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java.lang.Object | +--org.biojava.bio.program.gff.SimpleGFFRecord
A no-frills implementation of a GFFRecord.
Fields inherited from interface org.biojava.bio.program.gff.GFFRecord |
NO_FRAME,
NO_SCORE |
Constructor Summary | |
SimpleGFFRecord()
|
Method Summary | |
java.lang.String |
getComment()
The feature comment. |
int |
getEnd()
The end of this feature within the source sequence. |
java.lang.String |
getFeature()
The feature type filed. |
int |
getFrame()
The frame of the feature. |
java.util.Map |
getGroupAttributes()
A Map containing the group / attribute information. |
double |
getScore()
The score of the feature. |
java.lang.String |
getSeqName()
The sequence name field. |
java.lang.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(java.lang.String comment)
Set the comment to comment. |
void |
setEnd(int end)
Set the end coordinate to end. |
void |
setFeature(java.lang.String feature)
Set the feature type to type. |
void |
setFrame(int frame)
Set the frame to frame. |
void |
setGroupAttributes(java.util.Map ga)
Replace the group-attribute Map with ga. |
void |
setScore(double score)
Set the score to score. |
void |
setSeqName(java.lang.String seqName)
Set the sequence name to seqName. |
void |
setSource(java.lang.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 java.lang.String |
stringifyAttributes(java.util.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 |
public SimpleGFFRecord()
Method Detail |
public void setSeqName(java.lang.String seqName)
seqName
- the new namepublic java.lang.String getSeqName()
This should be the name of the sequence that this gff record is within.
public void setSource(java.lang.String source)
source
- the new sourcepublic java.lang.String getSource()
This is usualy a program name.
public void setFeature(java.lang.String feature)
feature
- the new feature typepublic java.lang.String getFeature()
This is something like "exon" - usualy corresponds to an EMBL term.
public void setStart(int start)
start
- the new start coordinatepublic int getStart()
public void setEnd(int end)
end
- the new end coordinatepublic int getEnd()
public void setScore(double 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.
score
- the new scorepublic double getScore()
For sequences that have no score, this will be set to GFFRecord.NO_SCORE.
public void setStrand(StrandedFeature.Strand strand)
strand
- the new Strandpublic StrandedFeature.Strand getStrand()
This will be one of GFFRecord.POSITIVE_STRAND, GFFRecord.NEGATIVE_STRAND, or GFFRecord.NO_STRAND.
public void setFrame(int frame) throws java.lang.IllegalArgumentException
The score must be one of {0, 1, 2}
or
GFFRecord.NO_FRAME.
score
- the new scorepublic int getFrame()
This will be one of {1, 2, 3}
or
GFFRecord.NO_FRAME.
public void setGroupAttributes(java.util.Map ga)
To efficiently add a key, call getGroupAttributes and modify the Map.
ga
- the new group-attribute Mappublic java.util.Map getGroupAttributes()
This will be a Map of group-names to List objects.
public void setComment(java.lang.String comment)
If you set it to null, then the comment for this line will be ignored.
the
- new commentpublic java.lang.String getComment()
public static java.lang.String stringifyAttributes(java.util.Map attMap)
attMap
- the Map of attributes and value lists
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