Package org.snpeff.genBank
Class Feature
- java.lang.Object
-
- org.snpeff.genBank.Feature
-
- All Implemented Interfaces:
java.lang.Iterable<FeatureCoordinates>
public class Feature extends java.lang.Object implements java.lang.Iterable<FeatureCoordinates>
A feature in a GenBank or EMBL file- Author:
- pablocingolani
-
-
Nested Class Summary
Nested Classes Modifier and Type Class Description static class
Feature.Type
-
Field Summary
Fields Modifier and Type Field Description static java.lang.String
COMPLEMENT_STRING
-
Constructor Summary
Constructors Constructor Description Feature(Feature.Type type, java.lang.String def)
Feature(Feature.Type type, java.lang.String def, int start, int end, boolean complement, int lineNum)
-
Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
add(FeatureCoordinates fc)
java.lang.String
get(java.lang.String name)
Get a qualifier by namejava.lang.String
getAasequence()
Get translated amino acid sequenceint
getEnd()
java.lang.String
getGeneId()
java.lang.String
getGeneName()
Get gene name from featureint
getStart()
java.lang.String
getTranscriptId()
Create a transcript ID based on a featureFeature.Type
getType()
boolean
hasMultipleCoordinates()
boolean
isComplement()
java.util.Iterator<FeatureCoordinates>
iterator()
java.lang.String
toString()
-
-
-
Field Detail
-
COMPLEMENT_STRING
public static final java.lang.String COMPLEMENT_STRING
- See Also:
- Constant Field Values
-
-
Constructor Detail
-
Feature
public Feature(Feature.Type type, java.lang.String def)
-
Feature
public Feature(Feature.Type type, java.lang.String def, int start, int end, boolean complement, int lineNum)
-
-
Method Detail
-
add
public void add(FeatureCoordinates fc)
-
get
public java.lang.String get(java.lang.String name)
Get a qualifier by name
-
getAasequence
public java.lang.String getAasequence()
Get translated amino acid sequence
-
getEnd
public int getEnd()
-
getGeneId
public java.lang.String getGeneId()
-
getGeneName
public java.lang.String getGeneName()
Get gene name from feature
-
getStart
public int getStart()
-
getTranscriptId
public java.lang.String getTranscriptId()
Create a transcript ID based on a feature
-
getType
public Feature.Type getType()
-
hasMultipleCoordinates
public boolean hasMultipleCoordinates()
-
isComplement
public boolean isComplement()
-
iterator
public java.util.Iterator<FeatureCoordinates> iterator()
- Specified by:
iterator
in interfacejava.lang.Iterable<FeatureCoordinates>
-
toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
-
-