank record from a 'GB' fileGenBank
(LineFileIterator lineFileIterator) -
Method Summary
Modifier and TypeMethodDescriptionprotected boolean
isNewFeature
(String line) Has this line a new feature?protected void
parseFieldLine
(String name, String valueOri, int fieldLineNum, int fileLineNum) Parse a feature linevoid
readFile()
Load and parse the contents of a data fileMethods inherited from class org.snpeff.genBank.Features
getAccession, getDate, getDefinition, getDivision, getFeatures, getKeywords, getLocusName, getMoleculeType, getOrganism, getReferences, getSequence, getSequenceLength, getShape, getSource, getVersion, isEmpty, iterator, open, parseFeatures, toString
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
Methods inherited from interface java.lang.Iterable
forEach, spliterator
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Field Details
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FEATURE_NAME_FIELD_LEN
public static final int FEATURE_NAME_FIELD_LEN- See Also:
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Constructor Details
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GenBank
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GenBank
Create a Genbank record from a 'GB' file
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Method Details
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isNewFeature
Has this line a new feature?- Specified by:
isNewFeature
in classFeatures
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parseFieldLine
Parse a feature line -
readFile
public void readFile()Load and parse the contents of a data file
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