Class SimpleGFFRecord
- java.lang.Object
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- org.biojava.bio.program.gff.SimpleGFFRecord
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- 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
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Field Summary
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Fields inherited from interface org.biojava.bio.program.gff.GFFRecord
NATURAL_ORDER, NO_FRAME, NO_SCORE
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Constructor Summary
Constructors Constructor Description SimpleGFFRecord()
Create a new SimpleGFFRecord with values set to null or zeroSimpleGFFRecord(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
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods 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.
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Constructor Detail
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SimpleGFFRecord
public SimpleGFFRecord(GFFRecord rec)
Create a new SimpleGFFRecord from GFFRecord object- Parameters:
rec
- - A GFFRecord object
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SimpleGFFRecord
public SimpleGFFRecord(String seqName, String source, String feature, int start, int end, double score, StrandedFeature.Strand strand, int frame, String comment, Map groupAttributes)
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SimpleGFFRecord
public SimpleGFFRecord()
Create a new SimpleGFFRecord with values set to null or zero
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Method Detail
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setSeqName
public void setSeqName(String seqName)
Set the sequence name to seqName.- Parameters:
seqName
- the new name
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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 interfaceGFFRecord
- Returns:
- the name of the sequence
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setSource
public void setSource(String source)
Set the feature source to source.- Parameters:
source
- the new source
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getSource
public String getSource()
Description copied from interface:GFFRecord
The source, or creator of this feature.This is usualy a program name.
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setFeature
public void setFeature(String feature)
Set the feature type to type.- Parameters:
feature
- the new feature type
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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 interfaceGFFRecord
- Returns:
- the feature type
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setStart
public void setStart(int start)
Set the start coordinate to start.- Parameters:
start
- the new start coordinate
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getStart
public int getStart()
Description copied from interface:GFFRecord
The start of this feature within the source sequence.
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setEnd
public void setEnd(int end)
Set the end coordinate to end.- Parameters:
end
- the new end coordinate
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getEnd
public int getEnd()
Description copied from interface:GFFRecord
The end of this feature within the source sequence.
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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
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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.
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setStrand
public void setStrand(StrandedFeature.Strand strand)
Set the strand to strand.- Parameters:
strand
- the new Strand
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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.
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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.
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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.
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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
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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 interfaceGFFRecord
- Returns:
- a Map containing the group and attribute info.
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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
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getComment
public String getComment()
Description copied from interface:GFFRecord
The feature comment.- Specified by:
getComment
in interfaceGFFRecord
- Returns:
- null or the feature comment
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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
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