Package org.snpeff.genBank
Class Features
java.lang.Object
org.snpeff.genBank.Features
A class representing a set of features
References: http://www.ebi.ac.uk/embl/Documentation/FT_definitions/feature_table.html
- Author:
- pablocingolani
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Field Summary
Fields -
Constructor Summary
ConstructorsConstructorDescriptionCreate features from a fileFeatures
(LineFileIterator lineFileIterator) Create features from a file -
Method Summary
Modifier and TypeMethodDescriptiongetDate()
int
getShape()
boolean
isEmpty()
protected abstract boolean
isNewFeature
(String line) Is there a new feature in this line?iterator()
protected void
Open a fileprotected void
Parse featuresprotected abstract void
readFile()
Load and parse the contents of a data file previously opened by 'open()' method.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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debug
public static boolean debug -
MAX_LEN_TO_SHOW
public static final int MAX_LEN_TO_SHOW- See Also:
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COMPLEMENT
- See Also:
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JOIN
- See Also:
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ORDER
- See Also:
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Constructor Details
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Features
Create features from a file -
Features
Create features from a file
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Method Details
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getAccession
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getDate
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getDefinition
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getDivision
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getFeatures
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getKeywords
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getLocusName
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getMoleculeType
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getOrganism
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getReferences
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getSequence
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getSequenceLength
public int getSequenceLength() -
getShape
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getSource
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getVersion
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isEmpty
public boolean isEmpty() -
isNewFeature
Is there a new feature in this line? -
iterator
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open
Open a file -
parseFeatures
protected void parseFeatures()Parse features -
readFile
protected abstract void readFile()Load and parse the contents of a data file previously opened by 'open()' method. -
toString
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