org.biojava.bio.program.gff

Interface GFFRecord

All Known Implementing Classes:

SimpleGFFRecord

public interface GFFRecord

A single GFF record.

This object has fields for each GFF field. It also defines a couple of useful constants.

GFF is described at http://www.sanger.ac.uk/Software/formats/GFF/

Author:

Matthew Pocock, Keith James (docs)

Field Summary

Fields

Modifier and Type	Field and Description
static Comparator	NATURAL_ORDER Comparator which defines a useful sort order for GFF records.
static int	NO_FRAME Deprecated. Use GFFTools.NO_FRAME instead
static double	NO_SCORE Deprecated. Use GFFTools.NO_SCORE instead

Method Summary

Methods

Modifier and Type	Method and Description
String	getComment() The feature comment.
int	getEnd() The end of this feature within the source sequence.
String	getFeature() The feature type filed.
int	getFrame() The frame of the feature.
Map	getGroupAttributes() A Map containing the group / attribute information.
double	getScore() The score of the feature.
String	getSeqName() The sequence name field.
String	getSource() The source, or creator of this feature.
int	getStart() The start of this feature within the source sequence.
StrandedFeature.Strand	getStrand() The strand of the feature.

Field Detail

NO_SCORE

static final double NO_SCORE

Deprecated. Use GFFTools.NO_SCORE instead

Flag to indicate that there is no score info.

NO_FRAME

static final int NO_FRAME

Deprecated. Use GFFTools.NO_FRAME instead

Flag to indicate that there is no frame info.

NATURAL_ORDER

static final Comparator NATURAL_ORDER

Comparator which defines a useful sort order for GFF records. GFFRecord properties are considered in the following order

1. Sequence name
2. Feature start
3. Feature end
4. Feature type
5. Feature source
6. The complete GFF line corresponding to this record

Two records are equal iff their GFF lines are character-for-character identical.

Since:

1.4

Method Detail

getSeqName

String getSeqName()

The sequence name field.

This should be the name of the sequence that this GFF record is within.

Returns:

the name of the sequence

getSource

String getSource()

The source, or creator of this feature.

This is usualy a program name.

Returns:

the feature source

getFeature

String getFeature()

The feature type filed.

This is something like "exon" - usualy corresponds to an EMBL term.

Returns:

the feature type

getStart

int getStart()

The start of this feature within the source sequence.

Returns:

the start index

getEnd

int getEnd()

The end of this feature within the source sequence.

Returns:

the end index

getScore

double getScore()

The score of the feature.

For sequences that have no score, this will be set to GFFRecord.NO_SCORE.

Returns:

the score, or NO_SCORE

getStrand

StrandedFeature.Strand getStrand()

The strand of the feature.

This will be one of GFFRecord.POSITIVE_STRAND, GFFRecord.NEGATIVE_STRAND, or GFFRecord.NO_STRAND.

Returns:

the strand field

getFrame

int getFrame()

The frame of the feature.

This will be one of {1, 2, 3} or GFFRecord.NO_FRAME.

Returns:

the frame field

getGroupAttributes

Map getGroupAttributes()

A Map containing the group / attribute information.

This will be a Map of group-names to List objects.

Returns:

a Map containing the group and attribute info.

getComment

String getComment()

The feature comment.

Returns:

null or the feature comment