Package htsjdk.tribble.bed

Class SimpleBEDFeature

java.lang.Object
htsjdk.tribble.bed.SimpleBEDFeature
All Implemented Interfaces:
Locatable, BEDFeature, Feature
Direct Known Subclasses:
FullBEDFeature
public class SimpleBEDFeature extends Object implements BEDFeature
Feature from a BED file without exon blocks.

  • Field Details

    • chr

      protected String chr

    • start

      protected int start

    • end

      protected int end

    • strand

      protected Strand strand

  • Constructor Details

    • SimpleBEDFeature

      public SimpleBEDFeature(int start, int end, String chr)

  • Method Details

    • getContig

      public String getContig()
      Description copied from interface: Locatable
      Gets the contig name for the contig this is mapped to. May return null if there is no unique mapping.
      Specified by:
      getContig in interface Locatable
      Returns:
      name of the contig this is mapped to, potentially null

    • getStart

      public int getStart()
      Specified by:
      getStart in interface Locatable
      Returns:
      1-based start position, undefined if getContig() == null

    • getEnd

      public int getEnd()
      Specified by:
      getEnd in interface Locatable
      Returns:
      1-based closed-ended position, undefined if getContig() == null

    • getStrand

      public Strand getStrand()
      Specified by:
      getStrand in interface BEDFeature

    • setStrand

      public void setStrand(Strand strand)

    • setChr

      public void setChr(String chr)

    • setStart

      public void setStart(int start)

    • setEnd

      public void setEnd(int end)

    • getType

      public String getType()
      Specified by:
      getType in interface BEDFeature

    • setType

      public void setType(String type)

    • getColor

      public Color getColor()
      Specified by:
      getColor in interface BEDFeature

    • setColor

      public void setColor(Color color)

    • getDescription

      public String getDescription()
      Specified by:
      getDescription in interface BEDFeature

    • setDescription

      public void setDescription(String description)

    • getName

      public String getName()
      Specified by:
      getName in interface BEDFeature

    • setName

      public void setName(String name)

    • getScore

      public float getScore()
      Specified by:
      getScore in interface BEDFeature

    • setScore

      public void setScore(float score)

    • getLink

      public String getLink()
      Specified by:
      getLink in interface BEDFeature

    • setLink

      public void setLink(String link)

    • getExons

      public List<FullBEDFeature.Exon> getExons()
      Specified by:
      getExons in interface BEDFeature