Package org.dishevelled.bio.feature.gff3

Class Gff3Record

java.lang.Object

org.dishevelled.bio.feature.gff3.Gff3Record

@Immutable
public final class Gff3Record
extends Object

GFF3 record.

Author:

Michael Heuer

Constructor Summary

Constructors

Constructor	Description
Gff3Record(String seqid, String source, String featureType, long start, long end, Double score, String strand, Integer phase, com.google.common.collect.ListMultimap<String,String> attributes)	Create a new GFF3 record.

Method Summary

Modifier and Type	Method	Description
boolean	equals(Object o)
com.google.common.collect.ListMultimap<String,String>	getAttributes()	Return the attributes for this GFF3 record.
long	getEnd()	Return the end for this GFF3 record in 0-based coordinate system, closed open range.
String	getFeatureType()	Return the feature type for this GFF3 record.
Integer	getPhase()	Return the phase for this GFF3 record, if any.
Double	getScore()	Return the score for this GFF3 record, if any.
String	getSeqid()	Return the seqid for this GFF3 record.
String	getSource()	Return the source for this GFF3 record.
long	getStart()	Return the start for this GFF3 record in 0-based coordinate system, closed open range.
String	getStrand()	Return the strand for this GFF3 record.
int	hashCode()
(package private) static boolean	isMissingValue(String value)	Return true if the specified value is the missing value (".").
(package private) static com.google.common.collect.ListMultimap<String,String>	parseAttributes(String attributes)	Parse the GFF3 attributes column into a list multimap of <String, String> entries.
com.google.common.collect.Range<Long>	toRange()	Return this GFF3 record as a 0-based coordinate system, closed open range.
String	toString()
static Gff3Record	valueOf(String value)	Return a new GFF3 record parsed from the specified value.
(package private) static String	writeAttributes(com.google.common.collect.ListMultimap<String,String> attributes)	Write the list multimap of <String, String> entries as GFF3 attributes column format.

Methods inherited from class java.lang.Object

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

Constructor Detail

Gff3Record

public Gff3Record(String seqid,
                  String source,
                  String featureType,
                  long start,
                  long end,
                  Double score,
                  String strand,
                  Integer phase,
                  com.google.common.collect.ListMultimap<String,String> attributes)

Create a new GFF3 record.

Parameters:

seqid - seqid, must not be null

source - source, must not be null

featureType - feature type, must not be null

start - start, must be at least 0L

end - end, must be at least zero, and greater than or equal to start

score - score

strand - strand, if present must be -, +, or ?

phase - phase, if present must be 0, 1, or 2

attributes - attributes, must not be null

Method Detail

getSeqid

public String getSeqid()

Return the seqid for this GFF3 record.

Returns:

the seqid for this GFF3 record

getSource

public String getSource()

Return the source for this GFF3 record.

Returns:

the source for this GFF3 record

getFeatureType

public String getFeatureType()

Return the feature type for this GFF3 record.

Returns:

the feature type for this GFF3 record

getStart

public long getStart()

Return the start for this GFF3 record in 0-based coordinate system, closed open range.

Returns:

the start for this GFF3 record in 0-based coordinate system, closed open range

getEnd

public long getEnd()

Return the end for this GFF3 record in 0-based coordinate system, closed open range.

Returns:

the end for this GFF3 record in 0-based coordinate system, closed open range

getScore

public Double getScore()

Return the score for this GFF3 record, if any.

Returns:

the score for this GFF3 record, if any

getStrand

public String getStrand()

Return the strand for this GFF3 record.

Returns:

the strand for this GFF3 record

getPhase

public Integer getPhase()

Return the phase for this GFF3 record, if any.

Returns:

the phase for this GFF3 record, if any

getAttributes

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

Return the attributes for this GFF3 record.

Returns:

the attributes for this GFF3 record

toRange

public com.google.common.collect.Range<Long> toRange()

Return this GFF3 record as a 0-based coordinate system, closed open range.

Returns:

this GFF3 record as a 0-based coordinate system, closed open range

hashCode

public int hashCode()

Overrides:

hashCode in class Object

equals

public boolean equals(Object o)

Overrides:

equals in class Object

toString

public String toString()

Overrides:

toString in class Object

parseAttributes

static com.google.common.collect.ListMultimap<String,String> parseAttributes(String attributes)

Parse the GFF3 attributes column into a list multimap of <String, String> entries.

Parameters:

attributes - attributes to parse, must not be null

Returns:

the GFF3 attributes column parsed into a list multimap of <String, String> entries

writeAttributes

static String writeAttributes(com.google.common.collect.ListMultimap<String,String> attributes)

Write the list multimap of <String, String> entries as GFF3 attributes column format.

Parameters:

attributes - attributes to write, must not be null

Returns:

the list multimap of <String, String> entries written as GFF3 attributes column format

isMissingValue

static boolean isMissingValue(String value)

Return true if the specified value is the missing value (".").

Parameters:

value - value

Returns:

true if the specified value is the missing value (".")

valueOf

public static Gff3Record valueOf(String value)

Return a new GFF3 record parsed from the specified value.

Parameters:

value - value to parse

Returns:

a new GFF3 record parsed from the specified value

Throws:

IllegalArgumentException - if the value is not valid GFF3 format

NumberFormatException - if a number valued field cannot be parsed as a number