Package htsjdk.tribble.gff

Class Gff3BaseData

java.lang.Object

htsjdk.tribble.gff.Gff3BaseData

All Implemented Interfaces:

Locatable

public class Gff3BaseData
extends Object
implements Locatable

Constructor Summary

Constructors

Constructor	Description
Gff3BaseData(String contig, String source, String type, int start, int end, Double score, Strand strand, int phase, Map<String,List<String>> attributes)

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object other)
List<String>	getAliases()
List<String>	getAttribute(String key)	get the values as List for the key, or an empty list if this key is not present
Map<String,List<String>>	getAttributes()
String	getContig()	Gets the contig name for the contig this is mapped to.
int	getEnd()
String	getId()
String	getName()
int	getPhase()
double	getScore()
String	getSource()
int	getStart()
Strand	getStrand()
String	getType()
Optional<String>	getUniqueAttribute(String key)	Most attributes in a GFF file are present just one time in a line, e.g.
boolean	hasAttribute(String key)	Returns true if this record contains an attribute for the specified key.
int	hashCode()

Methods inherited from class java.lang.Object

clone, finalize, getClass, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.util.Locatable

contains, contigsMatch, getLengthOnReference, overlaps, withinDistanceOf

Constructor Details

Gff3BaseData

public Gff3BaseData(String contig,
 String source,
 String type,
 int start,
 int end,
 Double score,
 Strand strand,
 int phase,
 Map<String,List<String>> attributes)

Method Details

equals

public boolean equals(Object other)

Overrides:

equals in class Object

hashCode

public int hashCode()

Overrides:

hashCode in class Object

getContig

public String getContig()

Description copied from interface: Locatable

Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.

Specified by:

getContig in interface Locatable

Returns:

name of the contig this is mapped to, potentially null

getSource

public String getSource()

getType

public String getType()

getStart

public int getStart()

Specified by:

getStart in interface Locatable

Returns:

1-based start position, undefined if getContig() == null

getEnd

public int getEnd()

Specified by:

getEnd in interface Locatable

Returns:

1-based closed-ended position, undefined if getContig() == null

getScore

public double getScore()

getStrand

public Strand getStrand()

getPhase

public int getPhase()

getAttributes

public Map<String,List<String>> getAttributes()

getAttribute

public List<String> getAttribute(String key)

get the values as List for the key, or an empty list if this key is not present

Parameters:

key - key whose presence in this map is to be tested

Returns:

the values as List, or an empty list if this key is not present

hasAttribute

public boolean hasAttribute(String key)

Returns true if this record contains an attribute for the specified key.

Parameters:

key - key whose presence in this map is to be tested

Returns:

true if this map contains an attribute for the specified key

getUniqueAttribute

public Optional<String> getUniqueAttribute(String key)

Most attributes in a GFF file are present just one time in a line, e.g. : gene_biotype, gene_name, etc ... This function returns an Optional.empty if the key is not present, an Optional.of(value) if there is only one value associated to the key, or it throws an IllegalArgumentException if there is more than one value.

Parameters:

key - key whose presence in the attributes is to be tested

Returns:

Optional<String> if this map contains zero or one attribute for the specified key

Throws:

IllegalArgumentException - if there is more than one value

getId

public String getId()

getName

public String getName()

getAliases

public List<String> getAliases()