Package org.snpeff.genBank
Class Features
- java.lang.Object
-
- org.snpeff.genBank.Features
-
-
Field Summary
Fields Modifier and Type Field Description static java.lang.String
COMPLEMENT
static boolean
debug
static java.lang.String
JOIN
static int
MAX_LEN_TO_SHOW
static java.lang.String
ORDER
-
Constructor Summary
Constructors Constructor Description Features(java.lang.String fileName)
Create features from a fileFeatures(LineFileIterator lineFileIterator)
Create features from a file
-
Method Summary
All Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description java.lang.String
getAccession()
java.lang.String
getDate()
java.lang.String
getDefinition()
java.lang.String
getDivision()
java.util.ArrayList<Feature>
getFeatures()
java.lang.String
getKeywords()
java.lang.String
getLocusName()
java.lang.String
getMoleculeType()
java.lang.String
getOrganism()
java.util.ArrayList<java.lang.StringBuffer>
getReferences()
java.lang.String
getSequence()
int
getSequenceLength()
java.lang.String
getShape()
java.lang.String
getSource()
java.lang.String
getVersion()
boolean
isEmpty()
protected abstract boolean
isNewFeature(java.lang.String line)
Is there a new feature in this line?java.util.Iterator<Feature>
iterator()
protected void
open(java.lang.String fileName)
Open a fileprotected void
parseFeatures()
Parse featuresprotected abstract void
readFile()
Load and parse the contents of a data file previously opened by 'open()' method.java.lang.String
toString()
-
-
-
Field Detail
-
debug
public static boolean debug
-
MAX_LEN_TO_SHOW
public static final int MAX_LEN_TO_SHOW
- See Also:
- Constant Field Values
-
COMPLEMENT
public static final java.lang.String COMPLEMENT
- See Also:
- Constant Field Values
-
JOIN
public static final java.lang.String JOIN
- See Also:
- Constant Field Values
-
ORDER
public static final java.lang.String ORDER
- See Also:
- Constant Field Values
-
-
Constructor Detail
-
Features
public Features(LineFileIterator lineFileIterator)
Create features from a file
-
Features
public Features(java.lang.String fileName)
Create features from a file
-
-
Method Detail
-
getAccession
public java.lang.String getAccession()
-
getDate
public java.lang.String getDate()
-
getDefinition
public java.lang.String getDefinition()
-
getDivision
public java.lang.String getDivision()
-
getFeatures
public java.util.ArrayList<Feature> getFeatures()
-
getKeywords
public java.lang.String getKeywords()
-
getLocusName
public java.lang.String getLocusName()
-
getMoleculeType
public java.lang.String getMoleculeType()
-
getOrganism
public java.lang.String getOrganism()
-
getReferences
public java.util.ArrayList<java.lang.StringBuffer> getReferences()
-
getSequence
public java.lang.String getSequence()
-
getSequenceLength
public int getSequenceLength()
-
getShape
public java.lang.String getShape()
-
getSource
public java.lang.String getSource()
-
getVersion
public java.lang.String getVersion()
-
isEmpty
public boolean isEmpty()
-
isNewFeature
protected abstract boolean isNewFeature(java.lang.String line)
Is there a new feature in this line?
-
iterator
public java.util.Iterator<Feature> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<Feature>
-
open
protected void open(java.lang.String fileName)
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
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
-
-