Class NextProtXmlAnnotation

java.lang.Object
org.snpeff.nextProt.NextProtXmlNode
org.snpeff.nextProt.NextProtXmlAnnotation

public class NextProtXmlAnnotation extends NextProtXmlNode
Mimics the 'annotation' tag in a NextProt XML file
Author:
Pablo Cingolani
  • Constructor Details

  • Method Details

    • addMarkers

      public void addMarkers(NextProtMarkerFactory markersFactory)
      Create all markers for this annotation
    • description

      public String description()
    • getCategory

      public String getCategory()
    • getCvTerm

      public CvTerm getCvTerm()
    • setCvTerm

      public void setCvTerm(CvTerm cvTerm)
    • getDescription

      public String getDescription()
    • setDescription

      public void setDescription(String description)
    • getLocations

      public List<Location> getLocations()
    • hasCvTerm

      public boolean hasCvTerm()
    • isEmpty

      public boolean isEmpty()
    • locationBeginPos

      public void locationBeginPos(Attributes attributes)
    • locationEnd

      public void locationEnd()
      End of location tag
    • locationEndPos

      public void locationEndPos(Attributes attributes)
    • locationIsoformStart

      public void locationIsoformStart(String accession)
    • locationStart

      public void locationStart(Attributes attributes)
    • name

      public String name()
      Return an annotation "name" Clean up characters to make them compatible with VCF annotations
    • toString

      public String toString()
      Overrides:
      toString in class Object
    • toString

      public String toString(String prefix)