de.charite.compbio.jannovar.impl.parse.gtfgff

Class FeatureRecord

java.lang.Object

de.charite.compbio.jannovar.impl.parse.gtfgff.FeatureRecord

All Implemented Interfaces:

Comparable<FeatureRecord>

public final class FeatureRecord
extends Object
implements Comparable<FeatureRecord>

Immutable class for describing a record from a GFF or GTF file. When comparing, features on the forward strand come before features on the reverse strand.

Author:

Manuel Holtgrewe

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	FeatureRecord.Strand Type for describing record strand

Constructor Summary

Constructors

Constructor and Description
FeatureRecord(String seqID, String source, String type, int begin, int end, String score, FeatureRecord.Strand strand, int phase, Map<String,String> attributes) Initialize the GFFRecord

Method Summary

Modifier and Type	Method and Description
int	compareTo(FeatureRecord o)
boolean	equals(Object obj)
com.google.common.collect.ImmutableMap<String,String>	getAttributes()
int	getBegin()
int	getEnd()
int	getPhase()
String	getScore()
String	getSeqID()
String	getSource()
FeatureRecord.Strand	getStrand()
String	getType()
int	hashCode()
void	setAttributes(com.google.common.collect.ImmutableMap<String,String> attributes)
String	toString()

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Constructor Detail

FeatureRecord

public FeatureRecord(String seqID,
                     String source,
                     String type,
                     int begin,
                     int end,
                     String score,
                     FeatureRecord.Strand strand,
                     int phase,
                     Map<String,String> attributes)

Initialize the GFFRecord

Method Detail

getAttributes

public com.google.common.collect.ImmutableMap<String,String> getAttributes()

setAttributes

public void setAttributes(com.google.common.collect.ImmutableMap<String,String> attributes)

getSeqID

public String getSeqID()

getSource

public String getSource()

getType

public String getType()

getBegin

public int getBegin()

getEnd

public int getEnd()

getScore

public String getScore()

getStrand

public FeatureRecord.Strand getStrand()

getPhase

public int getPhase()

toString

public String toString()

Overrides:

toString in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object obj)

Overrides:

equals in class Object

compareTo

public int compareTo(FeatureRecord o)

Specified by:

compareTo in interface Comparable<FeatureRecord>