Package org.snpeff.genBank
Class GenBank
- java.lang.Object
-
- org.snpeff.genBank.Features
-
- org.snpeff.genBank.GenBank
-
-
Field Summary
Fields Modifier and Type Field Description static int
FEATURE_NAME_FIELD_LEN
-
Fields inherited from class org.snpeff.genBank.Features
COMPLEMENT, debug, JOIN, MAX_LEN_TO_SHOW, ORDER
-
-
Constructor Summary
Constructors Constructor Description GenBank(java.lang.String fileName)
Create a Genbank record from a 'GB' fileGenBank(LineFileIterator lineFileIterator)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description protected boolean
isNewFeature(java.lang.String line)
Has this line a new feature?protected void
parseFieldLine(java.lang.String name, java.lang.String valueOri, int fieldLineNum, int fileLineNum)
Parse a feature linevoid
readFile()
Load and parse the contents of a data file-
Methods 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
-
-
-
-
Field Detail
-
FEATURE_NAME_FIELD_LEN
public static final int FEATURE_NAME_FIELD_LEN
- See Also:
- Constant Field Values
-
-
Constructor Detail
-
GenBank
public GenBank(LineFileIterator lineFileIterator)
-
GenBank
public GenBank(java.lang.String fileName)
Create a Genbank record from a 'GB' file
-
-
Method Detail
-
isNewFeature
protected boolean isNewFeature(java.lang.String line)
Has this line a new feature?- Specified by:
isNewFeature
in classFeatures
-
parseFieldLine
protected void parseFieldLine(java.lang.String name, java.lang.String valueOri, int fieldLineNum, int fileLineNum)
Parse a feature line
-
-