Package org.biojava.bio.program.gff

Class SimpleGFFRecord

java.lang.Object

org.biojava.bio.program.gff.SimpleGFFRecord

All Implemented Interfaces:

GFFRecord

public class SimpleGFFRecord
extends Object
implements GFFRecord

A no-frills implementation of a GFFRecord.

Author:

Matthew Pocock, Greg Cox, Aroul Ramadass, Len Trigg, Richard Holland

Field Summary

Fields inherited from interface org.biojava.bio.program.gff.GFFRecord

NATURAL_ORDER, NO_FRAME, NO_SCORE

Constructor Summary

Constructors

Constructor	Description
SimpleGFFRecord()	Create a new SimpleGFFRecord with values set to null or zero
SimpleGFFRecord(String seqName, String source, String feature, int start, int end, double score, StrandedFeature.Strand strand, int frame, String comment, Map groupAttributes)
SimpleGFFRecord(GFFRecord rec)	Create a new SimpleGFFRecord from GFFRecord object

Method Summary

Modifier and Type	Method	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.
void	setComment(String comment)	Set the comment to comment.
void	setEnd(int end)	Set the end coordinate to end.
void	setFeature(String feature)	Set the feature type to type.
void	setFrame(int frame)	Set the frame to frame.
void	setGroupAttributes(Map ga)	Replace the group-attribute Map with ga.
void	setScore(double score)	Set the score to score.
void	setSeqName(String seqName)	Set the sequence name to seqName.
void	setSource(String source)	Set the feature source to source.
void	setStart(int start)	Set the start coordinate to start.
void	setStrand(StrandedFeature.Strand strand)	Set the strand to strand.
static String	stringifyAttributes(Map attMap)	Create a String representation of attMap.

Methods inherited from class java.lang.Object

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

Constructor Detail

SimpleGFFRecord

public SimpleGFFRecord(GFFRecord rec)

Create a new SimpleGFFRecord from GFFRecord object

Parameters:

rec - - A GFFRecord object

SimpleGFFRecord

public SimpleGFFRecord(String seqName,
                       String source,
                       String feature,
                       int start,
                       int end,
                       double score,
                       StrandedFeature.Strand strand,
                       int frame,
                       String comment,
                       Map groupAttributes)

SimpleGFFRecord

public SimpleGFFRecord()

Create a new SimpleGFFRecord with values set to null or zero

Method Detail

setSeqName

public void setSeqName(String seqName)

Set the sequence name to seqName.

Parameters:

seqName - the new name

getSeqName

public String getSeqName()

Description copied from interface: GFFRecord

The sequence name field.

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

Specified by:

getSeqName in interface GFFRecord

Returns:

the name of the sequence

setSource

public void setSource(String source)

Set the feature source to source.

Parameters:

source - the new source

getSource

public String getSource()

Description copied from interface: GFFRecord

The source, or creator of this feature.

This is usualy a program name.

Specified by:

getSource in interface GFFRecord

Returns:

the feature source

setFeature

public void setFeature(String feature)

Set the feature type to type.

Parameters:

feature - the new feature type

getFeature

public String getFeature()

Description copied from interface: GFFRecord

The feature type filed.

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

Specified by:

getFeature in interface GFFRecord

Returns:

the feature type

setStart

public void setStart(int start)

Set the start coordinate to start.

Parameters:

start - the new start coordinate

getStart

public int getStart()

Description copied from interface: GFFRecord

The start of this feature within the source sequence.

Specified by:

getStart in interface GFFRecord

Returns:

the start index

setEnd

public void setEnd(int end)

Set the end coordinate to end.

Parameters:

end - the new end coordinate

getEnd

public int getEnd()

Description copied from interface: GFFRecord

The end of this feature within the source sequence.

Specified by:

getEnd in interface GFFRecord

Returns:

the end index

setScore

public void setScore(double score)

Set the score to score.

The score must be a double, inclusive of 0. If you wish to indicate that there is no score, then use GFFRecord.NO_SCORE.

Parameters:

score - the new score

getScore

public double getScore()

Description copied from interface: GFFRecord

The score of the feature.

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

Specified by:

getScore in interface GFFRecord

Returns:

the score, or NO_SCORE

setStrand

public void setStrand(StrandedFeature.Strand strand)

Set the strand to strand.

Parameters:

strand - the new Strand

getStrand

public StrandedFeature.Strand getStrand()

Description copied from interface: GFFRecord

The strand of the feature.

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

Specified by:

getStrand in interface GFFRecord

Returns:

the strand field

setFrame

public void setFrame(int frame)

Set the frame to frame.

The score must be one of {0, 1, 2} or GFFRecord.NO_FRAME.

Parameters:

frame - the frame

Throws:

IllegalArgumentException - if score is not valid.

getFrame

public int getFrame()

Description copied from interface: GFFRecord

The frame of the feature.

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

Specified by:

getFrame in interface GFFRecord

Returns:

the frame field

setGroupAttributes

public void setGroupAttributes(Map ga)

Replace the group-attribute Map with ga.

To efficiently add a key, call getGroupAttributes() and modify the Map.

Parameters:

ga - the new group-attribute Map

getGroupAttributes

public Map getGroupAttributes()

Description copied from interface: GFFRecord

A Map containing the group / attribute information.

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

Specified by:

getGroupAttributes in interface GFFRecord

Returns:

a Map containing the group and attribute info.

setComment

public void setComment(String comment)

Set the comment to comment.

If you set it to null, then the comment for this line will be ignored.

Parameters:

comment - the new comment

getComment

public String getComment()

Description copied from interface: GFFRecord

The feature comment.

Specified by:

getComment in interface GFFRecord

Returns:

null or the feature comment

stringifyAttributes

public static String stringifyAttributes(Map attMap)

Create a String representation of attMap. attMap is assumed to contain String keys and List values.

Parameters:

attMap - the Map of attributes and value lists

Returns:

a GFF attribute/value String