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

  • Constructor Details

  • Method Details

    • 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