Package 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)
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Field Summary
FieldsModifier and TypeFieldDescriptionstatic final Comparator
Comparator which defines a useful sort order for GFF records.static final int
Deprecated.Use GFFTools.NO_FRAME insteadstatic final double
Deprecated.Use GFFTools.NO_SCORE instead -
Method Summary
Modifier and TypeMethodDescriptionThe feature comment.int
getEnd()
The end of this feature within the source sequence.The feature type filed.int
getFrame()
The frame of the feature.A Map containing the group / attribute information.double
getScore()
The score of the feature.The sequence name field.The source, or creator of this feature.int
getStart()
The start of this feature within the source sequence.The strand of the feature.
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Field Details
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NO_SCORE
Deprecated.Use GFFTools.NO_SCORE insteadFlag to indicate that there is no score info. -
NO_FRAME
Deprecated.Use GFFTools.NO_FRAME insteadFlag to indicate that there is no frame info. -
NATURAL_ORDER
Comparator which defines a useful sort order for GFF records. GFFRecord properties are considered in the following order- Sequence name
- Feature start
- Feature end
- Feature type
- Feature source
- The complete GFF line corresponding to this record
Two records are equal iff their GFF lines are character-for-character identical.
- Since:
- 1.4
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Method Details
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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
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getSource
The source, or creator of this feature.This is usualy a program name.
- Returns:
- the feature source
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getFeature
The feature type filed.This is something like "exon" - usualy corresponds to an EMBL term.
- Returns:
- the feature type
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getStart
int getStart()The start of this feature within the source sequence.- Returns:
- the start index
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getEnd
int getEnd()The end of this feature within the source sequence.- Returns:
- the end index
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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
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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
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getFrame
int getFrame()The frame of the feature.This will be one of
{1, 2, 3}
or GFFRecord.NO_FRAME.- Returns:
- the frame field
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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.
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getComment
The feature comment.- Returns:
- null or the feature comment
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