org.biojava.bio.program.gff
Class SimpleGFFRecord

java.lang.Object
  extended byorg.biojava.bio.program.gff.SimpleGFFRecord
All Implemented Interfaces:
GFFRecord

public class SimpleGFFRecord
extends java.lang.Object
implements GFFRecord

A no-frills implementation of a GFFRecord.

Author:
Matthew Pocock, Greg Cox, Aroul Ramadass

Field Summary
 
Fields inherited from interface org.biojava.bio.program.gff.GFFRecord
NO_FRAME, NO_SCORE
 
Constructor Summary
SimpleGFFRecord()
          Create a new SimpleGFFRecord with values set to null or zero
SimpleGFFRecord(GFFRecord rec)
          Create a new SimpleGFFRecord from GFFRecord object
SimpleGFFRecord(java.lang.String seqName, java.lang.String source, java.lang.String feature, int start, int end, double score, StrandedFeature.Strand strand, int frame, java.lang.String comment, java.util.Map groupAttributes)
           
 
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

SimpleGFFRecord

public SimpleGFFRecord(GFFRecord rec)
Create a new SimpleGFFRecord from GFFRecord object

Parameters:
rec - - A GFFRecord object

SimpleGFFRecord

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

SimpleGFFRecord

public SimpleGFFRecord()
Create a new SimpleGFFRecord with values set to null or zero

Method Detail

setSeqName

public void setSeqName(java.lang.String seqName)
Set the sequence name to seqName.

Parameters:
seqName - the new name

getSeqName

public java.lang.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(java.lang.String source)
Set the feature source to source.

Parameters:
source - the new source

getSource

public java.lang.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(java.lang.String feature)
Set the feature type to type.

Parameters:
feature - the new feature type

getFeature

public java.lang.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)
              throws java.lang.IllegalArgumentException
Set the frame to frame.

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

Throws:
java.lang.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(java.util.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 java.util.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(java.lang.String comment)
Set the comment to comment.

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


getComment

public java.lang.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 java.lang.String stringifyAttributes(java.util.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